Mercurial > repos > galaxyp > openms_openswathdecoygenerator
comparison macros_autotest.xml @ 9:1814187218fe draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 20:15:46 +0000 |
| parents | |
| children | 965413f29bf5 |
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| 8:9f505cd4428f | 9:1814187218fe |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <macros> | |
| 3 <xml name="autotest_AccurateMassSearch"> | |
| 4 <test expect_num_outputs="2"> | |
| 5 <conditional name="adv_opts_cond"> | |
| 6 <param name="adv_opts_selector" value="advanced"/> | |
| 7 <param name="force" value="false"/> | |
| 8 <param name="test" value="true"/> | |
| 9 </conditional> | |
| 10 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> | |
| 11 <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 12 <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/> | |
| 13 <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/> | |
| 14 <section name="db"> | |
| 15 <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/> | |
| 16 <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/> | |
| 17 </section> | |
| 18 <section name="algorithm"> | |
| 19 <param name="mass_error_value" value="5.0"/> | |
| 20 <param name="mass_error_unit" value="ppm"/> | |
| 21 <param name="ionization_mode" value="positive"/> | |
| 22 <param name="isotopic_similarity" value="false"/> | |
| 23 <param name="use_feature_adducts" value="false"/> | |
| 24 <param name="keep_unidentified_masses" value="false"/> | |
| 25 <section name="mzTab"> | |
| 26 <param name="exportIsotopeIntensities" value="false"/> | |
| 27 </section> | |
| 28 </section> | |
| 29 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 30 <output name="ctd_out" ftype="xml"> | |
| 31 <assert_contents> | |
| 32 <is_valid_xml/> | |
| 33 </assert_contents> | |
| 34 </output> | |
| 35 </test> | |
| 36 <test expect_num_outputs="3"> | |
| 37 <conditional name="adv_opts_cond"> | |
| 38 <param name="adv_opts_selector" value="advanced"/> | |
| 39 <param name="force" value="false"/> | |
| 40 <param name="test" value="true"/> | |
| 41 </conditional> | |
| 42 <param name="in" value="AccurateMassSearch_2_input.featureXML"/> | |
| 43 <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 44 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 45 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> | |
| 46 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> | |
| 47 <section name="db"> | |
| 48 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> | |
| 49 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> | |
| 50 </section> | |
| 51 <section name="algorithm"> | |
| 52 <param name="mass_error_value" value="5.0"/> | |
| 53 <param name="mass_error_unit" value="ppm"/> | |
| 54 <param name="ionization_mode" value="positive"/> | |
| 55 <param name="isotopic_similarity" value="false"/> | |
| 56 <param name="use_feature_adducts" value="false"/> | |
| 57 <param name="keep_unidentified_masses" value="false"/> | |
| 58 <section name="mzTab"> | |
| 59 <param name="exportIsotopeIntensities" value="true"/> | |
| 60 </section> | |
| 61 </section> | |
| 62 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> | |
| 63 <output name="ctd_out" ftype="xml"> | |
| 64 <assert_contents> | |
| 65 <is_valid_xml/> | |
| 66 </assert_contents> | |
| 67 </output> | |
| 68 </test> | |
| 69 <test expect_num_outputs="3"> | |
| 70 <conditional name="adv_opts_cond"> | |
| 71 <param name="adv_opts_selector" value="advanced"/> | |
| 72 <param name="force" value="false"/> | |
| 73 <param name="test" value="true"/> | |
| 74 </conditional> | |
| 75 <param name="in" value="AccurateMassSearch_2_input.featureXML"/> | |
| 76 <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 77 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 78 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> | |
| 79 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> | |
| 80 <section name="db"> | |
| 81 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> | |
| 82 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> | |
| 83 </section> | |
| 84 <section name="algorithm"> | |
| 85 <param name="mass_error_value" value="5.0"/> | |
| 86 <param name="mass_error_unit" value="ppm"/> | |
| 87 <param name="ionization_mode" value="positive"/> | |
| 88 <param name="isotopic_similarity" value="false"/> | |
| 89 <param name="use_feature_adducts" value="false"/> | |
| 90 <param name="keep_unidentified_masses" value="false"/> | |
| 91 <section name="mzTab"> | |
| 92 <param name="exportIsotopeIntensities" value="false"/> | |
| 93 </section> | |
| 94 </section> | |
| 95 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> | |
| 96 <output name="ctd_out" ftype="xml"> | |
| 97 <assert_contents> | |
| 98 <is_valid_xml/> | |
| 99 </assert_contents> | |
| 100 </output> | |
| 101 </test> | |
| 102 </xml> | |
| 103 <xml name="autotest_AssayGeneratorMetabo"> | |
| 104 <test expect_num_outputs="2"> | |
| 105 <conditional name="adv_opts_cond"> | |
| 106 <param name="adv_opts_selector" value="advanced"/> | |
| 107 <param name="precursor_recalibration_window" value="0.1"/> | |
| 108 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 109 <param name="min_fragment_mz" value="0.0"/> | |
| 110 <param name="max_fragment_mz" value="2000.0"/> | |
| 111 <param name="force" value="false"/> | |
| 112 <param name="test" value="true"/> | |
| 113 </conditional> | |
| 114 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 115 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> | |
| 116 <param name="out_type" value="tsv"/> | |
| 117 <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 118 <param name="fragment_annotation" value="none"/> | |
| 119 <param name="method" value="highest_intensity"/> | |
| 120 <param name="use_exact_mass" value="false"/> | |
| 121 <param name="exclude_ms2_precursor" value="false"/> | |
| 122 <param name="precursor_mz_distance" value="0.0001"/> | |
| 123 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 124 <param name="use_known_unknowns" value="false"/> | |
| 125 <param name="min_transitions" value="1"/> | |
| 126 <param name="max_transitions" value="3"/> | |
| 127 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 128 <param name="transition_threshold" value="5.0"/> | |
| 129 <param name="out_workspace_directory" value=""/> | |
| 130 <section name="deisotoping"> | |
| 131 <param name="use_deisotoper" value="false"/> | |
| 132 <param name="fragment_tolerance" value="1.0"/> | |
| 133 <param name="fragment_unit" value="ppm"/> | |
| 134 <param name="min_charge" value="1"/> | |
| 135 <param name="max_charge" value="1"/> | |
| 136 <param name="min_isopeaks" value="2"/> | |
| 137 <param name="max_isopeaks" value="3"/> | |
| 138 <param name="keep_only_deisotoped" value="false"/> | |
| 139 <param name="annotate_charge" value="false"/> | |
| 140 </section> | |
| 141 <section name="preprocessing"> | |
| 142 <param name="filter_by_num_masstraces" value="1"/> | |
| 143 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 144 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 145 <param name="precursor_rt_tolerance" value="5"/> | |
| 146 <param name="isotope_pattern_iterations" value="3"/> | |
| 147 <param name="feature_only" value="false"/> | |
| 148 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 149 </section> | |
| 150 <section name="sirius"> | |
| 151 <param name="profile" value="qtof"/> | |
| 152 <param name="candidates" value="5"/> | |
| 153 <param name="database" value="all"/> | |
| 154 <param name="noise" value="0"/> | |
| 155 <param name="ppm_max" value="10"/> | |
| 156 <param name="isotope" value="both"/> | |
| 157 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 158 <param name="compound_timeout" value="10"/> | |
| 159 <param name="tree_timeout" value="0"/> | |
| 160 <param name="top_n_hits" value="10"/> | |
| 161 <param name="cores" value="1"/> | |
| 162 <param name="auto_charge" value="false"/> | |
| 163 <param name="ion_tree" value="false"/> | |
| 164 <param name="no_recalibration" value="false"/> | |
| 165 <param name="most_intense_ms2" value="false"/> | |
| 166 </section> | |
| 167 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 168 <output name="ctd_out" ftype="xml"> | |
| 169 <assert_contents> | |
| 170 <is_valid_xml/> | |
| 171 </assert_contents> | |
| 172 </output> | |
| 173 </test> | |
| 174 <test expect_num_outputs="2"> | |
| 175 <conditional name="adv_opts_cond"> | |
| 176 <param name="adv_opts_selector" value="advanced"/> | |
| 177 <param name="precursor_recalibration_window" value="0.1"/> | |
| 178 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 179 <param name="min_fragment_mz" value="0.0"/> | |
| 180 <param name="max_fragment_mz" value="2000.0"/> | |
| 181 <param name="force" value="false"/> | |
| 182 <param name="test" value="true"/> | |
| 183 </conditional> | |
| 184 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 185 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> | |
| 186 <param name="out_type" value="tsv"/> | |
| 187 <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 188 <param name="fragment_annotation" value="none"/> | |
| 189 <param name="method" value="highest_intensity"/> | |
| 190 <param name="use_exact_mass" value="false"/> | |
| 191 <param name="exclude_ms2_precursor" value="false"/> | |
| 192 <param name="precursor_mz_distance" value="0.0001"/> | |
| 193 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 194 <param name="use_known_unknowns" value="false"/> | |
| 195 <param name="min_transitions" value="1"/> | |
| 196 <param name="max_transitions" value="3"/> | |
| 197 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 198 <param name="transition_threshold" value="5.0"/> | |
| 199 <param name="out_workspace_directory" value=""/> | |
| 200 <section name="deisotoping"> | |
| 201 <param name="use_deisotoper" value="false"/> | |
| 202 <param name="fragment_tolerance" value="1.0"/> | |
| 203 <param name="fragment_unit" value="ppm"/> | |
| 204 <param name="min_charge" value="1"/> | |
| 205 <param name="max_charge" value="1"/> | |
| 206 <param name="min_isopeaks" value="2"/> | |
| 207 <param name="max_isopeaks" value="3"/> | |
| 208 <param name="keep_only_deisotoped" value="false"/> | |
| 209 <param name="annotate_charge" value="false"/> | |
| 210 </section> | |
| 211 <section name="preprocessing"> | |
| 212 <param name="filter_by_num_masstraces" value="1"/> | |
| 213 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 214 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 215 <param name="precursor_rt_tolerance" value="5"/> | |
| 216 <param name="isotope_pattern_iterations" value="3"/> | |
| 217 <param name="feature_only" value="false"/> | |
| 218 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 219 </section> | |
| 220 <section name="sirius"> | |
| 221 <param name="profile" value="qtof"/> | |
| 222 <param name="candidates" value="5"/> | |
| 223 <param name="database" value="all"/> | |
| 224 <param name="noise" value="0"/> | |
| 225 <param name="ppm_max" value="10"/> | |
| 226 <param name="isotope" value="both"/> | |
| 227 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 228 <param name="compound_timeout" value="10"/> | |
| 229 <param name="tree_timeout" value="0"/> | |
| 230 <param name="top_n_hits" value="10"/> | |
| 231 <param name="cores" value="1"/> | |
| 232 <param name="auto_charge" value="false"/> | |
| 233 <param name="ion_tree" value="false"/> | |
| 234 <param name="no_recalibration" value="false"/> | |
| 235 <param name="most_intense_ms2" value="false"/> | |
| 236 </section> | |
| 237 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 238 <output name="ctd_out" ftype="xml"> | |
| 239 <assert_contents> | |
| 240 <is_valid_xml/> | |
| 241 </assert_contents> | |
| 242 </output> | |
| 243 </test> | |
| 244 <test expect_num_outputs="2"> | |
| 245 <conditional name="adv_opts_cond"> | |
| 246 <param name="adv_opts_selector" value="advanced"/> | |
| 247 <param name="precursor_recalibration_window" value="0.1"/> | |
| 248 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 249 <param name="min_fragment_mz" value="0.0"/> | |
| 250 <param name="max_fragment_mz" value="2000.0"/> | |
| 251 <param name="force" value="false"/> | |
| 252 <param name="test" value="true"/> | |
| 253 </conditional> | |
| 254 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 255 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> | |
| 256 <param name="out_type" value="tsv"/> | |
| 257 <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 258 <param name="fragment_annotation" value="none"/> | |
| 259 <param name="method" value="consensus_spectrum"/> | |
| 260 <param name="use_exact_mass" value="false"/> | |
| 261 <param name="exclude_ms2_precursor" value="false"/> | |
| 262 <param name="precursor_mz_distance" value="0.0001"/> | |
| 263 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 264 <param name="use_known_unknowns" value="false"/> | |
| 265 <param name="min_transitions" value="1"/> | |
| 266 <param name="max_transitions" value="3"/> | |
| 267 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 268 <param name="transition_threshold" value="5.0"/> | |
| 269 <param name="out_workspace_directory" value=""/> | |
| 270 <section name="deisotoping"> | |
| 271 <param name="use_deisotoper" value="false"/> | |
| 272 <param name="fragment_tolerance" value="1.0"/> | |
| 273 <param name="fragment_unit" value="ppm"/> | |
| 274 <param name="min_charge" value="1"/> | |
| 275 <param name="max_charge" value="1"/> | |
| 276 <param name="min_isopeaks" value="2"/> | |
| 277 <param name="max_isopeaks" value="3"/> | |
| 278 <param name="keep_only_deisotoped" value="false"/> | |
| 279 <param name="annotate_charge" value="false"/> | |
| 280 </section> | |
| 281 <section name="preprocessing"> | |
| 282 <param name="filter_by_num_masstraces" value="1"/> | |
| 283 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 284 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 285 <param name="precursor_rt_tolerance" value="5"/> | |
| 286 <param name="isotope_pattern_iterations" value="3"/> | |
| 287 <param name="feature_only" value="false"/> | |
| 288 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 289 </section> | |
| 290 <section name="sirius"> | |
| 291 <param name="profile" value="qtof"/> | |
| 292 <param name="candidates" value="5"/> | |
| 293 <param name="database" value="all"/> | |
| 294 <param name="noise" value="0"/> | |
| 295 <param name="ppm_max" value="10"/> | |
| 296 <param name="isotope" value="both"/> | |
| 297 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 298 <param name="compound_timeout" value="10"/> | |
| 299 <param name="tree_timeout" value="0"/> | |
| 300 <param name="top_n_hits" value="10"/> | |
| 301 <param name="cores" value="1"/> | |
| 302 <param name="auto_charge" value="false"/> | |
| 303 <param name="ion_tree" value="false"/> | |
| 304 <param name="no_recalibration" value="false"/> | |
| 305 <param name="most_intense_ms2" value="false"/> | |
| 306 </section> | |
| 307 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 308 <output name="ctd_out" ftype="xml"> | |
| 309 <assert_contents> | |
| 310 <is_valid_xml/> | |
| 311 </assert_contents> | |
| 312 </output> | |
| 313 </test> | |
| 314 <test expect_num_outputs="2"> | |
| 315 <conditional name="adv_opts_cond"> | |
| 316 <param name="adv_opts_selector" value="advanced"/> | |
| 317 <param name="precursor_recalibration_window" value="0.1"/> | |
| 318 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 319 <param name="min_fragment_mz" value="0.0"/> | |
| 320 <param name="max_fragment_mz" value="2000.0"/> | |
| 321 <param name="force" value="false"/> | |
| 322 <param name="test" value="true"/> | |
| 323 </conditional> | |
| 324 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 325 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> | |
| 326 <param name="out_type" value="tsv"/> | |
| 327 <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 328 <param name="fragment_annotation" value="none"/> | |
| 329 <param name="method" value="consensus_spectrum"/> | |
| 330 <param name="use_exact_mass" value="false"/> | |
| 331 <param name="exclude_ms2_precursor" value="false"/> | |
| 332 <param name="precursor_mz_distance" value="0.0001"/> | |
| 333 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 334 <param name="use_known_unknowns" value="false"/> | |
| 335 <param name="min_transitions" value="1"/> | |
| 336 <param name="max_transitions" value="3"/> | |
| 337 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 338 <param name="transition_threshold" value="5.0"/> | |
| 339 <param name="out_workspace_directory" value=""/> | |
| 340 <section name="deisotoping"> | |
| 341 <param name="use_deisotoper" value="false"/> | |
| 342 <param name="fragment_tolerance" value="1.0"/> | |
| 343 <param name="fragment_unit" value="ppm"/> | |
| 344 <param name="min_charge" value="1"/> | |
| 345 <param name="max_charge" value="1"/> | |
| 346 <param name="min_isopeaks" value="2"/> | |
| 347 <param name="max_isopeaks" value="3"/> | |
| 348 <param name="keep_only_deisotoped" value="false"/> | |
| 349 <param name="annotate_charge" value="false"/> | |
| 350 </section> | |
| 351 <section name="preprocessing"> | |
| 352 <param name="filter_by_num_masstraces" value="1"/> | |
| 353 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 354 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 355 <param name="precursor_rt_tolerance" value="5"/> | |
| 356 <param name="isotope_pattern_iterations" value="3"/> | |
| 357 <param name="feature_only" value="false"/> | |
| 358 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 359 </section> | |
| 360 <section name="sirius"> | |
| 361 <param name="profile" value="qtof"/> | |
| 362 <param name="candidates" value="5"/> | |
| 363 <param name="database" value="all"/> | |
| 364 <param name="noise" value="0"/> | |
| 365 <param name="ppm_max" value="10"/> | |
| 366 <param name="isotope" value="both"/> | |
| 367 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 368 <param name="compound_timeout" value="10"/> | |
| 369 <param name="tree_timeout" value="0"/> | |
| 370 <param name="top_n_hits" value="10"/> | |
| 371 <param name="cores" value="1"/> | |
| 372 <param name="auto_charge" value="false"/> | |
| 373 <param name="ion_tree" value="false"/> | |
| 374 <param name="no_recalibration" value="false"/> | |
| 375 <param name="most_intense_ms2" value="false"/> | |
| 376 </section> | |
| 377 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 378 <output name="ctd_out" ftype="xml"> | |
| 379 <assert_contents> | |
| 380 <is_valid_xml/> | |
| 381 </assert_contents> | |
| 382 </output> | |
| 383 </test> | |
| 384 <test expect_num_outputs="2"> | |
| 385 <conditional name="adv_opts_cond"> | |
| 386 <param name="adv_opts_selector" value="advanced"/> | |
| 387 <param name="precursor_recalibration_window" value="0.1"/> | |
| 388 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 389 <param name="min_fragment_mz" value="0.0"/> | |
| 390 <param name="max_fragment_mz" value="2000.0"/> | |
| 391 <param name="force" value="false"/> | |
| 392 <param name="test" value="true"/> | |
| 393 </conditional> | |
| 394 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 395 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> | |
| 396 <param name="out_type" value="tsv"/> | |
| 397 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 398 <param name="fragment_annotation" value="none"/> | |
| 399 <param name="method" value="consensus_spectrum"/> | |
| 400 <param name="use_exact_mass" value="false"/> | |
| 401 <param name="exclude_ms2_precursor" value="false"/> | |
| 402 <param name="precursor_mz_distance" value="0.0001"/> | |
| 403 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 404 <param name="use_known_unknowns" value="true"/> | |
| 405 <param name="min_transitions" value="1"/> | |
| 406 <param name="max_transitions" value="3"/> | |
| 407 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 408 <param name="transition_threshold" value="5.0"/> | |
| 409 <param name="out_workspace_directory" value=""/> | |
| 410 <section name="deisotoping"> | |
| 411 <param name="use_deisotoper" value="false"/> | |
| 412 <param name="fragment_tolerance" value="1.0"/> | |
| 413 <param name="fragment_unit" value="ppm"/> | |
| 414 <param name="min_charge" value="1"/> | |
| 415 <param name="max_charge" value="1"/> | |
| 416 <param name="min_isopeaks" value="2"/> | |
| 417 <param name="max_isopeaks" value="3"/> | |
| 418 <param name="keep_only_deisotoped" value="false"/> | |
| 419 <param name="annotate_charge" value="false"/> | |
| 420 </section> | |
| 421 <section name="preprocessing"> | |
| 422 <param name="filter_by_num_masstraces" value="1"/> | |
| 423 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 424 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 425 <param name="precursor_rt_tolerance" value="5"/> | |
| 426 <param name="isotope_pattern_iterations" value="3"/> | |
| 427 <param name="feature_only" value="false"/> | |
| 428 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 429 </section> | |
| 430 <section name="sirius"> | |
| 431 <param name="profile" value="qtof"/> | |
| 432 <param name="candidates" value="5"/> | |
| 433 <param name="database" value="all"/> | |
| 434 <param name="noise" value="0"/> | |
| 435 <param name="ppm_max" value="10"/> | |
| 436 <param name="isotope" value="both"/> | |
| 437 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 438 <param name="compound_timeout" value="10"/> | |
| 439 <param name="tree_timeout" value="0"/> | |
| 440 <param name="top_n_hits" value="10"/> | |
| 441 <param name="cores" value="1"/> | |
| 442 <param name="auto_charge" value="false"/> | |
| 443 <param name="ion_tree" value="false"/> | |
| 444 <param name="no_recalibration" value="false"/> | |
| 445 <param name="most_intense_ms2" value="false"/> | |
| 446 </section> | |
| 447 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 448 <output name="ctd_out" ftype="xml"> | |
| 449 <assert_contents> | |
| 450 <is_valid_xml/> | |
| 451 </assert_contents> | |
| 452 </output> | |
| 453 </test> | |
| 454 <test expect_num_outputs="2"> | |
| 455 <conditional name="adv_opts_cond"> | |
| 456 <param name="adv_opts_selector" value="advanced"/> | |
| 457 <param name="precursor_recalibration_window" value="0.1"/> | |
| 458 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 459 <param name="min_fragment_mz" value="0.0"/> | |
| 460 <param name="max_fragment_mz" value="2000.0"/> | |
| 461 <param name="force" value="false"/> | |
| 462 <param name="test" value="true"/> | |
| 463 </conditional> | |
| 464 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 465 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> | |
| 466 <param name="out_type" value="tsv"/> | |
| 467 <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 468 <param name="fragment_annotation" value="sirius"/> | |
| 469 <param name="method" value="highest_intensity"/> | |
| 470 <param name="use_exact_mass" value="true"/> | |
| 471 <param name="exclude_ms2_precursor" value="false"/> | |
| 472 <param name="precursor_mz_distance" value="0.0001"/> | |
| 473 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 474 <param name="use_known_unknowns" value="false"/> | |
| 475 <param name="min_transitions" value="2"/> | |
| 476 <param name="max_transitions" value="3"/> | |
| 477 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 478 <param name="transition_threshold" value="3.0"/> | |
| 479 <param name="out_workspace_directory" value=""/> | |
| 480 <section name="deisotoping"> | |
| 481 <param name="use_deisotoper" value="false"/> | |
| 482 <param name="fragment_tolerance" value="1.0"/> | |
| 483 <param name="fragment_unit" value="ppm"/> | |
| 484 <param name="min_charge" value="1"/> | |
| 485 <param name="max_charge" value="1"/> | |
| 486 <param name="min_isopeaks" value="2"/> | |
| 487 <param name="max_isopeaks" value="3"/> | |
| 488 <param name="keep_only_deisotoped" value="false"/> | |
| 489 <param name="annotate_charge" value="false"/> | |
| 490 </section> | |
| 491 <section name="preprocessing"> | |
| 492 <param name="filter_by_num_masstraces" value="1"/> | |
| 493 <param name="precursor_mz_tolerance" value="10.0"/> | |
| 494 <param name="precursor_mz_tolerance_unit" value="ppm"/> | |
| 495 <param name="precursor_rt_tolerance" value="5"/> | |
| 496 <param name="isotope_pattern_iterations" value="3"/> | |
| 497 <param name="feature_only" value="true"/> | |
| 498 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 499 </section> | |
| 500 <section name="sirius"> | |
| 501 <param name="profile" value="qtof"/> | |
| 502 <param name="candidates" value="5"/> | |
| 503 <param name="database" value="all"/> | |
| 504 <param name="noise" value="0"/> | |
| 505 <param name="ppm_max" value="10"/> | |
| 506 <param name="isotope" value="both"/> | |
| 507 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 508 <param name="compound_timeout" value="100"/> | |
| 509 <param name="tree_timeout" value="0"/> | |
| 510 <param name="top_n_hits" value="10"/> | |
| 511 <param name="cores" value="1"/> | |
| 512 <param name="auto_charge" value="false"/> | |
| 513 <param name="ion_tree" value="false"/> | |
| 514 <param name="no_recalibration" value="false"/> | |
| 515 <param name="most_intense_ms2" value="false"/> | |
| 516 </section> | |
| 517 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 518 <output name="ctd_out" ftype="xml"> | |
| 519 <assert_contents> | |
| 520 <is_valid_xml/> | |
| 521 </assert_contents> | |
| 522 </output> | |
| 523 </test> | |
| 524 <test expect_num_outputs="2"> | |
| 525 <conditional name="adv_opts_cond"> | |
| 526 <param name="adv_opts_selector" value="advanced"/> | |
| 527 <param name="precursor_recalibration_window" value="0.1"/> | |
| 528 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 529 <param name="min_fragment_mz" value="0.0"/> | |
| 530 <param name="max_fragment_mz" value="2000.0"/> | |
| 531 <param name="force" value="false"/> | |
| 532 <param name="test" value="true"/> | |
| 533 </conditional> | |
| 534 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 535 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> | |
| 536 <param name="out_type" value="tsv"/> | |
| 537 <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 538 <param name="fragment_annotation" value="sirius"/> | |
| 539 <param name="method" value="highest_intensity"/> | |
| 540 <param name="use_exact_mass" value="true"/> | |
| 541 <param name="exclude_ms2_precursor" value="false"/> | |
| 542 <param name="precursor_mz_distance" value="0.0001"/> | |
| 543 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 544 <param name="use_known_unknowns" value="true"/> | |
| 545 <param name="min_transitions" value="2"/> | |
| 546 <param name="max_transitions" value="3"/> | |
| 547 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 548 <param name="transition_threshold" value="3.0"/> | |
| 549 <param name="out_workspace_directory" value=""/> | |
| 550 <section name="deisotoping"> | |
| 551 <param name="use_deisotoper" value="false"/> | |
| 552 <param name="fragment_tolerance" value="1.0"/> | |
| 553 <param name="fragment_unit" value="ppm"/> | |
| 554 <param name="min_charge" value="1"/> | |
| 555 <param name="max_charge" value="1"/> | |
| 556 <param name="min_isopeaks" value="2"/> | |
| 557 <param name="max_isopeaks" value="3"/> | |
| 558 <param name="keep_only_deisotoped" value="false"/> | |
| 559 <param name="annotate_charge" value="false"/> | |
| 560 </section> | |
| 561 <section name="preprocessing"> | |
| 562 <param name="filter_by_num_masstraces" value="1"/> | |
| 563 <param name="precursor_mz_tolerance" value="10.0"/> | |
| 564 <param name="precursor_mz_tolerance_unit" value="ppm"/> | |
| 565 <param name="precursor_rt_tolerance" value="5"/> | |
| 566 <param name="isotope_pattern_iterations" value="3"/> | |
| 567 <param name="feature_only" value="true"/> | |
| 568 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 569 </section> | |
| 570 <section name="sirius"> | |
| 571 <param name="profile" value="qtof"/> | |
| 572 <param name="candidates" value="5"/> | |
| 573 <param name="database" value="all"/> | |
| 574 <param name="noise" value="0"/> | |
| 575 <param name="ppm_max" value="10"/> | |
| 576 <param name="isotope" value="both"/> | |
| 577 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 578 <param name="compound_timeout" value="100"/> | |
| 579 <param name="tree_timeout" value="0"/> | |
| 580 <param name="top_n_hits" value="10"/> | |
| 581 <param name="cores" value="1"/> | |
| 582 <param name="auto_charge" value="false"/> | |
| 583 <param name="ion_tree" value="false"/> | |
| 584 <param name="no_recalibration" value="false"/> | |
| 585 <param name="most_intense_ms2" value="false"/> | |
| 586 </section> | |
| 587 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 588 <output name="ctd_out" ftype="xml"> | |
| 589 <assert_contents> | |
| 590 <is_valid_xml/> | |
| 591 </assert_contents> | |
| 592 </output> | |
| 593 </test> | |
| 594 <test expect_num_outputs="2"> | |
| 595 <conditional name="adv_opts_cond"> | |
| 596 <param name="adv_opts_selector" value="advanced"/> | |
| 597 <param name="precursor_recalibration_window" value="0.1"/> | |
| 598 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 599 <param name="min_fragment_mz" value="0.0"/> | |
| 600 <param name="max_fragment_mz" value="2000.0"/> | |
| 601 <param name="force" value="false"/> | |
| 602 <param name="test" value="true"/> | |
| 603 </conditional> | |
| 604 <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/> | |
| 605 <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/> | |
| 606 <param name="out_type" value="tsv"/> | |
| 607 <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 608 <param name="fragment_annotation" value="sirius"/> | |
| 609 <param name="method" value="highest_intensity"/> | |
| 610 <param name="use_exact_mass" value="true"/> | |
| 611 <param name="exclude_ms2_precursor" value="false"/> | |
| 612 <param name="precursor_mz_distance" value="0.0001"/> | |
| 613 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 614 <param name="use_known_unknowns" value="false"/> | |
| 615 <param name="min_transitions" value="2"/> | |
| 616 <param name="max_transitions" value="3"/> | |
| 617 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 618 <param name="transition_threshold" value="3.0"/> | |
| 619 <param name="out_workspace_directory" value=""/> | |
| 620 <section name="deisotoping"> | |
| 621 <param name="use_deisotoper" value="false"/> | |
| 622 <param name="fragment_tolerance" value="1.0"/> | |
| 623 <param name="fragment_unit" value="ppm"/> | |
| 624 <param name="min_charge" value="1"/> | |
| 625 <param name="max_charge" value="1"/> | |
| 626 <param name="min_isopeaks" value="2"/> | |
| 627 <param name="max_isopeaks" value="3"/> | |
| 628 <param name="keep_only_deisotoped" value="false"/> | |
| 629 <param name="annotate_charge" value="false"/> | |
| 630 </section> | |
| 631 <section name="preprocessing"> | |
| 632 <param name="filter_by_num_masstraces" value="1"/> | |
| 633 <param name="precursor_mz_tolerance" value="10.0"/> | |
| 634 <param name="precursor_mz_tolerance_unit" value="ppm"/> | |
| 635 <param name="precursor_rt_tolerance" value="5"/> | |
| 636 <param name="isotope_pattern_iterations" value="3"/> | |
| 637 <param name="feature_only" value="true"/> | |
| 638 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 639 </section> | |
| 640 <section name="sirius"> | |
| 641 <param name="profile" value="qtof"/> | |
| 642 <param name="candidates" value="5"/> | |
| 643 <param name="database" value="all"/> | |
| 644 <param name="noise" value="0"/> | |
| 645 <param name="ppm_max" value="10"/> | |
| 646 <param name="isotope" value="both"/> | |
| 647 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 648 <param name="compound_timeout" value="100"/> | |
| 649 <param name="tree_timeout" value="0"/> | |
| 650 <param name="top_n_hits" value="10"/> | |
| 651 <param name="cores" value="1"/> | |
| 652 <param name="auto_charge" value="false"/> | |
| 653 <param name="ion_tree" value="false"/> | |
| 654 <param name="no_recalibration" value="false"/> | |
| 655 <param name="most_intense_ms2" value="false"/> | |
| 656 </section> | |
| 657 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 658 <output name="ctd_out" ftype="xml"> | |
| 659 <assert_contents> | |
| 660 <is_valid_xml/> | |
| 661 </assert_contents> | |
| 662 </output> | |
| 663 </test> | |
| 664 <test expect_num_outputs="2"> | |
| 665 <conditional name="adv_opts_cond"> | |
| 666 <param name="adv_opts_selector" value="advanced"/> | |
| 667 <param name="precursor_recalibration_window" value="0.1"/> | |
| 668 <param name="precursor_recalibration_window_unit" value="Da"/> | |
| 669 <param name="min_fragment_mz" value="100.0"/> | |
| 670 <param name="max_fragment_mz" value="900.0"/> | |
| 671 <param name="force" value="false"/> | |
| 672 <param name="test" value="true"/> | |
| 673 </conditional> | |
| 674 <param name="in" value="AssayGeneratorMetabo_input.mzML"/> | |
| 675 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> | |
| 676 <param name="out_type" value="tsv"/> | |
| 677 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 678 <param name="fragment_annotation" value="sirius"/> | |
| 679 <param name="method" value="highest_intensity"/> | |
| 680 <param name="use_exact_mass" value="true"/> | |
| 681 <param name="exclude_ms2_precursor" value="false"/> | |
| 682 <param name="precursor_mz_distance" value="0.0001"/> | |
| 683 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 684 <param name="use_known_unknowns" value="false"/> | |
| 685 <param name="min_transitions" value="2"/> | |
| 686 <param name="max_transitions" value="3"/> | |
| 687 <param name="cosine_similarity_threshold" value="0.98"/> | |
| 688 <param name="transition_threshold" value="3.0"/> | |
| 689 <param name="out_workspace_directory" value=""/> | |
| 690 <section name="deisotoping"> | |
| 691 <param name="use_deisotoper" value="false"/> | |
| 692 <param name="fragment_tolerance" value="1.0"/> | |
| 693 <param name="fragment_unit" value="ppm"/> | |
| 694 <param name="min_charge" value="1"/> | |
| 695 <param name="max_charge" value="1"/> | |
| 696 <param name="min_isopeaks" value="2"/> | |
| 697 <param name="max_isopeaks" value="3"/> | |
| 698 <param name="keep_only_deisotoped" value="false"/> | |
| 699 <param name="annotate_charge" value="false"/> | |
| 700 </section> | |
| 701 <section name="preprocessing"> | |
| 702 <param name="filter_by_num_masstraces" value="1"/> | |
| 703 <param name="precursor_mz_tolerance" value="10.0"/> | |
| 704 <param name="precursor_mz_tolerance_unit" value="ppm"/> | |
| 705 <param name="precursor_rt_tolerance" value="5"/> | |
| 706 <param name="isotope_pattern_iterations" value="3"/> | |
| 707 <param name="feature_only" value="true"/> | |
| 708 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 709 </section> | |
| 710 <section name="sirius"> | |
| 711 <param name="profile" value="qtof"/> | |
| 712 <param name="candidates" value="5"/> | |
| 713 <param name="database" value="all"/> | |
| 714 <param name="noise" value="0"/> | |
| 715 <param name="ppm_max" value="10"/> | |
| 716 <param name="isotope" value="both"/> | |
| 717 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 718 <param name="compound_timeout" value="100"/> | |
| 719 <param name="tree_timeout" value="0"/> | |
| 720 <param name="top_n_hits" value="10"/> | |
| 721 <param name="cores" value="1"/> | |
| 722 <param name="auto_charge" value="false"/> | |
| 723 <param name="ion_tree" value="false"/> | |
| 724 <param name="no_recalibration" value="false"/> | |
| 725 <param name="most_intense_ms2" value="false"/> | |
| 726 </section> | |
| 727 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 728 <output name="ctd_out" ftype="xml"> | |
| 729 <assert_contents> | |
| 730 <is_valid_xml/> | |
| 731 </assert_contents> | |
| 732 </output> | |
| 733 </test> | |
| 734 </xml> | |
| 735 <xml name="autotest_BaselineFilter"> | |
| 736 <test expect_num_outputs="2"> | |
| 737 <conditional name="adv_opts_cond"> | |
| 738 <param name="adv_opts_selector" value="advanced"/> | |
| 739 <param name="force" value="false"/> | |
| 740 <param name="test" value="true"/> | |
| 741 </conditional> | |
| 742 <param name="in" value="BaselineFilter_input.mzML"/> | |
| 743 <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 744 <param name="struc_elem_length" value="1.5"/> | |
| 745 <param name="struc_elem_unit" value="Thomson"/> | |
| 746 <param name="method" value="tophat"/> | |
| 747 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 748 <output name="ctd_out" ftype="xml"> | |
| 749 <assert_contents> | |
| 750 <is_valid_xml/> | |
| 751 </assert_contents> | |
| 752 </output> | |
| 753 </test> | |
| 754 </xml> | |
| 755 <xml name="autotest_ClusterMassTracesByPrecursor"> | |
| 756 </xml> | |
| 757 <xml name="autotest_ClusterMassTraces"> | |
| 758 </xml> | |
| 759 <xml name="autotest_CometAdapter"> | |
| 760 <test expect_num_outputs="3"> | |
| 761 <conditional name="adv_opts_cond"> | |
| 762 <param name="adv_opts_selector" value="advanced"/> | |
| 763 <param name="fragment_bin_tolerance" value="1.0005"/> | |
| 764 <param name="fragment_bin_offset" value="0.25"/> | |
| 765 <param name="instrument" value="high_res"/> | |
| 766 <param name="use_A_ions" value="false"/> | |
| 767 <param name="use_B_ions" value="true"/> | |
| 768 <param name="use_C_ions" value="false"/> | |
| 769 <param name="use_X_ions" value="false"/> | |
| 770 <param name="use_Y_ions" value="true"/> | |
| 771 <param name="use_Z_ions" value="false"/> | |
| 772 <param name="use_NL_ions" value="false"/> | |
| 773 <param name="digest_mass_range" value="600:5000"/> | |
| 774 <param name="max_precursor_charge" value="5"/> | |
| 775 <param name="spectrum_batch_size" value="1000"/> | |
| 776 <param name="mass_offsets" value="0.0"/> | |
| 777 <param name="minimum_peaks" value="10"/> | |
| 778 <param name="minimum_intensity" value="0.0"/> | |
| 779 <param name="remove_precursor_peak" value="no"/> | |
| 780 <param name="remove_precursor_tolerance" value="1.5"/> | |
| 781 <param name="clear_mz_range" value="0:0"/> | |
| 782 <param name="max_variable_mods_in_peptide" value="5"/> | |
| 783 <param name="require_variable_mod" value="false"/> | |
| 784 <param name="force" value="false"/> | |
| 785 <param name="test" value="true"/> | |
| 786 </conditional> | |
| 787 <param name="in" value="spectra_comet.mzML"/> | |
| 788 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 789 <param name="database" value="proteins.fasta"/> | |
| 790 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 791 <param name="precursor_mass_tolerance" value="3.0"/> | |
| 792 <param name="precursor_error_units" value="ppm"/> | |
| 793 <param name="isotope_error" value="off"/> | |
| 794 <param name="enzyme" value="Trypsin"/> | |
| 795 <param name="num_enzyme_termini" value="fully"/> | |
| 796 <param name="allowed_missed_cleavages" value="1"/> | |
| 797 <param name="num_hits" value="5"/> | |
| 798 <param name="precursor_charge" value="0:0"/> | |
| 799 <param name="override_charge" value="keep any known"/> | |
| 800 <param name="ms_level" value="2"/> | |
| 801 <param name="activation_method" value="ALL"/> | |
| 802 <param name="max_fragment_charge" value="3"/> | |
| 803 <param name="clip_nterm_methionine" value="false"/> | |
| 804 <param name="fixed_modifications" value=""/> | |
| 805 <param name="variable_modifications" value=""/> | |
| 806 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> | |
| 807 <output name="ctd_out" ftype="xml"> | |
| 808 <assert_contents> | |
| 809 <is_valid_xml/> | |
| 810 </assert_contents> | |
| 811 </output> | |
| 812 </test> | |
| 813 <test expect_num_outputs="3"> | |
| 814 <conditional name="adv_opts_cond"> | |
| 815 <param name="adv_opts_selector" value="advanced"/> | |
| 816 <param name="fragment_bin_tolerance" value="1.0005"/> | |
| 817 <param name="fragment_bin_offset" value="0.25"/> | |
| 818 <param name="instrument" value="high_res"/> | |
| 819 <param name="use_A_ions" value="false"/> | |
| 820 <param name="use_B_ions" value="true"/> | |
| 821 <param name="use_C_ions" value="false"/> | |
| 822 <param name="use_X_ions" value="false"/> | |
| 823 <param name="use_Y_ions" value="true"/> | |
| 824 <param name="use_Z_ions" value="false"/> | |
| 825 <param name="use_NL_ions" value="false"/> | |
| 826 <param name="digest_mass_range" value="600:5000"/> | |
| 827 <param name="max_precursor_charge" value="5"/> | |
| 828 <param name="spectrum_batch_size" value="1000"/> | |
| 829 <param name="mass_offsets" value="0.0"/> | |
| 830 <param name="minimum_peaks" value="10"/> | |
| 831 <param name="minimum_intensity" value="0.0"/> | |
| 832 <param name="remove_precursor_peak" value="no"/> | |
| 833 <param name="remove_precursor_tolerance" value="1.5"/> | |
| 834 <param name="clear_mz_range" value="0:0"/> | |
| 835 <param name="max_variable_mods_in_peptide" value="5"/> | |
| 836 <param name="require_variable_mod" value="false"/> | |
| 837 <param name="force" value="false"/> | |
| 838 <param name="test" value="true"/> | |
| 839 </conditional> | |
| 840 <param name="in" value="CometAdapter_2_prepared.mzML"/> | |
| 841 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 842 <param name="database" value="CometAdapter_2_in.fasta"/> | |
| 843 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 844 <param name="precursor_mass_tolerance" value="3.0"/> | |
| 845 <param name="precursor_error_units" value="Da"/> | |
| 846 <param name="isotope_error" value="off"/> | |
| 847 <param name="enzyme" value="Trypsin"/> | |
| 848 <param name="num_enzyme_termini" value="fully"/> | |
| 849 <param name="allowed_missed_cleavages" value="1"/> | |
| 850 <param name="num_hits" value="5"/> | |
| 851 <param name="precursor_charge" value="0:0"/> | |
| 852 <param name="override_charge" value="keep any known"/> | |
| 853 <param name="ms_level" value="2"/> | |
| 854 <param name="activation_method" value="ALL"/> | |
| 855 <param name="max_fragment_charge" value="3"/> | |
| 856 <param name="clip_nterm_methionine" value="false"/> | |
| 857 <param name="fixed_modifications" value=""/> | |
| 858 <param name="variable_modifications" value=""/> | |
| 859 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> | |
| 860 <output name="ctd_out" ftype="xml"> | |
| 861 <assert_contents> | |
| 862 <is_valid_xml/> | |
| 863 </assert_contents> | |
| 864 </output> | |
| 865 </test> | |
| 866 <test expect_num_outputs="3"> | |
| 867 <conditional name="adv_opts_cond"> | |
| 868 <param name="adv_opts_selector" value="advanced"/> | |
| 869 <param name="fragment_bin_tolerance" value="0.02"/> | |
| 870 <param name="fragment_bin_offset" value="0.0"/> | |
| 871 <param name="instrument" value="high_res"/> | |
| 872 <param name="use_A_ions" value="false"/> | |
| 873 <param name="use_B_ions" value="true"/> | |
| 874 <param name="use_C_ions" value="false"/> | |
| 875 <param name="use_X_ions" value="false"/> | |
| 876 <param name="use_Y_ions" value="true"/> | |
| 877 <param name="use_Z_ions" value="false"/> | |
| 878 <param name="use_NL_ions" value="false"/> | |
| 879 <param name="digest_mass_range" value="600:5000"/> | |
| 880 <param name="max_precursor_charge" value="5"/> | |
| 881 <param name="spectrum_batch_size" value="20000"/> | |
| 882 <param name="mass_offsets" value="0.0"/> | |
| 883 <param name="minimum_peaks" value="10"/> | |
| 884 <param name="minimum_intensity" value="0.0"/> | |
| 885 <param name="remove_precursor_peak" value="no"/> | |
| 886 <param name="remove_precursor_tolerance" value="1.5"/> | |
| 887 <param name="clear_mz_range" value="0:0"/> | |
| 888 <param name="max_variable_mods_in_peptide" value="3"/> | |
| 889 <param name="require_variable_mod" value="false"/> | |
| 890 <param name="force" value="false"/> | |
| 891 <param name="test" value="true"/> | |
| 892 </conditional> | |
| 893 <param name="in" value="CometAdapter_3.mzML"/> | |
| 894 <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 895 <param name="database" value="CometAdapter_3.fasta"/> | |
| 896 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 897 <param name="precursor_mass_tolerance" value="5.0"/> | |
| 898 <param name="precursor_error_units" value="ppm"/> | |
| 899 <param name="isotope_error" value="off"/> | |
| 900 <param name="enzyme" value="Trypsin"/> | |
| 901 <param name="num_enzyme_termini" value="fully"/> | |
| 902 <param name="allowed_missed_cleavages" value="3"/> | |
| 903 <param name="num_hits" value="5"/> | |
| 904 <param name="precursor_charge" value="0:0"/> | |
| 905 <param name="override_charge" value="keep known search unknown"/> | |
| 906 <param name="ms_level" value="2"/> | |
| 907 <param name="activation_method" value="ALL"/> | |
| 908 <param name="max_fragment_charge" value="3"/> | |
| 909 <param name="clip_nterm_methionine" value="false"/> | |
| 910 <param name="fixed_modifications" value="Carbamidomethyl (C)"/> | |
| 911 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/> | |
| 912 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> | |
| 913 <output name="ctd_out" ftype="xml"> | |
| 914 <assert_contents> | |
| 915 <is_valid_xml/> | |
| 916 </assert_contents> | |
| 917 </output> | |
| 918 </test> | |
| 919 </xml> | |
| 920 <xml name="autotest_CompNovoCID"> | |
| 921 <test expect_num_outputs="2"> | |
| 922 <conditional name="adv_opts_cond"> | |
| 923 <param name="adv_opts_selector" value="advanced"/> | |
| 924 <param name="force" value="false"/> | |
| 925 <param name="test" value="true"/> | |
| 926 </conditional> | |
| 927 <param name="in" value="CompNovoCID_1_input.mzML"/> | |
| 928 <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 929 <section name="algorithm"> | |
| 930 <param name="max_number_aa_per_decomp" value="4"/> | |
| 931 <param name="tryptic_only" value="true"/> | |
| 932 <param name="precursor_mass_tolerance" value="0.3"/> | |
| 933 <param name="fragment_mass_tolerance" value="0.3"/> | |
| 934 <param name="max_number_pivot" value="9"/> | |
| 935 <param name="max_subscore_number" value="40"/> | |
| 936 <param name="decomp_weights_precision" value="0.01"/> | |
| 937 <param name="double_charged_iso_threshold" value="0.6"/> | |
| 938 <param name="max_mz" value="2000.0"/> | |
| 939 <param name="min_mz" value="200.0"/> | |
| 940 <param name="max_isotope_to_score" value="3"/> | |
| 941 <param name="max_decomp_weight" value="450.0"/> | |
| 942 <param name="max_isotope" value="3"/> | |
| 943 <param name="missed_cleavages" value="1"/> | |
| 944 <param name="number_of_hits" value="1"/> | |
| 945 <param name="estimate_precursor_mz" value="true"/> | |
| 946 <param name="number_of_prescoring_hits" value="250"/> | |
| 947 <param name="fixed_modifications" value=""/> | |
| 948 <param name="variable_modifications" value=""/> | |
| 949 <param name="residue_set" value="Natural19WithoutI"/> | |
| 950 </section> | |
| 951 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 952 <output name="ctd_out" ftype="xml"> | |
| 953 <assert_contents> | |
| 954 <is_valid_xml/> | |
| 955 </assert_contents> | |
| 956 </output> | |
| 957 </test> | |
| 958 </xml> | |
| 959 <xml name="autotest_CompNovo"> | |
| 960 <test expect_num_outputs="2"> | |
| 961 <conditional name="adv_opts_cond"> | |
| 962 <param name="adv_opts_selector" value="advanced"/> | |
| 963 <param name="force" value="false"/> | |
| 964 <param name="test" value="true"/> | |
| 965 </conditional> | |
| 966 <param name="in" value="CompNovo_1_input.mzML"/> | |
| 967 <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 968 <section name="algorithm"> | |
| 969 <param name="max_number_aa_per_decomp" value="4"/> | |
| 970 <param name="tryptic_only" value="true"/> | |
| 971 <param name="precursor_mass_tolerance" value="0.3"/> | |
| 972 <param name="fragment_mass_tolerance" value="0.3"/> | |
| 973 <param name="max_number_pivot" value="9"/> | |
| 974 <param name="max_subscore_number" value="40"/> | |
| 975 <param name="decomp_weights_precision" value="0.01"/> | |
| 976 <param name="double_charged_iso_threshold" value="0.6"/> | |
| 977 <param name="max_mz" value="2000.0"/> | |
| 978 <param name="min_mz" value="200.0"/> | |
| 979 <param name="max_isotope_to_score" value="3"/> | |
| 980 <param name="max_decomp_weight" value="450.0"/> | |
| 981 <param name="max_isotope" value="3"/> | |
| 982 <param name="missed_cleavages" value="1"/> | |
| 983 <param name="number_of_hits" value="1"/> | |
| 984 <param name="estimate_precursor_mz" value="true"/> | |
| 985 <param name="number_of_prescoring_hits" value="250"/> | |
| 986 <param name="fixed_modifications" value=""/> | |
| 987 <param name="variable_modifications" value=""/> | |
| 988 <param name="residue_set" value="Natural19WithoutI"/> | |
| 989 </section> | |
| 990 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 991 <output name="ctd_out" ftype="xml"> | |
| 992 <assert_contents> | |
| 993 <is_valid_xml/> | |
| 994 </assert_contents> | |
| 995 </output> | |
| 996 </test> | |
| 997 </xml> | |
| 998 <xml name="autotest_ConsensusID"> | |
| 999 <test expect_num_outputs="2"> | |
| 1000 <conditional name="adv_opts_cond"> | |
| 1001 <param name="adv_opts_selector" value="advanced"/> | |
| 1002 <param name="force" value="false"/> | |
| 1003 <param name="test" value="true"/> | |
| 1004 </conditional> | |
| 1005 <param name="in" value="ConsensusID_1_input.idXML"/> | |
| 1006 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1007 <param name="rt_delta" value="0.1"/> | |
| 1008 <param name="mz_delta" value="0.1"/> | |
| 1009 <param name="algorithm" value="PEPMatrix"/> | |
| 1010 <section name="filter"> | |
| 1011 <param name="considered_hits" value="0"/> | |
| 1012 <param name="min_support" value="0.0"/> | |
| 1013 <param name="count_empty" value="false"/> | |
| 1014 </section> | |
| 1015 <section name="PEPIons"> | |
| 1016 <param name="mass_tolerance" value="0.5"/> | |
| 1017 <param name="min_shared" value="2"/> | |
| 1018 </section> | |
| 1019 <section name="PEPMatrix"> | |
| 1020 <param name="matrix" value="PAM30MS"/> | |
| 1021 <param name="penalty" value="5"/> | |
| 1022 </section> | |
| 1023 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1024 <output name="ctd_out" ftype="xml"> | |
| 1025 <assert_contents> | |
| 1026 <is_valid_xml/> | |
| 1027 </assert_contents> | |
| 1028 </output> | |
| 1029 </test> | |
| 1030 <test expect_num_outputs="2"> | |
| 1031 <conditional name="adv_opts_cond"> | |
| 1032 <param name="adv_opts_selector" value="advanced"/> | |
| 1033 <param name="force" value="false"/> | |
| 1034 <param name="test" value="true"/> | |
| 1035 </conditional> | |
| 1036 <param name="in" value="ConsensusID_2_input.featureXML"/> | |
| 1037 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 1038 <param name="rt_delta" value="0.1"/> | |
| 1039 <param name="mz_delta" value="0.1"/> | |
| 1040 <param name="algorithm" value="average"/> | |
| 1041 <section name="filter"> | |
| 1042 <param name="considered_hits" value="0"/> | |
| 1043 <param name="min_support" value="0.0"/> | |
| 1044 <param name="count_empty" value="false"/> | |
| 1045 </section> | |
| 1046 <section name="PEPIons"> | |
| 1047 <param name="mass_tolerance" value="0.5"/> | |
| 1048 <param name="min_shared" value="2"/> | |
| 1049 </section> | |
| 1050 <section name="PEPMatrix"> | |
| 1051 <param name="matrix" value="identity"/> | |
| 1052 <param name="penalty" value="5"/> | |
| 1053 </section> | |
| 1054 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1055 <output name="ctd_out" ftype="xml"> | |
| 1056 <assert_contents> | |
| 1057 <is_valid_xml/> | |
| 1058 </assert_contents> | |
| 1059 </output> | |
| 1060 </test> | |
| 1061 <test expect_num_outputs="2"> | |
| 1062 <conditional name="adv_opts_cond"> | |
| 1063 <param name="adv_opts_selector" value="advanced"/> | |
| 1064 <param name="force" value="false"/> | |
| 1065 <param name="test" value="true"/> | |
| 1066 </conditional> | |
| 1067 <param name="in" value="ConsensusID_3_input.consensusXML"/> | |
| 1068 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 1069 <param name="rt_delta" value="0.1"/> | |
| 1070 <param name="mz_delta" value="0.1"/> | |
| 1071 <param name="algorithm" value="best"/> | |
| 1072 <section name="filter"> | |
| 1073 <param name="considered_hits" value="0"/> | |
| 1074 <param name="min_support" value="0.0"/> | |
| 1075 <param name="count_empty" value="false"/> | |
| 1076 </section> | |
| 1077 <section name="PEPIons"> | |
| 1078 <param name="mass_tolerance" value="0.5"/> | |
| 1079 <param name="min_shared" value="2"/> | |
| 1080 </section> | |
| 1081 <section name="PEPMatrix"> | |
| 1082 <param name="matrix" value="identity"/> | |
| 1083 <param name="penalty" value="5"/> | |
| 1084 </section> | |
| 1085 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1086 <output name="ctd_out" ftype="xml"> | |
| 1087 <assert_contents> | |
| 1088 <is_valid_xml/> | |
| 1089 </assert_contents> | |
| 1090 </output> | |
| 1091 </test> | |
| 1092 <test expect_num_outputs="2"> | |
| 1093 <conditional name="adv_opts_cond"> | |
| 1094 <param name="adv_opts_selector" value="advanced"/> | |
| 1095 <param name="force" value="false"/> | |
| 1096 <param name="test" value="true"/> | |
| 1097 </conditional> | |
| 1098 <param name="in" value="ConsensusID_1_input.idXML"/> | |
| 1099 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1100 <param name="rt_delta" value="0.1"/> | |
| 1101 <param name="mz_delta" value="0.1"/> | |
| 1102 <param name="algorithm" value="PEPMatrix"/> | |
| 1103 <section name="filter"> | |
| 1104 <param name="considered_hits" value="6"/> | |
| 1105 <param name="min_support" value="0.0"/> | |
| 1106 <param name="count_empty" value="false"/> | |
| 1107 </section> | |
| 1108 <section name="PEPIons"> | |
| 1109 <param name="mass_tolerance" value="0.5"/> | |
| 1110 <param name="min_shared" value="2"/> | |
| 1111 </section> | |
| 1112 <section name="PEPMatrix"> | |
| 1113 <param name="matrix" value="identity"/> | |
| 1114 <param name="penalty" value="5"/> | |
| 1115 </section> | |
| 1116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1117 <output name="ctd_out" ftype="xml"> | |
| 1118 <assert_contents> | |
| 1119 <is_valid_xml/> | |
| 1120 </assert_contents> | |
| 1121 </output> | |
| 1122 </test> | |
| 1123 <test expect_num_outputs="2"> | |
| 1124 <conditional name="adv_opts_cond"> | |
| 1125 <param name="adv_opts_selector" value="advanced"/> | |
| 1126 <param name="force" value="false"/> | |
| 1127 <param name="test" value="true"/> | |
| 1128 </conditional> | |
| 1129 <param name="in" value="ConsensusID_1_input.idXML"/> | |
| 1130 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1131 <param name="rt_delta" value="0.1"/> | |
| 1132 <param name="mz_delta" value="0.1"/> | |
| 1133 <param name="algorithm" value="PEPIons"/> | |
| 1134 <section name="filter"> | |
| 1135 <param name="considered_hits" value="0"/> | |
| 1136 <param name="min_support" value="0.0"/> | |
| 1137 <param name="count_empty" value="false"/> | |
| 1138 </section> | |
| 1139 <section name="PEPIons"> | |
| 1140 <param name="mass_tolerance" value="0.5"/> | |
| 1141 <param name="min_shared" value="2"/> | |
| 1142 </section> | |
| 1143 <section name="PEPMatrix"> | |
| 1144 <param name="matrix" value="identity"/> | |
| 1145 <param name="penalty" value="5"/> | |
| 1146 </section> | |
| 1147 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1148 <output name="ctd_out" ftype="xml"> | |
| 1149 <assert_contents> | |
| 1150 <is_valid_xml/> | |
| 1151 </assert_contents> | |
| 1152 </output> | |
| 1153 </test> | |
| 1154 <test expect_num_outputs="2"> | |
| 1155 <conditional name="adv_opts_cond"> | |
| 1156 <param name="adv_opts_selector" value="advanced"/> | |
| 1157 <param name="force" value="false"/> | |
| 1158 <param name="test" value="true"/> | |
| 1159 </conditional> | |
| 1160 <param name="in" value="ConsensusID_1_input.idXML"/> | |
| 1161 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1162 <param name="rt_delta" value="0.1"/> | |
| 1163 <param name="mz_delta" value="0.1"/> | |
| 1164 <param name="algorithm" value="best"/> | |
| 1165 <section name="filter"> | |
| 1166 <param name="considered_hits" value="0"/> | |
| 1167 <param name="min_support" value="0.5"/> | |
| 1168 <param name="count_empty" value="false"/> | |
| 1169 </section> | |
| 1170 <section name="PEPIons"> | |
| 1171 <param name="mass_tolerance" value="0.5"/> | |
| 1172 <param name="min_shared" value="2"/> | |
| 1173 </section> | |
| 1174 <section name="PEPMatrix"> | |
| 1175 <param name="matrix" value="identity"/> | |
| 1176 <param name="penalty" value="5"/> | |
| 1177 </section> | |
| 1178 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1179 <output name="ctd_out" ftype="xml"> | |
| 1180 <assert_contents> | |
| 1181 <is_valid_xml/> | |
| 1182 </assert_contents> | |
| 1183 </output> | |
| 1184 </test> | |
| 1185 </xml> | |
| 1186 <xml name="autotest_ConsensusMapNormalizer"> | |
| 1187 <test expect_num_outputs="2"> | |
| 1188 <conditional name="adv_opts_cond"> | |
| 1189 <param name="adv_opts_selector" value="advanced"/> | |
| 1190 <param name="accession_filter" value=""/> | |
| 1191 <param name="description_filter" value=""/> | |
| 1192 <param name="force" value="false"/> | |
| 1193 <param name="test" value="true"/> | |
| 1194 </conditional> | |
| 1195 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> | |
| 1196 <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 1197 <param name="algorithm_type" value="robust_regression"/> | |
| 1198 <param name="ratio_threshold" value="0.67"/> | |
| 1199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1200 <output name="ctd_out" ftype="xml"> | |
| 1201 <assert_contents> | |
| 1202 <is_valid_xml/> | |
| 1203 </assert_contents> | |
| 1204 </output> | |
| 1205 </test> | |
| 1206 </xml> | |
| 1207 <xml name="autotest_CruxAdapter"> | |
| 1208 <test expect_num_outputs="2"> | |
| 1209 <conditional name="adv_opts_cond"> | |
| 1210 <param name="adv_opts_selector" value="advanced"/> | |
| 1211 <param name="custom_enzyme" value=""/> | |
| 1212 <param name="decoy_prefix" value="decoy_"/> | |
| 1213 <param name="deisotope" value="false"/> | |
| 1214 <param name="report_decoys" value="false"/> | |
| 1215 <param name="force" value="false"/> | |
| 1216 <param name="test" value="true"/> | |
| 1217 </conditional> | |
| 1218 <param name="in" value="spectra_comet.mzML"/> | |
| 1219 <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1220 <param name="database" value="proteins.fasta"/> | |
| 1221 <param name="extra_index_args" value=""/> | |
| 1222 <param name="extra_search_args" value=""/> | |
| 1223 <param name="extra_percolator_args" value=""/> | |
| 1224 <param name="precursor_mass_tolerance" value="10.0"/> | |
| 1225 <param name="precursor_mass_units" value="ppm"/> | |
| 1226 <param name="fragment_bin_offset" value="0.0"/> | |
| 1227 <param name="fragment_bin_width" value="0.02"/> | |
| 1228 <param name="isotope_error" value=""/> | |
| 1229 <param name="run_percolator" value="false"/> | |
| 1230 <param name="enzyme" value="trypsin"/> | |
| 1231 <param name="digestion" value="full-digest"/> | |
| 1232 <param name="allowed_missed_cleavages" value="0"/> | |
| 1233 <param name="decoy_format" value="shuffle"/> | |
| 1234 <param name="keep_terminal_aminos" value="NC"/> | |
| 1235 <param name="cterm_modifications" value=""/> | |
| 1236 <param name="nterm_modifications" value=""/> | |
| 1237 <param name="modifications" value=""/> | |
| 1238 <param name="test_fdr" value="0.01"/> | |
| 1239 <param name="train_fdr" value="0.01"/> | |
| 1240 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1241 <output name="ctd_out" ftype="xml"> | |
| 1242 <assert_contents> | |
| 1243 <is_valid_xml/> | |
| 1244 </assert_contents> | |
| 1245 </output> | |
| 1246 </test> | |
| 1247 </xml> | |
| 1248 <xml name="autotest_CVInspector"> | |
| 1249 </xml> | |
| 1250 <xml name="autotest_DatabaseFilter"> | |
| 1251 <test expect_num_outputs="2"> | |
| 1252 <conditional name="adv_opts_cond"> | |
| 1253 <param name="adv_opts_selector" value="advanced"/> | |
| 1254 <param name="force" value="false"/> | |
| 1255 <param name="test" value="true"/> | |
| 1256 </conditional> | |
| 1257 <param name="in" value="DatabaseFilter_1.fasta"/> | |
| 1258 <param name="id" value="DatabaseFilter_1.idXML"/> | |
| 1259 <param name="method" value="whitelist"/> | |
| 1260 <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1261 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1262 <output name="ctd_out" ftype="xml"> | |
| 1263 <assert_contents> | |
| 1264 <is_valid_xml/> | |
| 1265 </assert_contents> | |
| 1266 </output> | |
| 1267 </test> | |
| 1268 <test expect_num_outputs="2"> | |
| 1269 <conditional name="adv_opts_cond"> | |
| 1270 <param name="adv_opts_selector" value="advanced"/> | |
| 1271 <param name="force" value="false"/> | |
| 1272 <param name="test" value="true"/> | |
| 1273 </conditional> | |
| 1274 <param name="in" value="DatabaseFilter_1.fasta"/> | |
| 1275 <param name="id" value="DatabaseFilter_1.idXML"/> | |
| 1276 <param name="method" value="blacklist"/> | |
| 1277 <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1278 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1279 <output name="ctd_out" ftype="xml"> | |
| 1280 <assert_contents> | |
| 1281 <is_valid_xml/> | |
| 1282 </assert_contents> | |
| 1283 </output> | |
| 1284 </test> | |
| 1285 <test expect_num_outputs="2"> | |
| 1286 <conditional name="adv_opts_cond"> | |
| 1287 <param name="adv_opts_selector" value="advanced"/> | |
| 1288 <param name="force" value="false"/> | |
| 1289 <param name="test" value="true"/> | |
| 1290 </conditional> | |
| 1291 <param name="in" value="DatabaseFilter_3.fasta"/> | |
| 1292 <param name="id" value="DatabaseFilter_3.mzid"/> | |
| 1293 <param name="method" value="whitelist"/> | |
| 1294 <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1295 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1296 <output name="ctd_out" ftype="xml"> | |
| 1297 <assert_contents> | |
| 1298 <is_valid_xml/> | |
| 1299 </assert_contents> | |
| 1300 </output> | |
| 1301 </test> | |
| 1302 <test expect_num_outputs="2"> | |
| 1303 <conditional name="adv_opts_cond"> | |
| 1304 <param name="adv_opts_selector" value="advanced"/> | |
| 1305 <param name="force" value="false"/> | |
| 1306 <param name="test" value="true"/> | |
| 1307 </conditional> | |
| 1308 <param name="in" value="DatabaseFilter_3.fasta"/> | |
| 1309 <param name="id" value="DatabaseFilter_3.mzid"/> | |
| 1310 <param name="method" value="blacklist"/> | |
| 1311 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1312 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1313 <output name="ctd_out" ftype="xml"> | |
| 1314 <assert_contents> | |
| 1315 <is_valid_xml/> | |
| 1316 </assert_contents> | |
| 1317 </output> | |
| 1318 </test> | |
| 1319 </xml> | |
| 1320 <xml name="autotest_Decharger"> | |
| 1321 <test expect_num_outputs="4"> | |
| 1322 <conditional name="adv_opts_cond"> | |
| 1323 <param name="adv_opts_selector" value="advanced"/> | |
| 1324 <param name="force" value="false"/> | |
| 1325 <param name="test" value="true"/> | |
| 1326 </conditional> | |
| 1327 <param name="in" value="Decharger_input.featureXML"/> | |
| 1328 <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 1329 <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 1330 <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 1331 <section name="algorithm"> | |
| 1332 <section name="FeatureDeconvolution"> | |
| 1333 <param name="charge_min" value="1"/> | |
| 1334 <param name="charge_max" value="10"/> | |
| 1335 <param name="charge_span_max" value="4"/> | |
| 1336 <param name="q_try" value="feature"/> | |
| 1337 <param name="retention_max_diff" value="1.0"/> | |
| 1338 <param name="retention_max_diff_local" value="1.0"/> | |
| 1339 <param name="mass_max_diff" value="0.1"/> | |
| 1340 <param name="potential_adducts" value=""H:+:0.7" "Na:+:0.1" "(2)H4H-4:0:0.1:-2:heavy""/> | |
| 1341 <param name="max_neutrals" value="0"/> | |
| 1342 <param name="max_minority_bound" value="2"/> | |
| 1343 <param name="min_rt_overlap" value="0.66"/> | |
| 1344 <param name="intensity_filter" value="false"/> | |
| 1345 <param name="negative_mode" value="false"/> | |
| 1346 <param name="default_map_label" value="decharged features"/> | |
| 1347 <param name="verbose_level" value="0"/> | |
| 1348 </section> | |
| 1349 </section> | |
| 1350 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/> | |
| 1351 <output name="ctd_out" ftype="xml"> | |
| 1352 <assert_contents> | |
| 1353 <is_valid_xml/> | |
| 1354 </assert_contents> | |
| 1355 </output> | |
| 1356 </test> | |
| 1357 </xml> | |
| 1358 <xml name="autotest_DecoyDatabase"> | |
| 1359 <test expect_num_outputs="2"> | |
| 1360 <conditional name="adv_opts_cond"> | |
| 1361 <param name="adv_opts_selector" value="advanced"/> | |
| 1362 <param name="shuffle_max_attempts" value="30"/> | |
| 1363 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 1364 <param name="seed" value="1"/> | |
| 1365 <param name="force" value="false"/> | |
| 1366 <param name="test" value="true"/> | |
| 1367 </conditional> | |
| 1368 <param name="in" value="DecoyDatabase_1.fasta"/> | |
| 1369 <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1370 <param name="decoy_string" value="DECOY_"/> | |
| 1371 <param name="decoy_string_position" value="prefix"/> | |
| 1372 <param name="only_decoy" value="true"/> | |
| 1373 <param name="type" value="protein"/> | |
| 1374 <param name="method" value="reverse"/> | |
| 1375 <param name="enzyme" value="Trypsin"/> | |
| 1376 <section name="Decoy"> | |
| 1377 <param name="non_shuffle_pattern" value=""/> | |
| 1378 <param name="keepPeptideNTerm" value="true"/> | |
| 1379 <param name="keepPeptideCTerm" value="true"/> | |
| 1380 </section> | |
| 1381 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1382 <output name="ctd_out" ftype="xml"> | |
| 1383 <assert_contents> | |
| 1384 <is_valid_xml/> | |
| 1385 </assert_contents> | |
| 1386 </output> | |
| 1387 </test> | |
| 1388 <test expect_num_outputs="2"> | |
| 1389 <conditional name="adv_opts_cond"> | |
| 1390 <param name="adv_opts_selector" value="advanced"/> | |
| 1391 <param name="shuffle_max_attempts" value="30"/> | |
| 1392 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 1393 <param name="seed" value="42"/> | |
| 1394 <param name="force" value="false"/> | |
| 1395 <param name="test" value="true"/> | |
| 1396 </conditional> | |
| 1397 <param name="in" value="DecoyDatabase_1.fasta"/> | |
| 1398 <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1399 <param name="decoy_string" value="blabla"/> | |
| 1400 <param name="decoy_string_position" value="prefix"/> | |
| 1401 <param name="only_decoy" value="false"/> | |
| 1402 <param name="type" value="protein"/> | |
| 1403 <param name="method" value="shuffle"/> | |
| 1404 <param name="enzyme" value="Trypsin"/> | |
| 1405 <section name="Decoy"> | |
| 1406 <param name="non_shuffle_pattern" value="KRP"/> | |
| 1407 <param name="keepPeptideNTerm" value="true"/> | |
| 1408 <param name="keepPeptideCTerm" value="true"/> | |
| 1409 </section> | |
| 1410 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1411 <output name="ctd_out" ftype="xml"> | |
| 1412 <assert_contents> | |
| 1413 <is_valid_xml/> | |
| 1414 </assert_contents> | |
| 1415 </output> | |
| 1416 </test> | |
| 1417 <test expect_num_outputs="2"> | |
| 1418 <conditional name="adv_opts_cond"> | |
| 1419 <param name="adv_opts_selector" value="advanced"/> | |
| 1420 <param name="shuffle_max_attempts" value="30"/> | |
| 1421 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 1422 <param name="seed" value="42"/> | |
| 1423 <param name="force" value="false"/> | |
| 1424 <param name="test" value="true"/> | |
| 1425 </conditional> | |
| 1426 <param name="in" value="DecoyDatabase_1.fasta"/> | |
| 1427 <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1428 <param name="decoy_string" value="blabla"/> | |
| 1429 <param name="decoy_string_position" value="prefix"/> | |
| 1430 <param name="only_decoy" value="false"/> | |
| 1431 <param name="type" value="protein"/> | |
| 1432 <param name="method" value="shuffle"/> | |
| 1433 <param name="enzyme" value="Chymotrypsin"/> | |
| 1434 <section name="Decoy"> | |
| 1435 <param name="non_shuffle_pattern" value="KR"/> | |
| 1436 <param name="keepPeptideNTerm" value="true"/> | |
| 1437 <param name="keepPeptideCTerm" value="true"/> | |
| 1438 </section> | |
| 1439 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1440 <output name="ctd_out" ftype="xml"> | |
| 1441 <assert_contents> | |
| 1442 <is_valid_xml/> | |
| 1443 </assert_contents> | |
| 1444 </output> | |
| 1445 </test> | |
| 1446 <test expect_num_outputs="2"> | |
| 1447 <conditional name="adv_opts_cond"> | |
| 1448 <param name="adv_opts_selector" value="advanced"/> | |
| 1449 <param name="shuffle_max_attempts" value="30"/> | |
| 1450 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 1451 <param name="seed" value="42"/> | |
| 1452 <param name="force" value="false"/> | |
| 1453 <param name="test" value="true"/> | |
| 1454 </conditional> | |
| 1455 <param name="in" value="DecoyDatabase_4.fasta"/> | |
| 1456 <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> | |
| 1457 <param name="decoy_string" value="blabla"/> | |
| 1458 <param name="decoy_string_position" value="prefix"/> | |
| 1459 <param name="only_decoy" value="false"/> | |
| 1460 <param name="type" value="RNA"/> | |
| 1461 <param name="method" value="reverse"/> | |
| 1462 <param name="enzyme" value="Trypsin"/> | |
| 1463 <section name="Decoy"> | |
| 1464 <param name="non_shuffle_pattern" value=""/> | |
| 1465 <param name="keepPeptideNTerm" value="true"/> | |
| 1466 <param name="keepPeptideCTerm" value="true"/> | |
| 1467 </section> | |
| 1468 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1469 <output name="ctd_out" ftype="xml"> | |
| 1470 <assert_contents> | |
| 1471 <is_valid_xml/> | |
| 1472 </assert_contents> | |
| 1473 </output> | |
| 1474 </test> | |
| 1475 </xml> | |
| 1476 <xml name="autotest_DeMeanderize"> | |
| 1477 </xml> | |
| 1478 <xml name="autotest_DTAExtractor"> | |
| 1479 <test expect_num_outputs="1"> | |
| 1480 <conditional name="adv_opts_cond"> | |
| 1481 <param name="adv_opts_selector" value="advanced"/> | |
| 1482 <param name="force" value="false"/> | |
| 1483 <param name="test" value="true"/> | |
| 1484 </conditional> | |
| 1485 <param name="in" value="DTAExtractor_1_input.mzML"/> | |
| 1486 <param name="out" value="DTAExtractor"/> | |
| 1487 <param name="mz" value=":"/> | |
| 1488 <param name="rt" value=":61"/> | |
| 1489 <param name="level" value="1,2,3"/> | |
| 1490 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1491 <output name="ctd_out" ftype="xml"> | |
| 1492 <assert_contents> | |
| 1493 <is_valid_xml/> | |
| 1494 </assert_contents> | |
| 1495 </output> | |
| 1496 </test> | |
| 1497 <test expect_num_outputs="1"> | |
| 1498 <conditional name="adv_opts_cond"> | |
| 1499 <param name="adv_opts_selector" value="advanced"/> | |
| 1500 <param name="force" value="false"/> | |
| 1501 <param name="test" value="true"/> | |
| 1502 </conditional> | |
| 1503 <param name="in" value="DTAExtractor_1_input.mzML"/> | |
| 1504 <param name="out" value="DTAExtractor"/> | |
| 1505 <param name="mz" value=":"/> | |
| 1506 <param name="rt" value=":"/> | |
| 1507 <param name="level" value="1"/> | |
| 1508 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1509 <output name="ctd_out" ftype="xml"> | |
| 1510 <assert_contents> | |
| 1511 <is_valid_xml/> | |
| 1512 </assert_contents> | |
| 1513 </output> | |
| 1514 </test> | |
| 1515 <test expect_num_outputs="1"> | |
| 1516 <conditional name="adv_opts_cond"> | |
| 1517 <param name="adv_opts_selector" value="advanced"/> | |
| 1518 <param name="force" value="false"/> | |
| 1519 <param name="test" value="true"/> | |
| 1520 </conditional> | |
| 1521 <param name="in" value="DTAExtractor_1_input.mzML"/> | |
| 1522 <param name="out" value="DTAExtractor"/> | |
| 1523 <param name="mz" value=":1000"/> | |
| 1524 <param name="rt" value=":"/> | |
| 1525 <param name="level" value="2"/> | |
| 1526 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1527 <output name="ctd_out" ftype="xml"> | |
| 1528 <assert_contents> | |
| 1529 <is_valid_xml/> | |
| 1530 </assert_contents> | |
| 1531 </output> | |
| 1532 </test> | |
| 1533 </xml> | |
| 1534 <xml name="autotest_EICExtractor"> | |
| 1535 </xml> | |
| 1536 <xml name="autotest_Epifany"> | |
| 1537 <test expect_num_outputs="2"> | |
| 1538 <conditional name="adv_opts_cond"> | |
| 1539 <param name="adv_opts_selector" value="advanced"/> | |
| 1540 <param name="conservative_fdr" value="true"/> | |
| 1541 <param name="min_psms_extreme_probability" value="0.0"/> | |
| 1542 <param name="force" value="false"/> | |
| 1543 <param name="test" value="true"/> | |
| 1544 </conditional> | |
| 1545 <param name="in" value="FidoAdapter_1_input.idXML"/> | |
| 1546 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1547 <param name="protein_fdr" value="false"/> | |
| 1548 <param name="greedy_group_resolution" value="none"/> | |
| 1549 <param name="max_psms_extreme_probability" value="1.0"/> | |
| 1550 <section name="algorithm"> | |
| 1551 <param name="psm_probability_cutoff" value="0.001"/> | |
| 1552 <param name="top_PSMs" value="1"/> | |
| 1553 <param name="update_PSM_probabilities" value="true"/> | |
| 1554 <param name="user_defined_priors" value="false"/> | |
| 1555 <param name="annotate_group_probabilities" value="true"/> | |
| 1556 <param name="use_ids_outside_features" value="false"/> | |
| 1557 <section name="model_parameters"> | |
| 1558 <param name="prot_prior" value="0.7"/> | |
| 1559 <param name="pep_emission" value="0.1"/> | |
| 1560 <param name="pep_spurious_emission" value="0.001"/> | |
| 1561 <param name="pep_prior" value="0.1"/> | |
| 1562 <param name="regularize" value="false"/> | |
| 1563 <param name="extended_model" value="false"/> | |
| 1564 </section> | |
| 1565 <section name="loopy_belief_propagation"> | |
| 1566 <param name="scheduling_type" value="priority"/> | |
| 1567 <param name="convergence_threshold" value="1e-05"/> | |
| 1568 <param name="dampening_lambda" value="0.001"/> | |
| 1569 <param name="max_nr_iterations" value="2147483647"/> | |
| 1570 <param name="p_norm_inference" value="1.0"/> | |
| 1571 </section> | |
| 1572 <section name="param_optimize"> | |
| 1573 <param name="aucweight" value="0.3"/> | |
| 1574 <param name="conservative_fdr" value="true"/> | |
| 1575 </section> | |
| 1576 </section> | |
| 1577 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1578 <output name="ctd_out" ftype="xml"> | |
| 1579 <assert_contents> | |
| 1580 <is_valid_xml/> | |
| 1581 </assert_contents> | |
| 1582 </output> | |
| 1583 </test> | |
| 1584 </xml> | |
| 1585 <xml name="autotest_ERPairFinder"> | |
| 1586 </xml> | |
| 1587 <xml name="autotest_ExternalCalibration"> | |
| 1588 <test expect_num_outputs="2"> | |
| 1589 <conditional name="adv_opts_cond"> | |
| 1590 <param name="adv_opts_selector" value="advanced"/> | |
| 1591 <param name="force" value="false"/> | |
| 1592 <param name="test" value="true"/> | |
| 1593 </conditional> | |
| 1594 <param name="in" value="ExternalCalibration_1_input.mzML"/> | |
| 1595 <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 1596 <param name="offset" value="-5.5"/> | |
| 1597 <param name="slope" value="0.0001"/> | |
| 1598 <param name="power" value="0.0"/> | |
| 1599 <param name="ms_level" value="1"/> | |
| 1600 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1601 <output name="ctd_out" ftype="xml"> | |
| 1602 <assert_contents> | |
| 1603 <is_valid_xml/> | |
| 1604 </assert_contents> | |
| 1605 </output> | |
| 1606 </test> | |
| 1607 <test expect_num_outputs="2"> | |
| 1608 <conditional name="adv_opts_cond"> | |
| 1609 <param name="adv_opts_selector" value="advanced"/> | |
| 1610 <param name="force" value="false"/> | |
| 1611 <param name="test" value="true"/> | |
| 1612 </conditional> | |
| 1613 <param name="in" value="ExternalCalibration_1_input.mzML"/> | |
| 1614 <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 1615 <param name="offset" value="-5.5"/> | |
| 1616 <param name="slope" value="0.0001"/> | |
| 1617 <param name="power" value="0.0"/> | |
| 1618 <param name="ms_level" value="2"/> | |
| 1619 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1620 <output name="ctd_out" ftype="xml"> | |
| 1621 <assert_contents> | |
| 1622 <is_valid_xml/> | |
| 1623 </assert_contents> | |
| 1624 </output> | |
| 1625 </test> | |
| 1626 </xml> | |
| 1627 <xml name="autotest_FalseDiscoveryRate"> | |
| 1628 <test expect_num_outputs="2"> | |
| 1629 <conditional name="adv_opts_cond"> | |
| 1630 <param name="adv_opts_selector" value="advanced"/> | |
| 1631 <param name="force" value="false"/> | |
| 1632 <param name="test" value="true"/> | |
| 1633 </conditional> | |
| 1634 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> | |
| 1635 <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1636 <param name="PSM" value="true"/> | |
| 1637 <param name="protein" value="false"/> | |
| 1638 <section name="FDR"> | |
| 1639 <param name="PSM" value="1.0"/> | |
| 1640 <param name="protein" value="1.0"/> | |
| 1641 <section name="cleanup"> | |
| 1642 <param name="remove_proteins_without_psms" value="true"/> | |
| 1643 <param name="remove_psms_without_proteins" value="true"/> | |
| 1644 <param name="remove_spectra_without_psms" value="true"/> | |
| 1645 </section> | |
| 1646 </section> | |
| 1647 <section name="algorithm"> | |
| 1648 <param name="no_qvalues" value="false"/> | |
| 1649 <param name="use_all_hits" value="false"/> | |
| 1650 <param name="split_charge_variants" value="false"/> | |
| 1651 <param name="treat_runs_separately" value="false"/> | |
| 1652 <param name="add_decoy_peptides" value="false"/> | |
| 1653 <param name="add_decoy_proteins" value="false"/> | |
| 1654 <param name="conservative" value="true"/> | |
| 1655 </section> | |
| 1656 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1657 <output name="ctd_out" ftype="xml"> | |
| 1658 <assert_contents> | |
| 1659 <is_valid_xml/> | |
| 1660 </assert_contents> | |
| 1661 </output> | |
| 1662 </test> | |
| 1663 <test expect_num_outputs="2"> | |
| 1664 <conditional name="adv_opts_cond"> | |
| 1665 <param name="adv_opts_selector" value="advanced"/> | |
| 1666 <param name="force" value="false"/> | |
| 1667 <param name="test" value="true"/> | |
| 1668 </conditional> | |
| 1669 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> | |
| 1670 <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1671 <param name="PSM" value="true"/> | |
| 1672 <param name="protein" value="false"/> | |
| 1673 <section name="FDR"> | |
| 1674 <param name="PSM" value="1.0"/> | |
| 1675 <param name="protein" value="1.0"/> | |
| 1676 <section name="cleanup"> | |
| 1677 <param name="remove_proteins_without_psms" value="true"/> | |
| 1678 <param name="remove_psms_without_proteins" value="true"/> | |
| 1679 <param name="remove_spectra_without_psms" value="true"/> | |
| 1680 </section> | |
| 1681 </section> | |
| 1682 <section name="algorithm"> | |
| 1683 <param name="no_qvalues" value="false"/> | |
| 1684 <param name="use_all_hits" value="false"/> | |
| 1685 <param name="split_charge_variants" value="false"/> | |
| 1686 <param name="treat_runs_separately" value="true"/> | |
| 1687 <param name="add_decoy_peptides" value="false"/> | |
| 1688 <param name="add_decoy_proteins" value="false"/> | |
| 1689 <param name="conservative" value="true"/> | |
| 1690 </section> | |
| 1691 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1692 <output name="ctd_out" ftype="xml"> | |
| 1693 <assert_contents> | |
| 1694 <is_valid_xml/> | |
| 1695 </assert_contents> | |
| 1696 </output> | |
| 1697 </test> | |
| 1698 <test expect_num_outputs="2"> | |
| 1699 <conditional name="adv_opts_cond"> | |
| 1700 <param name="adv_opts_selector" value="advanced"/> | |
| 1701 <param name="force" value="false"/> | |
| 1702 <param name="test" value="true"/> | |
| 1703 </conditional> | |
| 1704 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> | |
| 1705 <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1706 <param name="PSM" value="true"/> | |
| 1707 <param name="protein" value="false"/> | |
| 1708 <section name="FDR"> | |
| 1709 <param name="PSM" value="1.0"/> | |
| 1710 <param name="protein" value="1.0"/> | |
| 1711 <section name="cleanup"> | |
| 1712 <param name="remove_proteins_without_psms" value="true"/> | |
| 1713 <param name="remove_psms_without_proteins" value="true"/> | |
| 1714 <param name="remove_spectra_without_psms" value="true"/> | |
| 1715 </section> | |
| 1716 </section> | |
| 1717 <section name="algorithm"> | |
| 1718 <param name="no_qvalues" value="false"/> | |
| 1719 <param name="use_all_hits" value="false"/> | |
| 1720 <param name="split_charge_variants" value="true"/> | |
| 1721 <param name="treat_runs_separately" value="false"/> | |
| 1722 <param name="add_decoy_peptides" value="false"/> | |
| 1723 <param name="add_decoy_proteins" value="false"/> | |
| 1724 <param name="conservative" value="true"/> | |
| 1725 </section> | |
| 1726 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1727 <output name="ctd_out" ftype="xml"> | |
| 1728 <assert_contents> | |
| 1729 <is_valid_xml/> | |
| 1730 </assert_contents> | |
| 1731 </output> | |
| 1732 </test> | |
| 1733 <test expect_num_outputs="2"> | |
| 1734 <conditional name="adv_opts_cond"> | |
| 1735 <param name="adv_opts_selector" value="advanced"/> | |
| 1736 <param name="force" value="false"/> | |
| 1737 <param name="test" value="true"/> | |
| 1738 </conditional> | |
| 1739 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/> | |
| 1740 <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1741 <param name="PSM" value="true"/> | |
| 1742 <param name="protein" value="false"/> | |
| 1743 <section name="FDR"> | |
| 1744 <param name="PSM" value="1.0"/> | |
| 1745 <param name="protein" value="1.0"/> | |
| 1746 <section name="cleanup"> | |
| 1747 <param name="remove_proteins_without_psms" value="true"/> | |
| 1748 <param name="remove_psms_without_proteins" value="true"/> | |
| 1749 <param name="remove_spectra_without_psms" value="true"/> | |
| 1750 </section> | |
| 1751 </section> | |
| 1752 <section name="algorithm"> | |
| 1753 <param name="no_qvalues" value="false"/> | |
| 1754 <param name="use_all_hits" value="false"/> | |
| 1755 <param name="split_charge_variants" value="true"/> | |
| 1756 <param name="treat_runs_separately" value="false"/> | |
| 1757 <param name="add_decoy_peptides" value="false"/> | |
| 1758 <param name="add_decoy_proteins" value="false"/> | |
| 1759 <param name="conservative" value="true"/> | |
| 1760 </section> | |
| 1761 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1762 <output name="ctd_out" ftype="xml"> | |
| 1763 <assert_contents> | |
| 1764 <is_valid_xml/> | |
| 1765 </assert_contents> | |
| 1766 </output> | |
| 1767 </test> | |
| 1768 <test expect_num_outputs="2"> | |
| 1769 <conditional name="adv_opts_cond"> | |
| 1770 <param name="adv_opts_selector" value="advanced"/> | |
| 1771 <param name="force" value="true"/> | |
| 1772 <param name="test" value="true"/> | |
| 1773 </conditional> | |
| 1774 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/> | |
| 1775 <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1776 <param name="PSM" value="false"/> | |
| 1777 <param name="protein" value="true"/> | |
| 1778 <section name="FDR"> | |
| 1779 <param name="PSM" value="1.0"/> | |
| 1780 <param name="protein" value="1.0"/> | |
| 1781 <section name="cleanup"> | |
| 1782 <param name="remove_proteins_without_psms" value="true"/> | |
| 1783 <param name="remove_psms_without_proteins" value="true"/> | |
| 1784 <param name="remove_spectra_without_psms" value="true"/> | |
| 1785 </section> | |
| 1786 </section> | |
| 1787 <section name="algorithm"> | |
| 1788 <param name="no_qvalues" value="false"/> | |
| 1789 <param name="use_all_hits" value="false"/> | |
| 1790 <param name="split_charge_variants" value="false"/> | |
| 1791 <param name="treat_runs_separately" value="false"/> | |
| 1792 <param name="add_decoy_peptides" value="false"/> | |
| 1793 <param name="add_decoy_proteins" value="true"/> | |
| 1794 <param name="conservative" value="true"/> | |
| 1795 </section> | |
| 1796 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1797 <output name="ctd_out" ftype="xml"> | |
| 1798 <assert_contents> | |
| 1799 <is_valid_xml/> | |
| 1800 </assert_contents> | |
| 1801 </output> | |
| 1802 </test> | |
| 1803 <test expect_num_outputs="2"> | |
| 1804 <conditional name="adv_opts_cond"> | |
| 1805 <param name="adv_opts_selector" value="advanced"/> | |
| 1806 <param name="force" value="false"/> | |
| 1807 <param name="test" value="true"/> | |
| 1808 </conditional> | |
| 1809 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/> | |
| 1810 <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1811 <param name="PSM" value="true"/> | |
| 1812 <param name="protein" value="false"/> | |
| 1813 <section name="FDR"> | |
| 1814 <param name="PSM" value="0.05"/> | |
| 1815 <param name="protein" value="1.0"/> | |
| 1816 <section name="cleanup"> | |
| 1817 <param name="remove_proteins_without_psms" value="true"/> | |
| 1818 <param name="remove_psms_without_proteins" value="true"/> | |
| 1819 <param name="remove_spectra_without_psms" value="true"/> | |
| 1820 </section> | |
| 1821 </section> | |
| 1822 <section name="algorithm"> | |
| 1823 <param name="no_qvalues" value="false"/> | |
| 1824 <param name="use_all_hits" value="false"/> | |
| 1825 <param name="split_charge_variants" value="false"/> | |
| 1826 <param name="treat_runs_separately" value="false"/> | |
| 1827 <param name="add_decoy_peptides" value="false"/> | |
| 1828 <param name="add_decoy_proteins" value="false"/> | |
| 1829 <param name="conservative" value="true"/> | |
| 1830 </section> | |
| 1831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1832 <output name="ctd_out" ftype="xml"> | |
| 1833 <assert_contents> | |
| 1834 <is_valid_xml/> | |
| 1835 </assert_contents> | |
| 1836 </output> | |
| 1837 </test> | |
| 1838 <test expect_num_outputs="2"> | |
| 1839 <conditional name="adv_opts_cond"> | |
| 1840 <param name="adv_opts_selector" value="advanced"/> | |
| 1841 <param name="force" value="true"/> | |
| 1842 <param name="test" value="true"/> | |
| 1843 </conditional> | |
| 1844 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/> | |
| 1845 <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 1846 <param name="PSM" value="false"/> | |
| 1847 <param name="protein" value="true"/> | |
| 1848 <section name="FDR"> | |
| 1849 <param name="PSM" value="1.0"/> | |
| 1850 <param name="protein" value="0.3"/> | |
| 1851 <section name="cleanup"> | |
| 1852 <param name="remove_proteins_without_psms" value="true"/> | |
| 1853 <param name="remove_psms_without_proteins" value="true"/> | |
| 1854 <param name="remove_spectra_without_psms" value="true"/> | |
| 1855 </section> | |
| 1856 </section> | |
| 1857 <section name="algorithm"> | |
| 1858 <param name="no_qvalues" value="false"/> | |
| 1859 <param name="use_all_hits" value="false"/> | |
| 1860 <param name="split_charge_variants" value="false"/> | |
| 1861 <param name="treat_runs_separately" value="false"/> | |
| 1862 <param name="add_decoy_peptides" value="false"/> | |
| 1863 <param name="add_decoy_proteins" value="false"/> | |
| 1864 <param name="conservative" value="true"/> | |
| 1865 </section> | |
| 1866 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1867 <output name="ctd_out" ftype="xml"> | |
| 1868 <assert_contents> | |
| 1869 <is_valid_xml/> | |
| 1870 </assert_contents> | |
| 1871 </output> | |
| 1872 </test> | |
| 1873 </xml> | |
| 1874 <xml name="autotest_FeatureFinderCentroided"> | |
| 1875 <test expect_num_outputs="2"> | |
| 1876 <conditional name="adv_opts_cond"> | |
| 1877 <param name="adv_opts_selector" value="advanced"/> | |
| 1878 <param name="force" value="false"/> | |
| 1879 <param name="test" value="true"/> | |
| 1880 <param name="pseudo_rt_shift" value="500.0"/> | |
| 1881 </conditional> | |
| 1882 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> | |
| 1883 <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 1884 <section name="algorithm"> | |
| 1885 <section name="intensity"> | |
| 1886 <param name="bins" value="1"/> | |
| 1887 </section> | |
| 1888 <section name="mass_trace"> | |
| 1889 <param name="mz_tolerance" value="0.02"/> | |
| 1890 <param name="min_spectra" value="14"/> | |
| 1891 <param name="max_missing" value="1"/> | |
| 1892 <param name="slope_bound" value="0.1"/> | |
| 1893 </section> | |
| 1894 <section name="isotopic_pattern"> | |
| 1895 <param name="charge_low" value="2"/> | |
| 1896 <param name="charge_high" value="2"/> | |
| 1897 <param name="mz_tolerance" value="0.02"/> | |
| 1898 <param name="intensity_percentage" value="10.0"/> | |
| 1899 <param name="intensity_percentage_optional" value="0.1"/> | |
| 1900 <param name="optional_fit_improvement" value="2.0"/> | |
| 1901 <param name="mass_window_width" value="100.0"/> | |
| 1902 <param name="abundance_12C" value="98.93"/> | |
| 1903 <param name="abundance_14N" value="99.632"/> | |
| 1904 </section> | |
| 1905 <section name="seed"> | |
| 1906 <param name="min_score" value="0.8"/> | |
| 1907 </section> | |
| 1908 <section name="fit"> | |
| 1909 <param name="max_iterations" value="500"/> | |
| 1910 </section> | |
| 1911 <section name="feature"> | |
| 1912 <param name="min_score" value="0.7"/> | |
| 1913 <param name="min_isotope_fit" value="0.8"/> | |
| 1914 <param name="min_trace_score" value="0.5"/> | |
| 1915 <param name="min_rt_span" value="0.333"/> | |
| 1916 <param name="max_rt_span" value="2.5"/> | |
| 1917 <param name="rt_shape" value="symmetric"/> | |
| 1918 <param name="max_intersection" value="0.35"/> | |
| 1919 <param name="reported_mz" value="monoisotopic"/> | |
| 1920 </section> | |
| 1921 <section name="user-seed"> | |
| 1922 <param name="rt_tolerance" value="5.0"/> | |
| 1923 <param name="mz_tolerance" value="1.1"/> | |
| 1924 <param name="min_score" value="0.5"/> | |
| 1925 </section> | |
| 1926 </section> | |
| 1927 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1928 <output name="ctd_out" ftype="xml"> | |
| 1929 <assert_contents> | |
| 1930 <is_valid_xml/> | |
| 1931 </assert_contents> | |
| 1932 </output> | |
| 1933 </test> | |
| 1934 </xml> | |
| 1935 <xml name="autotest_FeatureFinderIdentification"> | |
| 1936 <test expect_num_outputs="2"> | |
| 1937 <conditional name="adv_opts_cond"> | |
| 1938 <param name="adv_opts_selector" value="advanced"/> | |
| 1939 <param name="force" value="false"/> | |
| 1940 <param name="test" value="true"/> | |
| 1941 </conditional> | |
| 1942 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> | |
| 1943 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> | |
| 1944 <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 1945 <section name="extract"> | |
| 1946 <param name="batch_size" value="1000"/> | |
| 1947 <param name="mz_window" value="0.1"/> | |
| 1948 <param name="n_isotopes" value="2"/> | |
| 1949 <param name="isotope_pmin" value="0.0"/> | |
| 1950 <param name="rt_quantile" value="0.95"/> | |
| 1951 <param name="rt_window" value="0.0"/> | |
| 1952 </section> | |
| 1953 <section name="detect"> | |
| 1954 <param name="peak_width" value="60.0"/> | |
| 1955 <param name="min_peak_width" value="0.2"/> | |
| 1956 <param name="signal_to_noise" value="0.8"/> | |
| 1957 <param name="mapping_tolerance" value="0.0"/> | |
| 1958 </section> | |
| 1959 <section name="svm"> | |
| 1960 <param name="samples" value="0"/> | |
| 1961 <param name="no_selection" value="false"/> | |
| 1962 <param name="kernel" value="RBF"/> | |
| 1963 <param name="xval" value="5"/> | |
| 1964 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> | |
| 1965 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> | |
| 1966 <param name="epsilon" value="0.001"/> | |
| 1967 <param name="cache_size" value="100.0"/> | |
| 1968 <param name="no_shrinking" value="false"/> | |
| 1969 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> | |
| 1970 <param name="min_prob" value="0.0"/> | |
| 1971 </section> | |
| 1972 <section name="model"> | |
| 1973 <param name="type" value="none"/> | |
| 1974 <param name="add_zeros" value="0.2"/> | |
| 1975 <param name="unweighted_fit" value="false"/> | |
| 1976 <param name="no_imputation" value="false"/> | |
| 1977 <section name="check"> | |
| 1978 <param name="min_area" value="1.0"/> | |
| 1979 <param name="boundaries" value="0.5"/> | |
| 1980 <param name="width" value="10.0"/> | |
| 1981 <param name="asymmetry" value="10.0"/> | |
| 1982 </section> | |
| 1983 </section> | |
| 1984 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 1985 <output name="ctd_out" ftype="xml"> | |
| 1986 <assert_contents> | |
| 1987 <is_valid_xml/> | |
| 1988 </assert_contents> | |
| 1989 </output> | |
| 1990 </test> | |
| 1991 <test expect_num_outputs="2"> | |
| 1992 <conditional name="adv_opts_cond"> | |
| 1993 <param name="adv_opts_selector" value="advanced"/> | |
| 1994 <param name="force" value="false"/> | |
| 1995 <param name="test" value="true"/> | |
| 1996 </conditional> | |
| 1997 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> | |
| 1998 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> | |
| 1999 <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2000 <section name="extract"> | |
| 2001 <param name="batch_size" value="1000"/> | |
| 2002 <param name="mz_window" value="0.1"/> | |
| 2003 <param name="n_isotopes" value="2"/> | |
| 2004 <param name="isotope_pmin" value="0.0"/> | |
| 2005 <param name="rt_quantile" value="0.95"/> | |
| 2006 <param name="rt_window" value="0.0"/> | |
| 2007 </section> | |
| 2008 <section name="detect"> | |
| 2009 <param name="peak_width" value="60.0"/> | |
| 2010 <param name="min_peak_width" value="0.2"/> | |
| 2011 <param name="signal_to_noise" value="0.8"/> | |
| 2012 <param name="mapping_tolerance" value="0.0"/> | |
| 2013 </section> | |
| 2014 <section name="svm"> | |
| 2015 <param name="samples" value="0"/> | |
| 2016 <param name="no_selection" value="false"/> | |
| 2017 <param name="kernel" value="RBF"/> | |
| 2018 <param name="xval" value="5"/> | |
| 2019 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> | |
| 2020 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> | |
| 2021 <param name="epsilon" value="0.001"/> | |
| 2022 <param name="cache_size" value="100.0"/> | |
| 2023 <param name="no_shrinking" value="false"/> | |
| 2024 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> | |
| 2025 <param name="min_prob" value="0.0"/> | |
| 2026 </section> | |
| 2027 <section name="model"> | |
| 2028 <param name="type" value="symmetric"/> | |
| 2029 <param name="add_zeros" value="0.2"/> | |
| 2030 <param name="unweighted_fit" value="false"/> | |
| 2031 <param name="no_imputation" value="false"/> | |
| 2032 <section name="check"> | |
| 2033 <param name="min_area" value="1.0"/> | |
| 2034 <param name="boundaries" value="0.5"/> | |
| 2035 <param name="width" value="10.0"/> | |
| 2036 <param name="asymmetry" value="10.0"/> | |
| 2037 </section> | |
| 2038 </section> | |
| 2039 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 2040 <output name="ctd_out" ftype="xml"> | |
| 2041 <assert_contents> | |
| 2042 <is_valid_xml/> | |
| 2043 </assert_contents> | |
| 2044 </output> | |
| 2045 </test> | |
| 2046 <test expect_num_outputs="2"> | |
| 2047 <conditional name="adv_opts_cond"> | |
| 2048 <param name="adv_opts_selector" value="advanced"/> | |
| 2049 <param name="force" value="false"/> | |
| 2050 <param name="test" value="true"/> | |
| 2051 </conditional> | |
| 2052 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> | |
| 2053 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> | |
| 2054 <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2055 <section name="extract"> | |
| 2056 <param name="batch_size" value="10"/> | |
| 2057 <param name="mz_window" value="0.1"/> | |
| 2058 <param name="n_isotopes" value="2"/> | |
| 2059 <param name="isotope_pmin" value="0.0"/> | |
| 2060 <param name="rt_quantile" value="0.95"/> | |
| 2061 <param name="rt_window" value="0.0"/> | |
| 2062 </section> | |
| 2063 <section name="detect"> | |
| 2064 <param name="peak_width" value="60.0"/> | |
| 2065 <param name="min_peak_width" value="0.2"/> | |
| 2066 <param name="signal_to_noise" value="0.8"/> | |
| 2067 <param name="mapping_tolerance" value="0.0"/> | |
| 2068 </section> | |
| 2069 <section name="svm"> | |
| 2070 <param name="samples" value="0"/> | |
| 2071 <param name="no_selection" value="false"/> | |
| 2072 <param name="kernel" value="RBF"/> | |
| 2073 <param name="xval" value="5"/> | |
| 2074 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> | |
| 2075 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> | |
| 2076 <param name="epsilon" value="0.001"/> | |
| 2077 <param name="cache_size" value="100.0"/> | |
| 2078 <param name="no_shrinking" value="false"/> | |
| 2079 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> | |
| 2080 <param name="min_prob" value="0.0"/> | |
| 2081 </section> | |
| 2082 <section name="model"> | |
| 2083 <param name="type" value="none"/> | |
| 2084 <param name="add_zeros" value="0.2"/> | |
| 2085 <param name="unweighted_fit" value="false"/> | |
| 2086 <param name="no_imputation" value="false"/> | |
| 2087 <section name="check"> | |
| 2088 <param name="min_area" value="1.0"/> | |
| 2089 <param name="boundaries" value="0.5"/> | |
| 2090 <param name="width" value="10.0"/> | |
| 2091 <param name="asymmetry" value="10.0"/> | |
| 2092 </section> | |
| 2093 </section> | |
| 2094 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 2095 <output name="ctd_out" ftype="xml"> | |
| 2096 <assert_contents> | |
| 2097 <is_valid_xml/> | |
| 2098 </assert_contents> | |
| 2099 </output> | |
| 2100 </test> | |
| 2101 </xml> | |
| 2102 <xml name="autotest_FeatureFinderIsotopeWavelet"> | |
| 2103 </xml> | |
| 2104 <xml name="autotest_FeatureFinderMetaboIdent"> | |
| 2105 <test expect_num_outputs="2"> | |
| 2106 <conditional name="adv_opts_cond"> | |
| 2107 <param name="adv_opts_selector" value="advanced"/> | |
| 2108 <param name="force" value="false"/> | |
| 2109 <param name="test" value="true"/> | |
| 2110 </conditional> | |
| 2111 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/> | |
| 2112 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/> | |
| 2113 <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2114 <section name="extract"> | |
| 2115 <param name="mz_window" value="5.0"/> | |
| 2116 <param name="n_isotopes" value="2"/> | |
| 2117 <param name="isotope_pmin" value="0.0"/> | |
| 2118 <param name="rt_window" value="20.0"/> | |
| 2119 </section> | |
| 2120 <section name="detect"> | |
| 2121 <param name="peak_width" value="3.0"/> | |
| 2122 <param name="min_peak_width" value="0.2"/> | |
| 2123 <param name="signal_to_noise" value="0.8"/> | |
| 2124 </section> | |
| 2125 <section name="model"> | |
| 2126 <param name="type" value="symmetric"/> | |
| 2127 <param name="add_zeros" value="0.2"/> | |
| 2128 <param name="unweighted_fit" value="false"/> | |
| 2129 <param name="no_imputation" value="false"/> | |
| 2130 <section name="check"> | |
| 2131 <param name="min_area" value="1.0"/> | |
| 2132 <param name="boundaries" value="0.5"/> | |
| 2133 <param name="width" value="10.0"/> | |
| 2134 <param name="asymmetry" value="10.0"/> | |
| 2135 </section> | |
| 2136 </section> | |
| 2137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 2138 <output name="ctd_out" ftype="xml"> | |
| 2139 <assert_contents> | |
| 2140 <is_valid_xml/> | |
| 2141 </assert_contents> | |
| 2142 </output> | |
| 2143 </test> | |
| 2144 </xml> | |
| 2145 <xml name="autotest_FeatureFinderMetabo"> | |
| 2146 <test expect_num_outputs="2"> | |
| 2147 <conditional name="adv_opts_cond"> | |
| 2148 <param name="adv_opts_selector" value="advanced"/> | |
| 2149 <param name="force" value="false"/> | |
| 2150 <param name="test" value="true"/> | |
| 2151 </conditional> | |
| 2152 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> | |
| 2153 <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2154 <section name="algorithm"> | |
| 2155 <section name="common"> | |
| 2156 <param name="noise_threshold_int" value="10.0"/> | |
| 2157 <param name="chrom_peak_snr" value="3.0"/> | |
| 2158 <param name="chrom_fwhm" value="5.0"/> | |
| 2159 </section> | |
| 2160 <section name="mtd"> | |
| 2161 <param name="mass_error_ppm" value="20.0"/> | |
| 2162 <param name="reestimate_mt_sd" value="true"/> | |
| 2163 <param name="quant_method" value="area"/> | |
| 2164 <param name="trace_termination_criterion" value="outlier"/> | |
| 2165 <param name="trace_termination_outliers" value="5"/> | |
| 2166 <param name="min_sample_rate" value="0.5"/> | |
| 2167 <param name="min_trace_length" value="5.0"/> | |
| 2168 <param name="max_trace_length" value="300.0"/> | |
| 2169 </section> | |
| 2170 <section name="epd"> | |
| 2171 <param name="enabled" value="true"/> | |
| 2172 <param name="width_filtering" value="off"/> | |
| 2173 <param name="min_fwhm" value="3.0"/> | |
| 2174 <param name="max_fwhm" value="60.0"/> | |
| 2175 <param name="masstrace_snr_filtering" value="false"/> | |
| 2176 </section> | |
| 2177 <section name="ffm"> | |
| 2178 <param name="local_rt_range" value="10.0"/> | |
| 2179 <param name="local_mz_range" value="6.5"/> | |
| 2180 <param name="charge_lower_bound" value="1"/> | |
| 2181 <param name="charge_upper_bound" value="3"/> | |
| 2182 <param name="report_summed_ints" value="false"/> | |
| 2183 <param name="enable_RT_filtering" value="true"/> | |
| 2184 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> | |
| 2185 <param name="mz_scoring_13C" value="true"/> | |
| 2186 <param name="use_smoothed_intensities" value="true"/> | |
| 2187 <param name="report_convex_hulls" value="false"/> | |
| 2188 <param name="remove_single_traces" value="false"/> | |
| 2189 <param name="mz_scoring_by_elements" value="false"/> | |
| 2190 <param name="elements" value="CHNOPS"/> | |
| 2191 </section> | |
| 2192 </section> | |
| 2193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 2194 <output name="ctd_out" ftype="xml"> | |
| 2195 <assert_contents> | |
| 2196 <is_valid_xml/> | |
| 2197 </assert_contents> | |
| 2198 </output> | |
| 2199 </test> | |
| 2200 <test expect_num_outputs="2"> | |
| 2201 <conditional name="adv_opts_cond"> | |
| 2202 <param name="adv_opts_selector" value="advanced"/> | |
| 2203 <param name="force" value="false"/> | |
| 2204 <param name="test" value="true"/> | |
| 2205 </conditional> | |
| 2206 <param name="in" value="FeatureFinderMetabo_2_input.mzML"/> | |
| 2207 <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2208 <section name="algorithm"> | |
| 2209 <section name="common"> | |
| 2210 <param name="noise_threshold_int" value="100.0"/> | |
| 2211 <param name="chrom_peak_snr" value="0.0"/> | |
| 2212 <param name="chrom_fwhm" value="100.0"/> | |
| 2213 </section> | |
| 2214 <section name="mtd"> | |
| 2215 <param name="mass_error_ppm" value="5.0"/> | |
| 2216 <param name="reestimate_mt_sd" value="true"/> | |
| 2217 <param name="quant_method" value="median"/> | |
| 2218 <param name="trace_termination_criterion" value="sample_rate"/> | |
| 2219 <param name="trace_termination_outliers" value="2"/> | |
| 2220 <param name="min_sample_rate" value="0.01"/> | |
| 2221 <param name="min_trace_length" value="30.0"/> | |
| 2222 <param name="max_trace_length" value="3000.0"/> | |
| 2223 </section> | |
| 2224 <section name="epd"> | |
| 2225 <param name="enabled" value="false"/> | |
| 2226 <param name="width_filtering" value="off"/> | |
| 2227 <param name="min_fwhm" value="10.0"/> | |
| 2228 <param name="max_fwhm" value="80.0"/> | |
| 2229 <param name="masstrace_snr_filtering" value="false"/> | |
| 2230 </section> | |
| 2231 <section name="ffm"> | |
| 2232 <param name="local_rt_range" value="10.0"/> | |
| 2233 <param name="local_mz_range" value="4.5"/> | |
| 2234 <param name="charge_lower_bound" value="1"/> | |
| 2235 <param name="charge_upper_bound" value="3"/> | |
| 2236 <param name="report_summed_ints" value="false"/> | |
| 2237 <param name="enable_RT_filtering" value="false"/> | |
| 2238 <param name="isotope_filtering_model" value="none"/> | |
| 2239 <param name="mz_scoring_13C" value="false"/> | |
| 2240 <param name="use_smoothed_intensities" value="false"/> | |
| 2241 <param name="report_convex_hulls" value="true"/> | |
| 2242 <param name="remove_single_traces" value="false"/> | |
| 2243 <param name="mz_scoring_by_elements" value="false"/> | |
| 2244 <param name="elements" value="CHNOPS"/> | |
| 2245 </section> | |
| 2246 </section> | |
| 2247 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 2248 <output name="ctd_out" ftype="xml"> | |
| 2249 <assert_contents> | |
| 2250 <is_valid_xml/> | |
| 2251 </assert_contents> | |
| 2252 </output> | |
| 2253 </test> | |
| 2254 <test expect_num_outputs="3"> | |
| 2255 <conditional name="adv_opts_cond"> | |
| 2256 <param name="adv_opts_selector" value="advanced"/> | |
| 2257 <param name="force" value="false"/> | |
| 2258 <param name="test" value="true"/> | |
| 2259 </conditional> | |
| 2260 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> | |
| 2261 <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2262 <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 2263 <section name="algorithm"> | |
| 2264 <section name="common"> | |
| 2265 <param name="noise_threshold_int" value="10.0"/> | |
| 2266 <param name="chrom_peak_snr" value="3.0"/> | |
| 2267 <param name="chrom_fwhm" value="5.0"/> | |
| 2268 </section> | |
| 2269 <section name="mtd"> | |
| 2270 <param name="mass_error_ppm" value="5.0"/> | |
| 2271 <param name="reestimate_mt_sd" value="true"/> | |
| 2272 <param name="quant_method" value="area"/> | |
| 2273 <param name="trace_termination_criterion" value="outlier"/> | |
| 2274 <param name="trace_termination_outliers" value="5"/> | |
| 2275 <param name="min_sample_rate" value="0.5"/> | |
| 2276 <param name="min_trace_length" value="5.0"/> | |
| 2277 <param name="max_trace_length" value="-1.0"/> | |
| 2278 </section> | |
| 2279 <section name="epd"> | |
| 2280 <param name="enabled" value="true"/> | |
| 2281 <param name="width_filtering" value="fixed"/> | |
| 2282 <param name="min_fwhm" value="3.0"/> | |
| 2283 <param name="max_fwhm" value="60.0"/> | |
| 2284 <param name="masstrace_snr_filtering" value="false"/> | |
| 2285 </section> | |
| 2286 <section name="ffm"> | |
| 2287 <param name="local_rt_range" value="10.0"/> | |
| 2288 <param name="local_mz_range" value="6.5"/> | |
| 2289 <param name="charge_lower_bound" value="1"/> | |
| 2290 <param name="charge_upper_bound" value="3"/> | |
| 2291 <param name="report_summed_ints" value="false"/> | |
| 2292 <param name="enable_RT_filtering" value="true"/> | |
| 2293 <param name="isotope_filtering_model" value="none"/> | |
| 2294 <param name="mz_scoring_13C" value="true"/> | |
| 2295 <param name="use_smoothed_intensities" value="true"/> | |
| 2296 <param name="report_convex_hulls" value="true"/> | |
| 2297 <param name="remove_single_traces" value="false"/> | |
| 2298 <param name="mz_scoring_by_elements" value="false"/> | |
| 2299 <param name="elements" value="CHNOPS"/> | |
| 2300 </section> | |
| 2301 </section> | |
| 2302 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> | |
| 2303 <output name="ctd_out" ftype="xml"> | |
| 2304 <assert_contents> | |
| 2305 <is_valid_xml/> | |
| 2306 </assert_contents> | |
| 2307 </output> | |
| 2308 </test> | |
| 2309 <test expect_num_outputs="3"> | |
| 2310 <conditional name="adv_opts_cond"> | |
| 2311 <param name="adv_opts_selector" value="advanced"/> | |
| 2312 <param name="force" value="false"/> | |
| 2313 <param name="test" value="true"/> | |
| 2314 </conditional> | |
| 2315 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> | |
| 2316 <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2317 <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 2318 <section name="algorithm"> | |
| 2319 <section name="common"> | |
| 2320 <param name="noise_threshold_int" value="10.0"/> | |
| 2321 <param name="chrom_peak_snr" value="3.0"/> | |
| 2322 <param name="chrom_fwhm" value="5.0"/> | |
| 2323 </section> | |
| 2324 <section name="mtd"> | |
| 2325 <param name="mass_error_ppm" value="5.0"/> | |
| 2326 <param name="reestimate_mt_sd" value="true"/> | |
| 2327 <param name="quant_method" value="area"/> | |
| 2328 <param name="trace_termination_criterion" value="outlier"/> | |
| 2329 <param name="trace_termination_outliers" value="5"/> | |
| 2330 <param name="min_sample_rate" value="0.5"/> | |
| 2331 <param name="min_trace_length" value="5.0"/> | |
| 2332 <param name="max_trace_length" value="-1.0"/> | |
| 2333 </section> | |
| 2334 <section name="epd"> | |
| 2335 <param name="enabled" value="true"/> | |
| 2336 <param name="width_filtering" value="fixed"/> | |
| 2337 <param name="min_fwhm" value="3.0"/> | |
| 2338 <param name="max_fwhm" value="60.0"/> | |
| 2339 <param name="masstrace_snr_filtering" value="false"/> | |
| 2340 </section> | |
| 2341 <section name="ffm"> | |
| 2342 <param name="local_rt_range" value="10.0"/> | |
| 2343 <param name="local_mz_range" value="6.5"/> | |
| 2344 <param name="charge_lower_bound" value="1"/> | |
| 2345 <param name="charge_upper_bound" value="3"/> | |
| 2346 <param name="report_summed_ints" value="false"/> | |
| 2347 <param name="enable_RT_filtering" value="true"/> | |
| 2348 <param name="isotope_filtering_model" value="none"/> | |
| 2349 <param name="mz_scoring_13C" value="true"/> | |
| 2350 <param name="use_smoothed_intensities" value="true"/> | |
| 2351 <param name="report_convex_hulls" value="true"/> | |
| 2352 <param name="remove_single_traces" value="true"/> | |
| 2353 <param name="mz_scoring_by_elements" value="false"/> | |
| 2354 <param name="elements" value="CHNOPS"/> | |
| 2355 </section> | |
| 2356 </section> | |
| 2357 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> | |
| 2358 <output name="ctd_out" ftype="xml"> | |
| 2359 <assert_contents> | |
| 2360 <is_valid_xml/> | |
| 2361 </assert_contents> | |
| 2362 </output> | |
| 2363 </test> | |
| 2364 <test expect_num_outputs="2"> | |
| 2365 <conditional name="adv_opts_cond"> | |
| 2366 <param name="adv_opts_selector" value="advanced"/> | |
| 2367 <param name="force" value="false"/> | |
| 2368 <param name="test" value="true"/> | |
| 2369 </conditional> | |
| 2370 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> | |
| 2371 <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2372 <section name="algorithm"> | |
| 2373 <section name="common"> | |
| 2374 <param name="noise_threshold_int" value="10.0"/> | |
| 2375 <param name="chrom_peak_snr" value="3.0"/> | |
| 2376 <param name="chrom_fwhm" value="5.0"/> | |
| 2377 </section> | |
| 2378 <section name="mtd"> | |
| 2379 <param name="mass_error_ppm" value="20.0"/> | |
| 2380 <param name="reestimate_mt_sd" value="true"/> | |
| 2381 <param name="quant_method" value="max_height"/> | |
| 2382 <param name="trace_termination_criterion" value="outlier"/> | |
| 2383 <param name="trace_termination_outliers" value="5"/> | |
| 2384 <param name="min_sample_rate" value="0.5"/> | |
| 2385 <param name="min_trace_length" value="5.0"/> | |
| 2386 <param name="max_trace_length" value="300.0"/> | |
| 2387 </section> | |
| 2388 <section name="epd"> | |
| 2389 <param name="enabled" value="true"/> | |
| 2390 <param name="width_filtering" value="off"/> | |
| 2391 <param name="min_fwhm" value="3.0"/> | |
| 2392 <param name="max_fwhm" value="60.0"/> | |
| 2393 <param name="masstrace_snr_filtering" value="false"/> | |
| 2394 </section> | |
| 2395 <section name="ffm"> | |
| 2396 <param name="local_rt_range" value="10.0"/> | |
| 2397 <param name="local_mz_range" value="6.5"/> | |
| 2398 <param name="charge_lower_bound" value="1"/> | |
| 2399 <param name="charge_upper_bound" value="3"/> | |
| 2400 <param name="report_summed_ints" value="false"/> | |
| 2401 <param name="enable_RT_filtering" value="true"/> | |
| 2402 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> | |
| 2403 <param name="mz_scoring_13C" value="true"/> | |
| 2404 <param name="use_smoothed_intensities" value="true"/> | |
| 2405 <param name="report_convex_hulls" value="false"/> | |
| 2406 <param name="remove_single_traces" value="false"/> | |
| 2407 <param name="mz_scoring_by_elements" value="false"/> | |
| 2408 <param name="elements" value="CHNOPS"/> | |
| 2409 </section> | |
| 2410 </section> | |
| 2411 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 2412 <output name="ctd_out" ftype="xml"> | |
| 2413 <assert_contents> | |
| 2414 <is_valid_xml/> | |
| 2415 </assert_contents> | |
| 2416 </output> | |
| 2417 </test> | |
| 2418 </xml> | |
| 2419 <xml name="autotest_FeatureFinderMRM"> | |
| 2420 <test expect_num_outputs="2"> | |
| 2421 <conditional name="adv_opts_cond"> | |
| 2422 <param name="adv_opts_selector" value="advanced"/> | |
| 2423 <param name="force" value="false"/> | |
| 2424 <param name="test" value="true"/> | |
| 2425 </conditional> | |
| 2426 <param name="in" value="FeatureFinderMRM_1_input.mzML"/> | |
| 2427 <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2428 <section name="algorithm"> | |
| 2429 <param name="min_rt_distance" value="10.0"/> | |
| 2430 <param name="min_num_peaks_per_feature" value="5"/> | |
| 2431 <param name="min_signal_to_noise_ratio" value="2.0"/> | |
| 2432 <param name="write_debug_files" value="false"/> | |
| 2433 <param name="resample_traces" value="false"/> | |
| 2434 <param name="write_debuginfo" value="false"/> | |
| 2435 </section> | |
| 2436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 2437 <output name="ctd_out" ftype="xml"> | |
| 2438 <assert_contents> | |
| 2439 <is_valid_xml/> | |
| 2440 </assert_contents> | |
| 2441 </output> | |
| 2442 </test> | |
| 2443 </xml> | |
| 2444 <xml name="autotest_FeatureFinderMultiplex"> | |
| 2445 <test expect_num_outputs="3"> | |
| 2446 <conditional name="adv_opts_cond"> | |
| 2447 <param name="adv_opts_selector" value="advanced"/> | |
| 2448 <param name="force" value="false"/> | |
| 2449 <param name="test" value="true"/> | |
| 2450 </conditional> | |
| 2451 <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/> | |
| 2452 <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2453 <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2454 <section name="algorithm"> | |
| 2455 <param name="labels" value="[Dimethyl0][Dimethyl8]"/> | |
| 2456 <param name="charge" value="1:4"/> | |
| 2457 <param name="isotopes_per_peptide" value="3:6"/> | |
| 2458 <param name="rt_typical" value="90.0"/> | |
| 2459 <param name="rt_band" value="10.0"/> | |
| 2460 <param name="rt_min" value="5.0"/> | |
| 2461 <param name="mz_tolerance" value="40.0"/> | |
| 2462 <param name="mz_unit" value="ppm"/> | |
| 2463 <param name="intensity_cutoff" value="10.0"/> | |
| 2464 <param name="peptide_similarity" value="0.8"/> | |
| 2465 <param name="averagine_similarity" value="0.75"/> | |
| 2466 <param name="averagine_similarity_scaling" value="0.75"/> | |
| 2467 <param name="missed_cleavages" value="1"/> | |
| 2468 <param name="spectrum_type" value="automatic"/> | |
| 2469 <param name="averagine_type" value="peptide"/> | |
| 2470 <param name="knock_out" value="false"/> | |
| 2471 </section> | |
| 2472 <section name="labels"> | |
| 2473 <param name="Arg6" value="6.0201290268"/> | |
| 2474 <param name="Arg10" value="10.0082686"/> | |
| 2475 <param name="Lys4" value="4.0251069836"/> | |
| 2476 <param name="Lys6" value="6.0201290268"/> | |
| 2477 <param name="Lys8" value="8.0141988132"/> | |
| 2478 <param name="Leu3" value="3.01883"/> | |
| 2479 <param name="Dimethyl0" value="28.0313"/> | |
| 2480 <param name="Dimethyl4" value="32.056407"/> | |
| 2481 <param name="Dimethyl6" value="34.063117"/> | |
| 2482 <param name="Dimethyl8" value="36.07567"/> | |
| 2483 <param name="ICPL0" value="105.021464"/> | |
| 2484 <param name="ICPL4" value="109.046571"/> | |
| 2485 <param name="ICPL6" value="111.041593"/> | |
| 2486 <param name="ICPL10" value="115.0667"/> | |
| 2487 </section> | |
| 2488 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2489 <output name="ctd_out" ftype="xml"> | |
| 2490 <assert_contents> | |
| 2491 <is_valid_xml/> | |
| 2492 </assert_contents> | |
| 2493 </output> | |
| 2494 </test> | |
| 2495 <test expect_num_outputs="3"> | |
| 2496 <conditional name="adv_opts_cond"> | |
| 2497 <param name="adv_opts_selector" value="advanced"/> | |
| 2498 <param name="force" value="false"/> | |
| 2499 <param name="test" value="true"/> | |
| 2500 </conditional> | |
| 2501 <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/> | |
| 2502 <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2503 <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2504 <section name="algorithm"> | |
| 2505 <param name="labels" value="[][Lys8,Arg10]"/> | |
| 2506 <param name="charge" value="1:4"/> | |
| 2507 <param name="isotopes_per_peptide" value="3:6"/> | |
| 2508 <param name="rt_typical" value="40.0"/> | |
| 2509 <param name="rt_band" value="5.0"/> | |
| 2510 <param name="rt_min" value="2.0"/> | |
| 2511 <param name="mz_tolerance" value="6.0"/> | |
| 2512 <param name="mz_unit" value="ppm"/> | |
| 2513 <param name="intensity_cutoff" value="1000.0"/> | |
| 2514 <param name="peptide_similarity" value="0.5"/> | |
| 2515 <param name="averagine_similarity" value="0.4"/> | |
| 2516 <param name="averagine_similarity_scaling" value="0.75"/> | |
| 2517 <param name="missed_cleavages" value="0"/> | |
| 2518 <param name="spectrum_type" value="automatic"/> | |
| 2519 <param name="averagine_type" value="peptide"/> | |
| 2520 <param name="knock_out" value="false"/> | |
| 2521 </section> | |
| 2522 <section name="labels"> | |
| 2523 <param name="Arg6" value="6.0201290268"/> | |
| 2524 <param name="Arg10" value="10.0082686"/> | |
| 2525 <param name="Lys4" value="4.0251069836"/> | |
| 2526 <param name="Lys6" value="6.0201290268"/> | |
| 2527 <param name="Lys8" value="8.0141988132"/> | |
| 2528 <param name="Leu3" value="3.01883"/> | |
| 2529 <param name="Dimethyl0" value="28.0313"/> | |
| 2530 <param name="Dimethyl4" value="32.056407"/> | |
| 2531 <param name="Dimethyl6" value="34.063117"/> | |
| 2532 <param name="Dimethyl8" value="36.07567"/> | |
| 2533 <param name="ICPL0" value="105.021464"/> | |
| 2534 <param name="ICPL4" value="109.046571"/> | |
| 2535 <param name="ICPL6" value="111.041593"/> | |
| 2536 <param name="ICPL10" value="115.0667"/> | |
| 2537 </section> | |
| 2538 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2539 <output name="ctd_out" ftype="xml"> | |
| 2540 <assert_contents> | |
| 2541 <is_valid_xml/> | |
| 2542 </assert_contents> | |
| 2543 </output> | |
| 2544 </test> | |
| 2545 <test expect_num_outputs="3"> | |
| 2546 <conditional name="adv_opts_cond"> | |
| 2547 <param name="adv_opts_selector" value="advanced"/> | |
| 2548 <param name="force" value="false"/> | |
| 2549 <param name="test" value="true"/> | |
| 2550 </conditional> | |
| 2551 <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/> | |
| 2552 <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2553 <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2554 <section name="algorithm"> | |
| 2555 <param name="labels" value="[]"/> | |
| 2556 <param name="charge" value="5:15"/> | |
| 2557 <param name="isotopes_per_peptide" value="5:10"/> | |
| 2558 <param name="rt_typical" value="45.0"/> | |
| 2559 <param name="rt_band" value="5.0"/> | |
| 2560 <param name="rt_min" value="2.0"/> | |
| 2561 <param name="mz_tolerance" value="6.0"/> | |
| 2562 <param name="mz_unit" value="ppm"/> | |
| 2563 <param name="intensity_cutoff" value="200.0"/> | |
| 2564 <param name="peptide_similarity" value="0.5"/> | |
| 2565 <param name="averagine_similarity" value="0.4"/> | |
| 2566 <param name="averagine_similarity_scaling" value="0.75"/> | |
| 2567 <param name="missed_cleavages" value="0"/> | |
| 2568 <param name="spectrum_type" value="automatic"/> | |
| 2569 <param name="averagine_type" value="RNA"/> | |
| 2570 <param name="knock_out" value="false"/> | |
| 2571 </section> | |
| 2572 <section name="labels"> | |
| 2573 <param name="Arg6" value="6.0201290268"/> | |
| 2574 <param name="Arg10" value="10.0082686"/> | |
| 2575 <param name="Lys4" value="4.0251069836"/> | |
| 2576 <param name="Lys6" value="6.0201290268"/> | |
| 2577 <param name="Lys8" value="8.0141988132"/> | |
| 2578 <param name="Leu3" value="3.01883"/> | |
| 2579 <param name="Dimethyl0" value="28.0313"/> | |
| 2580 <param name="Dimethyl4" value="32.056407"/> | |
| 2581 <param name="Dimethyl6" value="34.063117"/> | |
| 2582 <param name="Dimethyl8" value="36.07567"/> | |
| 2583 <param name="ICPL0" value="105.021464"/> | |
| 2584 <param name="ICPL4" value="109.046571"/> | |
| 2585 <param name="ICPL6" value="111.041593"/> | |
| 2586 <param name="ICPL10" value="115.0667"/> | |
| 2587 </section> | |
| 2588 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2589 <output name="ctd_out" ftype="xml"> | |
| 2590 <assert_contents> | |
| 2591 <is_valid_xml/> | |
| 2592 </assert_contents> | |
| 2593 </output> | |
| 2594 </test> | |
| 2595 <test expect_num_outputs="3"> | |
| 2596 <conditional name="adv_opts_cond"> | |
| 2597 <param name="adv_opts_selector" value="advanced"/> | |
| 2598 <param name="force" value="false"/> | |
| 2599 <param name="test" value="true"/> | |
| 2600 </conditional> | |
| 2601 <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/> | |
| 2602 <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2603 <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2604 <section name="algorithm"> | |
| 2605 <param name="labels" value="[]"/> | |
| 2606 <param name="charge" value="5:15"/> | |
| 2607 <param name="isotopes_per_peptide" value="5:10"/> | |
| 2608 <param name="rt_typical" value="45.0"/> | |
| 2609 <param name="rt_band" value="5.0"/> | |
| 2610 <param name="rt_min" value="2.0"/> | |
| 2611 <param name="mz_tolerance" value="6.0"/> | |
| 2612 <param name="mz_unit" value="ppm"/> | |
| 2613 <param name="intensity_cutoff" value="200.0"/> | |
| 2614 <param name="peptide_similarity" value="0.5"/> | |
| 2615 <param name="averagine_similarity" value="0.4"/> | |
| 2616 <param name="averagine_similarity_scaling" value="0.75"/> | |
| 2617 <param name="missed_cleavages" value="0"/> | |
| 2618 <param name="spectrum_type" value="automatic"/> | |
| 2619 <param name="averagine_type" value="DNA"/> | |
| 2620 <param name="knock_out" value="false"/> | |
| 2621 </section> | |
| 2622 <section name="labels"> | |
| 2623 <param name="Arg6" value="6.0201290268"/> | |
| 2624 <param name="Arg10" value="10.0082686"/> | |
| 2625 <param name="Lys4" value="4.0251069836"/> | |
| 2626 <param name="Lys6" value="6.0201290268"/> | |
| 2627 <param name="Lys8" value="8.0141988132"/> | |
| 2628 <param name="Leu3" value="3.01883"/> | |
| 2629 <param name="Dimethyl0" value="28.0313"/> | |
| 2630 <param name="Dimethyl4" value="32.056407"/> | |
| 2631 <param name="Dimethyl6" value="34.063117"/> | |
| 2632 <param name="Dimethyl8" value="36.07567"/> | |
| 2633 <param name="ICPL0" value="105.021464"/> | |
| 2634 <param name="ICPL4" value="109.046571"/> | |
| 2635 <param name="ICPL6" value="111.041593"/> | |
| 2636 <param name="ICPL10" value="115.0667"/> | |
| 2637 </section> | |
| 2638 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2639 <output name="ctd_out" ftype="xml"> | |
| 2640 <assert_contents> | |
| 2641 <is_valid_xml/> | |
| 2642 </assert_contents> | |
| 2643 </output> | |
| 2644 </test> | |
| 2645 <test expect_num_outputs="3"> | |
| 2646 <conditional name="adv_opts_cond"> | |
| 2647 <param name="adv_opts_selector" value="advanced"/> | |
| 2648 <param name="force" value="false"/> | |
| 2649 <param name="test" value="true"/> | |
| 2650 </conditional> | |
| 2651 <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/> | |
| 2652 <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2653 <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2654 <section name="algorithm"> | |
| 2655 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> | |
| 2656 <param name="charge" value="1:5"/> | |
| 2657 <param name="isotopes_per_peptide" value="3:6"/> | |
| 2658 <param name="rt_typical" value="50.0"/> | |
| 2659 <param name="rt_band" value="3.0"/> | |
| 2660 <param name="rt_min" value="8.0"/> | |
| 2661 <param name="mz_tolerance" value="10.0"/> | |
| 2662 <param name="mz_unit" value="ppm"/> | |
| 2663 <param name="intensity_cutoff" value="10000000.0"/> | |
| 2664 <param name="peptide_similarity" value="0.95"/> | |
| 2665 <param name="averagine_similarity" value="0.8"/> | |
| 2666 <param name="averagine_similarity_scaling" value="0.95"/> | |
| 2667 <param name="missed_cleavages" value="3"/> | |
| 2668 <param name="spectrum_type" value="profile"/> | |
| 2669 <param name="averagine_type" value="peptide"/> | |
| 2670 <param name="knock_out" value="false"/> | |
| 2671 </section> | |
| 2672 <section name="labels"> | |
| 2673 <param name="Arg6" value="6.0201290268"/> | |
| 2674 <param name="Arg10" value="10.0082686"/> | |
| 2675 <param name="Lys4" value="4.0251069836"/> | |
| 2676 <param name="Lys6" value="6.0201290268"/> | |
| 2677 <param name="Lys8" value="8.0141988132"/> | |
| 2678 <param name="Leu3" value="3.01883"/> | |
| 2679 <param name="Dimethyl0" value="28.0313"/> | |
| 2680 <param name="Dimethyl4" value="32.056407"/> | |
| 2681 <param name="Dimethyl6" value="34.063117"/> | |
| 2682 <param name="Dimethyl8" value="36.07567"/> | |
| 2683 <param name="ICPL0" value="105.021464"/> | |
| 2684 <param name="ICPL4" value="109.046571"/> | |
| 2685 <param name="ICPL6" value="111.041593"/> | |
| 2686 <param name="ICPL10" value="115.0667"/> | |
| 2687 </section> | |
| 2688 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2689 <output name="ctd_out" ftype="xml"> | |
| 2690 <assert_contents> | |
| 2691 <is_valid_xml/> | |
| 2692 </assert_contents> | |
| 2693 </output> | |
| 2694 </test> | |
| 2695 <test expect_num_outputs="3"> | |
| 2696 <conditional name="adv_opts_cond"> | |
| 2697 <param name="adv_opts_selector" value="advanced"/> | |
| 2698 <param name="force" value="false"/> | |
| 2699 <param name="test" value="true"/> | |
| 2700 </conditional> | |
| 2701 <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/> | |
| 2702 <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2703 <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2704 <section name="algorithm"> | |
| 2705 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> | |
| 2706 <param name="charge" value="1:5"/> | |
| 2707 <param name="isotopes_per_peptide" value="3:6"/> | |
| 2708 <param name="rt_typical" value="50.0"/> | |
| 2709 <param name="rt_band" value="3.0"/> | |
| 2710 <param name="rt_min" value="8.0"/> | |
| 2711 <param name="mz_tolerance" value="10.0"/> | |
| 2712 <param name="mz_unit" value="ppm"/> | |
| 2713 <param name="intensity_cutoff" value="10000000.0"/> | |
| 2714 <param name="peptide_similarity" value="0.95"/> | |
| 2715 <param name="averagine_similarity" value="0.8"/> | |
| 2716 <param name="averagine_similarity_scaling" value="1.0"/> | |
| 2717 <param name="missed_cleavages" value="3"/> | |
| 2718 <param name="spectrum_type" value="profile"/> | |
| 2719 <param name="averagine_type" value="peptide"/> | |
| 2720 <param name="knock_out" value="false"/> | |
| 2721 </section> | |
| 2722 <section name="labels"> | |
| 2723 <param name="Arg6" value="6.0201290268"/> | |
| 2724 <param name="Arg10" value="10.0082686"/> | |
| 2725 <param name="Lys4" value="4.0251069836"/> | |
| 2726 <param name="Lys6" value="6.0201290268"/> | |
| 2727 <param name="Lys8" value="8.0141988132"/> | |
| 2728 <param name="Leu3" value="3.01883"/> | |
| 2729 <param name="Dimethyl0" value="28.0313"/> | |
| 2730 <param name="Dimethyl4" value="32.056407"/> | |
| 2731 <param name="Dimethyl6" value="34.063117"/> | |
| 2732 <param name="Dimethyl8" value="36.07567"/> | |
| 2733 <param name="ICPL0" value="105.021464"/> | |
| 2734 <param name="ICPL4" value="109.046571"/> | |
| 2735 <param name="ICPL6" value="111.041593"/> | |
| 2736 <param name="ICPL10" value="115.0667"/> | |
| 2737 </section> | |
| 2738 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2739 <output name="ctd_out" ftype="xml"> | |
| 2740 <assert_contents> | |
| 2741 <is_valid_xml/> | |
| 2742 </assert_contents> | |
| 2743 </output> | |
| 2744 </test> | |
| 2745 <test expect_num_outputs="3"> | |
| 2746 <conditional name="adv_opts_cond"> | |
| 2747 <param name="adv_opts_selector" value="advanced"/> | |
| 2748 <param name="force" value="false"/> | |
| 2749 <param name="test" value="true"/> | |
| 2750 </conditional> | |
| 2751 <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/> | |
| 2752 <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2753 <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2754 <section name="algorithm"> | |
| 2755 <param name="labels" value="[][Dimethyl4]"/> | |
| 2756 <param name="charge" value="1:4"/> | |
| 2757 <param name="isotopes_per_peptide" value="3:6"/> | |
| 2758 <param name="rt_typical" value="40.0"/> | |
| 2759 <param name="rt_band" value="5.0"/> | |
| 2760 <param name="rt_min" value="2.0"/> | |
| 2761 <param name="mz_tolerance" value="6.0"/> | |
| 2762 <param name="mz_unit" value="ppm"/> | |
| 2763 <param name="intensity_cutoff" value="1000.0"/> | |
| 2764 <param name="peptide_similarity" value="0.5"/> | |
| 2765 <param name="averagine_similarity" value="0.4"/> | |
| 2766 <param name="averagine_similarity_scaling" value="0.75"/> | |
| 2767 <param name="missed_cleavages" value="0"/> | |
| 2768 <param name="spectrum_type" value="automatic"/> | |
| 2769 <param name="averagine_type" value="peptide"/> | |
| 2770 <param name="knock_out" value="false"/> | |
| 2771 </section> | |
| 2772 <section name="labels"> | |
| 2773 <param name="Arg6" value="6.0201290268"/> | |
| 2774 <param name="Arg10" value="10.0082686"/> | |
| 2775 <param name="Lys4" value="4.0251069836"/> | |
| 2776 <param name="Lys6" value="6.0201290268"/> | |
| 2777 <param name="Lys8" value="8.0141988132"/> | |
| 2778 <param name="Leu3" value="3.01883"/> | |
| 2779 <param name="Dimethyl0" value="28.0313"/> | |
| 2780 <param name="Dimethyl4" value="31.0094"/> | |
| 2781 <param name="Dimethyl6" value="34.063117"/> | |
| 2782 <param name="Dimethyl8" value="36.07567"/> | |
| 2783 <param name="ICPL0" value="105.021464"/> | |
| 2784 <param name="ICPL4" value="109.046571"/> | |
| 2785 <param name="ICPL6" value="111.041593"/> | |
| 2786 <param name="ICPL10" value="115.0667"/> | |
| 2787 </section> | |
| 2788 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2789 <output name="ctd_out" ftype="xml"> | |
| 2790 <assert_contents> | |
| 2791 <is_valid_xml/> | |
| 2792 </assert_contents> | |
| 2793 </output> | |
| 2794 </test> | |
| 2795 <test expect_num_outputs="3"> | |
| 2796 <conditional name="adv_opts_cond"> | |
| 2797 <param name="adv_opts_selector" value="advanced"/> | |
| 2798 <param name="force" value="false"/> | |
| 2799 <param name="test" value="true"/> | |
| 2800 </conditional> | |
| 2801 <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/> | |
| 2802 <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2803 <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2804 <section name="algorithm"> | |
| 2805 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> | |
| 2806 <param name="charge" value="1:7"/> | |
| 2807 <param name="isotopes_per_peptide" value="3:8"/> | |
| 2808 <param name="rt_typical" value="50.0"/> | |
| 2809 <param name="rt_band" value="3.0"/> | |
| 2810 <param name="rt_min" value="8.0"/> | |
| 2811 <param name="mz_tolerance" value="10.0"/> | |
| 2812 <param name="mz_unit" value="ppm"/> | |
| 2813 <param name="intensity_cutoff" value="10.0"/> | |
| 2814 <param name="peptide_similarity" value="0.2"/> | |
| 2815 <param name="averagine_similarity" value="0.25"/> | |
| 2816 <param name="averagine_similarity_scaling" value="0.95"/> | |
| 2817 <param name="missed_cleavages" value="4"/> | |
| 2818 <param name="spectrum_type" value="automatic"/> | |
| 2819 <param name="averagine_type" value="peptide"/> | |
| 2820 <param name="knock_out" value="true"/> | |
| 2821 </section> | |
| 2822 <section name="labels"> | |
| 2823 <param name="Arg6" value="6.0201290268"/> | |
| 2824 <param name="Arg10" value="10.0082686"/> | |
| 2825 <param name="Lys4" value="4.0251069836"/> | |
| 2826 <param name="Lys6" value="6.0201290268"/> | |
| 2827 <param name="Lys8" value="8.0141988132"/> | |
| 2828 <param name="Leu3" value="3.01883"/> | |
| 2829 <param name="Dimethyl0" value="28.0313"/> | |
| 2830 <param name="Dimethyl4" value="32.056407"/> | |
| 2831 <param name="Dimethyl6" value="34.063117"/> | |
| 2832 <param name="Dimethyl8" value="36.07567"/> | |
| 2833 <param name="ICPL0" value="105.021464"/> | |
| 2834 <param name="ICPL4" value="109.046571"/> | |
| 2835 <param name="ICPL6" value="111.041593"/> | |
| 2836 <param name="ICPL10" value="115.0667"/> | |
| 2837 </section> | |
| 2838 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2839 <output name="ctd_out" ftype="xml"> | |
| 2840 <assert_contents> | |
| 2841 <is_valid_xml/> | |
| 2842 </assert_contents> | |
| 2843 </output> | |
| 2844 </test> | |
| 2845 <test expect_num_outputs="3"> | |
| 2846 <conditional name="adv_opts_cond"> | |
| 2847 <param name="adv_opts_selector" value="advanced"/> | |
| 2848 <param name="force" value="false"/> | |
| 2849 <param name="test" value="true"/> | |
| 2850 </conditional> | |
| 2851 <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/> | |
| 2852 <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2853 <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2854 <section name="algorithm"> | |
| 2855 <param name="labels" value="[0][6.03705]"/> | |
| 2856 <param name="charge" value="2:8"/> | |
| 2857 <param name="isotopes_per_peptide" value="3:8"/> | |
| 2858 <param name="rt_typical" value="40.0"/> | |
| 2859 <param name="rt_band" value="0.0"/> | |
| 2860 <param name="rt_min" value="4.0"/> | |
| 2861 <param name="mz_tolerance" value="10.0"/> | |
| 2862 <param name="mz_unit" value="ppm"/> | |
| 2863 <param name="intensity_cutoff" value="1000.0"/> | |
| 2864 <param name="peptide_similarity" value="0.5"/> | |
| 2865 <param name="averagine_similarity" value="0.4"/> | |
| 2866 <param name="averagine_similarity_scaling" value="0.95"/> | |
| 2867 <param name="missed_cleavages" value="0"/> | |
| 2868 <param name="spectrum_type" value="centroid"/> | |
| 2869 <param name="averagine_type" value="peptide"/> | |
| 2870 <param name="knock_out" value="false"/> | |
| 2871 </section> | |
| 2872 <section name="labels"> | |
| 2873 <param name="Arg6" value="6.0201290268"/> | |
| 2874 <param name="Arg10" value="10.0082686"/> | |
| 2875 <param name="Lys4" value="4.0251069836"/> | |
| 2876 <param name="Lys6" value="6.0201290268"/> | |
| 2877 <param name="Lys8" value="8.0141988132"/> | |
| 2878 <param name="Leu3" value="3.01883"/> | |
| 2879 <param name="Dimethyl0" value="28.0313"/> | |
| 2880 <param name="Dimethyl4" value="32.056407"/> | |
| 2881 <param name="Dimethyl6" value="34.063117"/> | |
| 2882 <param name="Dimethyl8" value="36.07567"/> | |
| 2883 <param name="ICPL0" value="105.021464"/> | |
| 2884 <param name="ICPL4" value="109.046571"/> | |
| 2885 <param name="ICPL6" value="111.041593"/> | |
| 2886 <param name="ICPL10" value="115.0667"/> | |
| 2887 </section> | |
| 2888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2889 <output name="ctd_out" ftype="xml"> | |
| 2890 <assert_contents> | |
| 2891 <is_valid_xml/> | |
| 2892 </assert_contents> | |
| 2893 </output> | |
| 2894 </test> | |
| 2895 <test expect_num_outputs="3"> | |
| 2896 <conditional name="adv_opts_cond"> | |
| 2897 <param name="adv_opts_selector" value="advanced"/> | |
| 2898 <param name="force" value="false"/> | |
| 2899 <param name="test" value="true"/> | |
| 2900 </conditional> | |
| 2901 <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/> | |
| 2902 <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2903 <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 2904 <section name="algorithm"> | |
| 2905 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> | |
| 2906 <param name="charge" value="1:7"/> | |
| 2907 <param name="isotopes_per_peptide" value="3:6"/> | |
| 2908 <param name="rt_typical" value="50.0"/> | |
| 2909 <param name="rt_band" value="5.0"/> | |
| 2910 <param name="rt_min" value="8.0"/> | |
| 2911 <param name="mz_tolerance" value="6.0"/> | |
| 2912 <param name="mz_unit" value="ppm"/> | |
| 2913 <param name="intensity_cutoff" value="10.0"/> | |
| 2914 <param name="peptide_similarity" value="0.4"/> | |
| 2915 <param name="averagine_similarity" value="0.5"/> | |
| 2916 <param name="averagine_similarity_scaling" value="0.95"/> | |
| 2917 <param name="missed_cleavages" value="3"/> | |
| 2918 <param name="spectrum_type" value="profile"/> | |
| 2919 <param name="averagine_type" value="peptide"/> | |
| 2920 <param name="knock_out" value="true"/> | |
| 2921 </section> | |
| 2922 <section name="labels"> | |
| 2923 <param name="Arg6" value="6.0201290268"/> | |
| 2924 <param name="Arg10" value="10.0082686"/> | |
| 2925 <param name="Lys4" value="4.0251069836"/> | |
| 2926 <param name="Lys6" value="6.0201290268"/> | |
| 2927 <param name="Lys8" value="8.0141988132"/> | |
| 2928 <param name="Leu3" value="3.01883"/> | |
| 2929 <param name="Dimethyl0" value="28.0313"/> | |
| 2930 <param name="Dimethyl4" value="32.056407"/> | |
| 2931 <param name="Dimethyl6" value="34.063117"/> | |
| 2932 <param name="Dimethyl8" value="36.07567"/> | |
| 2933 <param name="ICPL0" value="105.021464"/> | |
| 2934 <param name="ICPL4" value="109.046571"/> | |
| 2935 <param name="ICPL6" value="111.041593"/> | |
| 2936 <param name="ICPL10" value="115.0667"/> | |
| 2937 </section> | |
| 2938 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> | |
| 2939 <output name="ctd_out" ftype="xml"> | |
| 2940 <assert_contents> | |
| 2941 <is_valid_xml/> | |
| 2942 </assert_contents> | |
| 2943 </output> | |
| 2944 </test> | |
| 2945 <test expect_num_outputs="2"> | |
| 2946 <conditional name="adv_opts_cond"> | |
| 2947 <param name="adv_opts_selector" value="advanced"/> | |
| 2948 <param name="force" value="false"/> | |
| 2949 <param name="test" value="true"/> | |
| 2950 </conditional> | |
| 2951 <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/> | |
| 2952 <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 2953 <section name="algorithm"> | |
| 2954 <param name="labels" value="[]"/> | |
| 2955 <param name="charge" value="1:4"/> | |
| 2956 <param name="isotopes_per_peptide" value="3:6"/> | |
| 2957 <param name="rt_typical" value="1e-05"/> | |
| 2958 <param name="rt_band" value="0.0"/> | |
| 2959 <param name="rt_min" value="0.0"/> | |
| 2960 <param name="mz_tolerance" value="10.0"/> | |
| 2961 <param name="mz_unit" value="ppm"/> | |
| 2962 <param name="intensity_cutoff" value="1000.0"/> | |
| 2963 <param name="peptide_similarity" value="0.5"/> | |
| 2964 <param name="averagine_similarity" value="0.7"/> | |
| 2965 <param name="averagine_similarity_scaling" value="0.95"/> | |
| 2966 <param name="missed_cleavages" value="0"/> | |
| 2967 <param name="spectrum_type" value="automatic"/> | |
| 2968 <param name="averagine_type" value="peptide"/> | |
| 2969 <param name="knock_out" value="false"/> | |
| 2970 </section> | |
| 2971 <section name="labels"> | |
| 2972 <param name="Arg6" value="6.0201290268"/> | |
| 2973 <param name="Arg10" value="10.0082686"/> | |
| 2974 <param name="Lys4" value="4.0251069836"/> | |
| 2975 <param name="Lys6" value="6.0201290268"/> | |
| 2976 <param name="Lys8" value="8.0141988132"/> | |
| 2977 <param name="Leu3" value="3.01883"/> | |
| 2978 <param name="Dimethyl0" value="28.0313"/> | |
| 2979 <param name="Dimethyl4" value="32.056407"/> | |
| 2980 <param name="Dimethyl6" value="34.063117"/> | |
| 2981 <param name="Dimethyl8" value="36.07567"/> | |
| 2982 <param name="ICPL0" value="105.021464"/> | |
| 2983 <param name="ICPL4" value="109.046571"/> | |
| 2984 <param name="ICPL6" value="111.041593"/> | |
| 2985 <param name="ICPL10" value="115.0667"/> | |
| 2986 </section> | |
| 2987 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 2988 <output name="ctd_out" ftype="xml"> | |
| 2989 <assert_contents> | |
| 2990 <is_valid_xml/> | |
| 2991 </assert_contents> | |
| 2992 </output> | |
| 2993 </test> | |
| 2994 </xml> | |
| 2995 <xml name="autotest_FeatureFinderSuperHirn"> | |
| 2996 <test expect_num_outputs="2"> | |
| 2997 <conditional name="adv_opts_cond"> | |
| 2998 <param name="adv_opts_selector" value="advanced"/> | |
| 2999 <param name="force" value="false"/> | |
| 3000 <param name="test" value="true"/> | |
| 3001 </conditional> | |
| 3002 <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/> | |
| 3003 <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 3004 <section name="algorithm"> | |
| 3005 <section name="centroiding"> | |
| 3006 <param name="active" value="false"/> | |
| 3007 <param name="window_width" value="5"/> | |
| 3008 <param name="absolute_isotope_mass_precision" value="0.01"/> | |
| 3009 <param name="relative_isotope_mass_precision" value="10.0"/> | |
| 3010 <param name="minimal_peak_height" value="0.0"/> | |
| 3011 <param name="min_ms_signal_intensity" value="50.0"/> | |
| 3012 </section> | |
| 3013 <section name="ms1"> | |
| 3014 <param name="precursor_detection_scan_levels" value="1"/> | |
| 3015 <param name="max_inter_scan_distance" value="0"/> | |
| 3016 <param name="tr_resolution" value="0.01"/> | |
| 3017 <param name="intensity_threshold" value="1000.0"/> | |
| 3018 <param name="max_inter_scan_rt_distance" value="0.1"/> | |
| 3019 <param name="min_nb_cluster_members" value="4"/> | |
| 3020 <param name="detectable_isotope_factor" value="0.05"/> | |
| 3021 <param name="intensity_cv" value="0.9"/> | |
| 3022 <param name="retention_time_tolerance" value="0.5"/> | |
| 3023 <param name="mz_tolerance" value="0.0"/> | |
| 3024 </section> | |
| 3025 <section name="ms1_feature_merger"> | |
| 3026 <param name="active" value="true"/> | |
| 3027 <param name="tr_resolution" value="0.01"/> | |
| 3028 <param name="initial_apex_tr_tolerance" value="5.0"/> | |
| 3029 <param name="feature_merging_tr_tolerance" value="1.0"/> | |
| 3030 <param name="intensity_variation_percentage" value="25.0"/> | |
| 3031 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> | |
| 3032 </section> | |
| 3033 <section name="ms1_feature_selection_options"> | |
| 3034 <param name="start_elution_window" value="0.0"/> | |
| 3035 <param name="end_elution_window" value="180.0"/> | |
| 3036 <param name="mz_range_min" value="0.0"/> | |
| 3037 <param name="mz_range_max" value="2000.0"/> | |
| 3038 <param name="chrg_range_min" value="1"/> | |
| 3039 <param name="chrg_range_max" value="5"/> | |
| 3040 </section> | |
| 3041 </section> | |
| 3042 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3043 <output name="ctd_out" ftype="xml"> | |
| 3044 <assert_contents> | |
| 3045 <is_valid_xml/> | |
| 3046 </assert_contents> | |
| 3047 </output> | |
| 3048 </test> | |
| 3049 <test expect_num_outputs="2"> | |
| 3050 <conditional name="adv_opts_cond"> | |
| 3051 <param name="adv_opts_selector" value="advanced"/> | |
| 3052 <param name="force" value="false"/> | |
| 3053 <param name="test" value="true"/> | |
| 3054 </conditional> | |
| 3055 <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/> | |
| 3056 <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 3057 <section name="algorithm"> | |
| 3058 <section name="centroiding"> | |
| 3059 <param name="active" value="true"/> | |
| 3060 <param name="window_width" value="5"/> | |
| 3061 <param name="absolute_isotope_mass_precision" value="0.01"/> | |
| 3062 <param name="relative_isotope_mass_precision" value="10.0"/> | |
| 3063 <param name="minimal_peak_height" value="0.0"/> | |
| 3064 <param name="min_ms_signal_intensity" value="50.0"/> | |
| 3065 </section> | |
| 3066 <section name="ms1"> | |
| 3067 <param name="precursor_detection_scan_levels" value="1"/> | |
| 3068 <param name="max_inter_scan_distance" value="0"/> | |
| 3069 <param name="tr_resolution" value="0.01"/> | |
| 3070 <param name="intensity_threshold" value="1000.0"/> | |
| 3071 <param name="max_inter_scan_rt_distance" value="0.1"/> | |
| 3072 <param name="min_nb_cluster_members" value="4"/> | |
| 3073 <param name="detectable_isotope_factor" value="0.05"/> | |
| 3074 <param name="intensity_cv" value="0.9"/> | |
| 3075 <param name="retention_time_tolerance" value="0.5"/> | |
| 3076 <param name="mz_tolerance" value="0.0"/> | |
| 3077 </section> | |
| 3078 <section name="ms1_feature_merger"> | |
| 3079 <param name="active" value="true"/> | |
| 3080 <param name="tr_resolution" value="0.01"/> | |
| 3081 <param name="initial_apex_tr_tolerance" value="5.0"/> | |
| 3082 <param name="feature_merging_tr_tolerance" value="1.0"/> | |
| 3083 <param name="intensity_variation_percentage" value="25.0"/> | |
| 3084 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> | |
| 3085 </section> | |
| 3086 <section name="ms1_feature_selection_options"> | |
| 3087 <param name="start_elution_window" value="0.0"/> | |
| 3088 <param name="end_elution_window" value="180.0"/> | |
| 3089 <param name="mz_range_min" value="0.0"/> | |
| 3090 <param name="mz_range_max" value="2000.0"/> | |
| 3091 <param name="chrg_range_min" value="1"/> | |
| 3092 <param name="chrg_range_max" value="5"/> | |
| 3093 </section> | |
| 3094 </section> | |
| 3095 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3096 <output name="ctd_out" ftype="xml"> | |
| 3097 <assert_contents> | |
| 3098 <is_valid_xml/> | |
| 3099 </assert_contents> | |
| 3100 </output> | |
| 3101 </test> | |
| 3102 </xml> | |
| 3103 <xml name="autotest_FeatureLinkerLabeled"> | |
| 3104 <test expect_num_outputs="2"> | |
| 3105 <conditional name="adv_opts_cond"> | |
| 3106 <param name="adv_opts_selector" value="advanced"/> | |
| 3107 <param name="force" value="false"/> | |
| 3108 <param name="test" value="true"/> | |
| 3109 </conditional> | |
| 3110 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> | |
| 3111 <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3112 <section name="algorithm"> | |
| 3113 <param name="rt_estimate" value="false"/> | |
| 3114 <param name="rt_pair_dist" value="-1.0"/> | |
| 3115 <param name="rt_dev_low" value="0.4"/> | |
| 3116 <param name="rt_dev_high" value="0.4"/> | |
| 3117 <param name="mz_pair_dists" value="8.0"/> | |
| 3118 <param name="mz_dev" value="0.1"/> | |
| 3119 <param name="mrm" value="false"/> | |
| 3120 </section> | |
| 3121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3122 <output name="ctd_out" ftype="xml"> | |
| 3123 <assert_contents> | |
| 3124 <is_valid_xml/> | |
| 3125 </assert_contents> | |
| 3126 </output> | |
| 3127 </test> | |
| 3128 <test expect_num_outputs="2"> | |
| 3129 <conditional name="adv_opts_cond"> | |
| 3130 <param name="adv_opts_selector" value="advanced"/> | |
| 3131 <param name="force" value="false"/> | |
| 3132 <param name="test" value="true"/> | |
| 3133 </conditional> | |
| 3134 <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/> | |
| 3135 <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3136 <section name="algorithm"> | |
| 3137 <param name="rt_estimate" value="true"/> | |
| 3138 <param name="rt_pair_dist" value="-121.0382"/> | |
| 3139 <param name="rt_dev_low" value="123.3965"/> | |
| 3140 <param name="rt_dev_high" value="123.3965"/> | |
| 3141 <param name="mz_pair_dists" value="4.0"/> | |
| 3142 <param name="mz_dev" value="0.1"/> | |
| 3143 <param name="mrm" value="false"/> | |
| 3144 </section> | |
| 3145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3146 <output name="ctd_out" ftype="xml"> | |
| 3147 <assert_contents> | |
| 3148 <is_valid_xml/> | |
| 3149 </assert_contents> | |
| 3150 </output> | |
| 3151 </test> | |
| 3152 </xml> | |
| 3153 <xml name="autotest_FeatureLinkerUnlabeledKD"> | |
| 3154 <test expect_num_outputs="2"> | |
| 3155 <conditional name="adv_opts_cond"> | |
| 3156 <param name="adv_opts_selector" value="advanced"/> | |
| 3157 <param name="force" value="false"/> | |
| 3158 <param name="test" value="true"/> | |
| 3159 </conditional> | |
| 3160 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> | |
| 3161 <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3162 <param name="keep_subelements" value="false"/> | |
| 3163 <section name="algorithm"> | |
| 3164 <param name="mz_unit" value="Da"/> | |
| 3165 <param name="nr_partitions" value="1"/> | |
| 3166 <section name="warp"> | |
| 3167 <param name="enabled" value="false"/> | |
| 3168 <param name="rt_tol" value="100.0"/> | |
| 3169 <param name="mz_tol" value="0.3"/> | |
| 3170 <param name="max_pairwise_log_fc" value="0.5"/> | |
| 3171 <param name="min_rel_cc_size" value="0.5"/> | |
| 3172 <param name="max_nr_conflicts" value="0"/> | |
| 3173 </section> | |
| 3174 <section name="link"> | |
| 3175 <param name="rt_tol" value="100.0"/> | |
| 3176 <param name="mz_tol" value="0.3"/> | |
| 3177 <param name="charge_merging" value="With_charge_zero"/> | |
| 3178 <param name="adduct_merging" value="Any"/> | |
| 3179 </section> | |
| 3180 <section name="distance_RT"> | |
| 3181 <param name="exponent" value="1.0"/> | |
| 3182 <param name="weight" value="1.0"/> | |
| 3183 </section> | |
| 3184 <section name="distance_MZ"> | |
| 3185 <param name="exponent" value="2.0"/> | |
| 3186 <param name="weight" value="1.0"/> | |
| 3187 </section> | |
| 3188 <section name="distance_intensity"> | |
| 3189 <param name="exponent" value="1.0"/> | |
| 3190 <param name="weight" value="1.0"/> | |
| 3191 <param name="log_transform" value="enabled"/> | |
| 3192 </section> | |
| 3193 <section name="LOWESS"> | |
| 3194 <param name="span" value="0.666666666666667"/> | |
| 3195 <param name="num_iterations" value="3"/> | |
| 3196 <param name="delta" value="-1.0"/> | |
| 3197 <param name="interpolation_type" value="cspline"/> | |
| 3198 <param name="extrapolation_type" value="four-point-linear"/> | |
| 3199 </section> | |
| 3200 </section> | |
| 3201 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3202 <output name="ctd_out" ftype="xml"> | |
| 3203 <assert_contents> | |
| 3204 <is_valid_xml/> | |
| 3205 </assert_contents> | |
| 3206 </output> | |
| 3207 </test> | |
| 3208 <test expect_num_outputs="2"> | |
| 3209 <conditional name="adv_opts_cond"> | |
| 3210 <param name="adv_opts_selector" value="advanced"/> | |
| 3211 <param name="force" value="false"/> | |
| 3212 <param name="test" value="true"/> | |
| 3213 </conditional> | |
| 3214 <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/> | |
| 3215 <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3216 <param name="keep_subelements" value="true"/> | |
| 3217 <section name="algorithm"> | |
| 3218 <param name="mz_unit" value="Da"/> | |
| 3219 <param name="nr_partitions" value="99999"/> | |
| 3220 <section name="warp"> | |
| 3221 <param name="enabled" value="false"/> | |
| 3222 <param name="rt_tol" value="100.0"/> | |
| 3223 <param name="mz_tol" value="0.3"/> | |
| 3224 <param name="max_pairwise_log_fc" value="0.5"/> | |
| 3225 <param name="min_rel_cc_size" value="0.5"/> | |
| 3226 <param name="max_nr_conflicts" value="0"/> | |
| 3227 </section> | |
| 3228 <section name="link"> | |
| 3229 <param name="rt_tol" value="100.0"/> | |
| 3230 <param name="mz_tol" value="0.3"/> | |
| 3231 <param name="charge_merging" value="With_charge_zero"/> | |
| 3232 <param name="adduct_merging" value="Any"/> | |
| 3233 </section> | |
| 3234 <section name="distance_RT"> | |
| 3235 <param name="exponent" value="1.0"/> | |
| 3236 <param name="weight" value="1.0"/> | |
| 3237 </section> | |
| 3238 <section name="distance_MZ"> | |
| 3239 <param name="exponent" value="2.0"/> | |
| 3240 <param name="weight" value="1.0"/> | |
| 3241 </section> | |
| 3242 <section name="distance_intensity"> | |
| 3243 <param name="exponent" value="1.0"/> | |
| 3244 <param name="weight" value="1.0"/> | |
| 3245 <param name="log_transform" value="enabled"/> | |
| 3246 </section> | |
| 3247 <section name="LOWESS"> | |
| 3248 <param name="span" value="0.666666666666667"/> | |
| 3249 <param name="num_iterations" value="3"/> | |
| 3250 <param name="delta" value="-1.0"/> | |
| 3251 <param name="interpolation_type" value="cspline"/> | |
| 3252 <param name="extrapolation_type" value="four-point-linear"/> | |
| 3253 </section> | |
| 3254 </section> | |
| 3255 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3256 <output name="ctd_out" ftype="xml"> | |
| 3257 <assert_contents> | |
| 3258 <is_valid_xml/> | |
| 3259 </assert_contents> | |
| 3260 </output> | |
| 3261 </test> | |
| 3262 <test expect_num_outputs="2"> | |
| 3263 <conditional name="adv_opts_cond"> | |
| 3264 <param name="adv_opts_selector" value="advanced"/> | |
| 3265 <param name="force" value="false"/> | |
| 3266 <param name="test" value="true"/> | |
| 3267 </conditional> | |
| 3268 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> | |
| 3269 <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3270 <param name="keep_subelements" value="false"/> | |
| 3271 <section name="algorithm"> | |
| 3272 <param name="mz_unit" value="Da"/> | |
| 3273 <param name="nr_partitions" value="100"/> | |
| 3274 <section name="warp"> | |
| 3275 <param name="enabled" value="false"/> | |
| 3276 <param name="rt_tol" value="100.0"/> | |
| 3277 <param name="mz_tol" value="0.3"/> | |
| 3278 <param name="max_pairwise_log_fc" value="0.5"/> | |
| 3279 <param name="min_rel_cc_size" value="0.5"/> | |
| 3280 <param name="max_nr_conflicts" value="0"/> | |
| 3281 </section> | |
| 3282 <section name="link"> | |
| 3283 <param name="rt_tol" value="100.0"/> | |
| 3284 <param name="mz_tol" value="0.3"/> | |
| 3285 <param name="charge_merging" value="With_charge_zero"/> | |
| 3286 <param name="adduct_merging" value="Any"/> | |
| 3287 </section> | |
| 3288 <section name="distance_RT"> | |
| 3289 <param name="exponent" value="1.0"/> | |
| 3290 <param name="weight" value="1.0"/> | |
| 3291 </section> | |
| 3292 <section name="distance_MZ"> | |
| 3293 <param name="exponent" value="2.0"/> | |
| 3294 <param name="weight" value="1.0"/> | |
| 3295 </section> | |
| 3296 <section name="distance_intensity"> | |
| 3297 <param name="exponent" value="1.0"/> | |
| 3298 <param name="weight" value="1.0"/> | |
| 3299 <param name="log_transform" value="enabled"/> | |
| 3300 </section> | |
| 3301 <section name="LOWESS"> | |
| 3302 <param name="span" value="0.666666666666667"/> | |
| 3303 <param name="num_iterations" value="3"/> | |
| 3304 <param name="delta" value="-1.0"/> | |
| 3305 <param name="interpolation_type" value="cspline"/> | |
| 3306 <param name="extrapolation_type" value="four-point-linear"/> | |
| 3307 </section> | |
| 3308 </section> | |
| 3309 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3310 <output name="ctd_out" ftype="xml"> | |
| 3311 <assert_contents> | |
| 3312 <is_valid_xml/> | |
| 3313 </assert_contents> | |
| 3314 </output> | |
| 3315 </test> | |
| 3316 <test expect_num_outputs="2"> | |
| 3317 <conditional name="adv_opts_cond"> | |
| 3318 <param name="adv_opts_selector" value="advanced"/> | |
| 3319 <param name="force" value="false"/> | |
| 3320 <param name="test" value="true"/> | |
| 3321 </conditional> | |
| 3322 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> | |
| 3323 <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3324 <param name="keep_subelements" value="false"/> | |
| 3325 <section name="algorithm"> | |
| 3326 <param name="mz_unit" value="ppm"/> | |
| 3327 <param name="nr_partitions" value="100"/> | |
| 3328 <section name="warp"> | |
| 3329 <param name="enabled" value="true"/> | |
| 3330 <param name="rt_tol" value="100.0"/> | |
| 3331 <param name="mz_tol" value="5.0"/> | |
| 3332 <param name="max_pairwise_log_fc" value="0.5"/> | |
| 3333 <param name="min_rel_cc_size" value="0.5"/> | |
| 3334 <param name="max_nr_conflicts" value="0"/> | |
| 3335 </section> | |
| 3336 <section name="link"> | |
| 3337 <param name="rt_tol" value="30.0"/> | |
| 3338 <param name="mz_tol" value="10.0"/> | |
| 3339 <param name="charge_merging" value="Identical"/> | |
| 3340 <param name="adduct_merging" value="Any"/> | |
| 3341 </section> | |
| 3342 <section name="distance_RT"> | |
| 3343 <param name="exponent" value="1.0"/> | |
| 3344 <param name="weight" value="1.0"/> | |
| 3345 </section> | |
| 3346 <section name="distance_MZ"> | |
| 3347 <param name="exponent" value="2.0"/> | |
| 3348 <param name="weight" value="1.0"/> | |
| 3349 </section> | |
| 3350 <section name="distance_intensity"> | |
| 3351 <param name="exponent" value="1.0"/> | |
| 3352 <param name="weight" value="1.0"/> | |
| 3353 <param name="log_transform" value="enabled"/> | |
| 3354 </section> | |
| 3355 <section name="LOWESS"> | |
| 3356 <param name="span" value="0.666666666666667"/> | |
| 3357 <param name="num_iterations" value="3"/> | |
| 3358 <param name="delta" value="-1.0"/> | |
| 3359 <param name="interpolation_type" value="cspline"/> | |
| 3360 <param name="extrapolation_type" value="four-point-linear"/> | |
| 3361 </section> | |
| 3362 </section> | |
| 3363 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3364 <output name="ctd_out" ftype="xml"> | |
| 3365 <assert_contents> | |
| 3366 <is_valid_xml/> | |
| 3367 </assert_contents> | |
| 3368 </output> | |
| 3369 </test> | |
| 3370 <test expect_num_outputs="2"> | |
| 3371 <conditional name="adv_opts_cond"> | |
| 3372 <param name="adv_opts_selector" value="advanced"/> | |
| 3373 <param name="force" value="false"/> | |
| 3374 <param name="test" value="true"/> | |
| 3375 </conditional> | |
| 3376 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> | |
| 3377 <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3378 <param name="keep_subelements" value="false"/> | |
| 3379 <section name="algorithm"> | |
| 3380 <param name="mz_unit" value="ppm"/> | |
| 3381 <param name="nr_partitions" value="100"/> | |
| 3382 <section name="warp"> | |
| 3383 <param name="enabled" value="true"/> | |
| 3384 <param name="rt_tol" value="100.0"/> | |
| 3385 <param name="mz_tol" value="5.0"/> | |
| 3386 <param name="max_pairwise_log_fc" value="0.5"/> | |
| 3387 <param name="min_rel_cc_size" value="0.5"/> | |
| 3388 <param name="max_nr_conflicts" value="0"/> | |
| 3389 </section> | |
| 3390 <section name="link"> | |
| 3391 <param name="rt_tol" value="30.0"/> | |
| 3392 <param name="mz_tol" value="10.0"/> | |
| 3393 <param name="charge_merging" value="With_charge_zero"/> | |
| 3394 <param name="adduct_merging" value="Any"/> | |
| 3395 </section> | |
| 3396 <section name="distance_RT"> | |
| 3397 <param name="exponent" value="1.0"/> | |
| 3398 <param name="weight" value="1.0"/> | |
| 3399 </section> | |
| 3400 <section name="distance_MZ"> | |
| 3401 <param name="exponent" value="2.0"/> | |
| 3402 <param name="weight" value="1.0"/> | |
| 3403 </section> | |
| 3404 <section name="distance_intensity"> | |
| 3405 <param name="exponent" value="1.0"/> | |
| 3406 <param name="weight" value="1.0"/> | |
| 3407 <param name="log_transform" value="enabled"/> | |
| 3408 </section> | |
| 3409 <section name="LOWESS"> | |
| 3410 <param name="span" value="0.666666666666667"/> | |
| 3411 <param name="num_iterations" value="3"/> | |
| 3412 <param name="delta" value="-1.0"/> | |
| 3413 <param name="interpolation_type" value="cspline"/> | |
| 3414 <param name="extrapolation_type" value="four-point-linear"/> | |
| 3415 </section> | |
| 3416 </section> | |
| 3417 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3418 <output name="ctd_out" ftype="xml"> | |
| 3419 <assert_contents> | |
| 3420 <is_valid_xml/> | |
| 3421 </assert_contents> | |
| 3422 </output> | |
| 3423 </test> | |
| 3424 <test expect_num_outputs="2"> | |
| 3425 <conditional name="adv_opts_cond"> | |
| 3426 <param name="adv_opts_selector" value="advanced"/> | |
| 3427 <param name="force" value="false"/> | |
| 3428 <param name="test" value="true"/> | |
| 3429 </conditional> | |
| 3430 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> | |
| 3431 <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3432 <param name="keep_subelements" value="false"/> | |
| 3433 <section name="algorithm"> | |
| 3434 <param name="mz_unit" value="ppm"/> | |
| 3435 <param name="nr_partitions" value="100"/> | |
| 3436 <section name="warp"> | |
| 3437 <param name="enabled" value="true"/> | |
| 3438 <param name="rt_tol" value="100.0"/> | |
| 3439 <param name="mz_tol" value="5.0"/> | |
| 3440 <param name="max_pairwise_log_fc" value="0.5"/> | |
| 3441 <param name="min_rel_cc_size" value="0.5"/> | |
| 3442 <param name="max_nr_conflicts" value="0"/> | |
| 3443 </section> | |
| 3444 <section name="link"> | |
| 3445 <param name="rt_tol" value="30.0"/> | |
| 3446 <param name="mz_tol" value="10.0"/> | |
| 3447 <param name="charge_merging" value="Any"/> | |
| 3448 <param name="adduct_merging" value="With_unknown_adducts"/> | |
| 3449 </section> | |
| 3450 <section name="distance_RT"> | |
| 3451 <param name="exponent" value="1.0"/> | |
| 3452 <param name="weight" value="1.0"/> | |
| 3453 </section> | |
| 3454 <section name="distance_MZ"> | |
| 3455 <param name="exponent" value="2.0"/> | |
| 3456 <param name="weight" value="1.0"/> | |
| 3457 </section> | |
| 3458 <section name="distance_intensity"> | |
| 3459 <param name="exponent" value="1.0"/> | |
| 3460 <param name="weight" value="1.0"/> | |
| 3461 <param name="log_transform" value="enabled"/> | |
| 3462 </section> | |
| 3463 <section name="LOWESS"> | |
| 3464 <param name="span" value="0.666666666666667"/> | |
| 3465 <param name="num_iterations" value="3"/> | |
| 3466 <param name="delta" value="-1.0"/> | |
| 3467 <param name="interpolation_type" value="cspline"/> | |
| 3468 <param name="extrapolation_type" value="four-point-linear"/> | |
| 3469 </section> | |
| 3470 </section> | |
| 3471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3472 <output name="ctd_out" ftype="xml"> | |
| 3473 <assert_contents> | |
| 3474 <is_valid_xml/> | |
| 3475 </assert_contents> | |
| 3476 </output> | |
| 3477 </test> | |
| 3478 <test expect_num_outputs="2"> | |
| 3479 <conditional name="adv_opts_cond"> | |
| 3480 <param name="adv_opts_selector" value="advanced"/> | |
| 3481 <param name="force" value="false"/> | |
| 3482 <param name="test" value="true"/> | |
| 3483 </conditional> | |
| 3484 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> | |
| 3485 <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3486 <param name="keep_subelements" value="false"/> | |
| 3487 <section name="algorithm"> | |
| 3488 <param name="mz_unit" value="ppm"/> | |
| 3489 <param name="nr_partitions" value="100"/> | |
| 3490 <section name="warp"> | |
| 3491 <param name="enabled" value="true"/> | |
| 3492 <param name="rt_tol" value="100.0"/> | |
| 3493 <param name="mz_tol" value="5.0"/> | |
| 3494 <param name="max_pairwise_log_fc" value="0.5"/> | |
| 3495 <param name="min_rel_cc_size" value="0.5"/> | |
| 3496 <param name="max_nr_conflicts" value="0"/> | |
| 3497 </section> | |
| 3498 <section name="link"> | |
| 3499 <param name="rt_tol" value="30.0"/> | |
| 3500 <param name="mz_tol" value="10.0"/> | |
| 3501 <param name="charge_merging" value="Any"/> | |
| 3502 <param name="adduct_merging" value="Identical"/> | |
| 3503 </section> | |
| 3504 <section name="distance_RT"> | |
| 3505 <param name="exponent" value="1.0"/> | |
| 3506 <param name="weight" value="1.0"/> | |
| 3507 </section> | |
| 3508 <section name="distance_MZ"> | |
| 3509 <param name="exponent" value="2.0"/> | |
| 3510 <param name="weight" value="1.0"/> | |
| 3511 </section> | |
| 3512 <section name="distance_intensity"> | |
| 3513 <param name="exponent" value="1.0"/> | |
| 3514 <param name="weight" value="1.0"/> | |
| 3515 <param name="log_transform" value="enabled"/> | |
| 3516 </section> | |
| 3517 <section name="LOWESS"> | |
| 3518 <param name="span" value="0.666666666666667"/> | |
| 3519 <param name="num_iterations" value="3"/> | |
| 3520 <param name="delta" value="-1.0"/> | |
| 3521 <param name="interpolation_type" value="cspline"/> | |
| 3522 <param name="extrapolation_type" value="four-point-linear"/> | |
| 3523 </section> | |
| 3524 </section> | |
| 3525 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3526 <output name="ctd_out" ftype="xml"> | |
| 3527 <assert_contents> | |
| 3528 <is_valid_xml/> | |
| 3529 </assert_contents> | |
| 3530 </output> | |
| 3531 </test> | |
| 3532 </xml> | |
| 3533 <xml name="autotest_FeatureLinkerUnlabeledQT"> | |
| 3534 <test expect_num_outputs="2"> | |
| 3535 <conditional name="adv_opts_cond"> | |
| 3536 <param name="adv_opts_selector" value="advanced"/> | |
| 3537 <param name="force" value="false"/> | |
| 3538 <param name="test" value="true"/> | |
| 3539 </conditional> | |
| 3540 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> | |
| 3541 <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3542 <param name="keep_subelements" value="false"/> | |
| 3543 <section name="algorithm"> | |
| 3544 <param name="use_identifications" value="false"/> | |
| 3545 <param name="nr_partitions" value="100"/> | |
| 3546 <param name="ignore_charge" value="false"/> | |
| 3547 <param name="ignore_adduct" value="true"/> | |
| 3548 <section name="distance_RT"> | |
| 3549 <param name="max_difference" value="100.0"/> | |
| 3550 <param name="exponent" value="1.0"/> | |
| 3551 <param name="weight" value="1.0"/> | |
| 3552 </section> | |
| 3553 <section name="distance_MZ"> | |
| 3554 <param name="max_difference" value="0.3"/> | |
| 3555 <param name="unit" value="Da"/> | |
| 3556 <param name="exponent" value="2.0"/> | |
| 3557 <param name="weight" value="1.0"/> | |
| 3558 </section> | |
| 3559 <section name="distance_intensity"> | |
| 3560 <param name="exponent" value="1.0"/> | |
| 3561 <param name="weight" value="0.0"/> | |
| 3562 <param name="log_transform" value="disabled"/> | |
| 3563 </section> | |
| 3564 </section> | |
| 3565 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3566 <output name="ctd_out" ftype="xml"> | |
| 3567 <assert_contents> | |
| 3568 <is_valid_xml/> | |
| 3569 </assert_contents> | |
| 3570 </output> | |
| 3571 </test> | |
| 3572 <test expect_num_outputs="2"> | |
| 3573 <conditional name="adv_opts_cond"> | |
| 3574 <param name="adv_opts_selector" value="advanced"/> | |
| 3575 <param name="force" value="false"/> | |
| 3576 <param name="test" value="true"/> | |
| 3577 </conditional> | |
| 3578 <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/> | |
| 3579 <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3580 <param name="keep_subelements" value="true"/> | |
| 3581 <section name="algorithm"> | |
| 3582 <param name="use_identifications" value="false"/> | |
| 3583 <param name="nr_partitions" value="100"/> | |
| 3584 <param name="ignore_charge" value="false"/> | |
| 3585 <param name="ignore_adduct" value="true"/> | |
| 3586 <section name="distance_RT"> | |
| 3587 <param name="max_difference" value="100.0"/> | |
| 3588 <param name="exponent" value="1.0"/> | |
| 3589 <param name="weight" value="1.0"/> | |
| 3590 </section> | |
| 3591 <section name="distance_MZ"> | |
| 3592 <param name="max_difference" value="0.3"/> | |
| 3593 <param name="unit" value="Da"/> | |
| 3594 <param name="exponent" value="2.0"/> | |
| 3595 <param name="weight" value="1.0"/> | |
| 3596 </section> | |
| 3597 <section name="distance_intensity"> | |
| 3598 <param name="exponent" value="1.0"/> | |
| 3599 <param name="weight" value="0.0"/> | |
| 3600 <param name="log_transform" value="disabled"/> | |
| 3601 </section> | |
| 3602 </section> | |
| 3603 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3604 <output name="ctd_out" ftype="xml"> | |
| 3605 <assert_contents> | |
| 3606 <is_valid_xml/> | |
| 3607 </assert_contents> | |
| 3608 </output> | |
| 3609 </test> | |
| 3610 <test expect_num_outputs="2"> | |
| 3611 <conditional name="adv_opts_cond"> | |
| 3612 <param name="adv_opts_selector" value="advanced"/> | |
| 3613 <param name="force" value="false"/> | |
| 3614 <param name="test" value="true"/> | |
| 3615 </conditional> | |
| 3616 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> | |
| 3617 <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3618 <param name="keep_subelements" value="false"/> | |
| 3619 <section name="algorithm"> | |
| 3620 <param name="use_identifications" value="false"/> | |
| 3621 <param name="nr_partitions" value="99999"/> | |
| 3622 <param name="ignore_charge" value="false"/> | |
| 3623 <param name="ignore_adduct" value="true"/> | |
| 3624 <section name="distance_RT"> | |
| 3625 <param name="max_difference" value="100.0"/> | |
| 3626 <param name="exponent" value="1.0"/> | |
| 3627 <param name="weight" value="1.0"/> | |
| 3628 </section> | |
| 3629 <section name="distance_MZ"> | |
| 3630 <param name="max_difference" value="0.3"/> | |
| 3631 <param name="unit" value="Da"/> | |
| 3632 <param name="exponent" value="2.0"/> | |
| 3633 <param name="weight" value="1.0"/> | |
| 3634 </section> | |
| 3635 <section name="distance_intensity"> | |
| 3636 <param name="exponent" value="1.0"/> | |
| 3637 <param name="weight" value="0.0"/> | |
| 3638 <param name="log_transform" value="disabled"/> | |
| 3639 </section> | |
| 3640 </section> | |
| 3641 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3642 <output name="ctd_out" ftype="xml"> | |
| 3643 <assert_contents> | |
| 3644 <is_valid_xml/> | |
| 3645 </assert_contents> | |
| 3646 </output> | |
| 3647 </test> | |
| 3648 <test expect_num_outputs="2"> | |
| 3649 <conditional name="adv_opts_cond"> | |
| 3650 <param name="adv_opts_selector" value="advanced"/> | |
| 3651 <param name="force" value="false"/> | |
| 3652 <param name="test" value="true"/> | |
| 3653 </conditional> | |
| 3654 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> | |
| 3655 <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3656 <param name="keep_subelements" value="false"/> | |
| 3657 <section name="algorithm"> | |
| 3658 <param name="use_identifications" value="true"/> | |
| 3659 <param name="nr_partitions" value="100"/> | |
| 3660 <param name="ignore_charge" value="false"/> | |
| 3661 <param name="ignore_adduct" value="true"/> | |
| 3662 <section name="distance_RT"> | |
| 3663 <param name="max_difference" value="100.0"/> | |
| 3664 <param name="exponent" value="1.0"/> | |
| 3665 <param name="weight" value="1.0"/> | |
| 3666 </section> | |
| 3667 <section name="distance_MZ"> | |
| 3668 <param name="max_difference" value="0.3"/> | |
| 3669 <param name="unit" value="Da"/> | |
| 3670 <param name="exponent" value="2.0"/> | |
| 3671 <param name="weight" value="1.0"/> | |
| 3672 </section> | |
| 3673 <section name="distance_intensity"> | |
| 3674 <param name="exponent" value="1.0"/> | |
| 3675 <param name="weight" value="0.0"/> | |
| 3676 <param name="log_transform" value="disabled"/> | |
| 3677 </section> | |
| 3678 </section> | |
| 3679 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3680 <output name="ctd_out" ftype="xml"> | |
| 3681 <assert_contents> | |
| 3682 <is_valid_xml/> | |
| 3683 </assert_contents> | |
| 3684 </output> | |
| 3685 </test> | |
| 3686 <test expect_num_outputs="2"> | |
| 3687 <conditional name="adv_opts_cond"> | |
| 3688 <param name="adv_opts_selector" value="advanced"/> | |
| 3689 <param name="force" value="false"/> | |
| 3690 <param name="test" value="true"/> | |
| 3691 </conditional> | |
| 3692 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> | |
| 3693 <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3694 <param name="keep_subelements" value="false"/> | |
| 3695 <section name="algorithm"> | |
| 3696 <param name="use_identifications" value="false"/> | |
| 3697 <param name="nr_partitions" value="100"/> | |
| 3698 <param name="ignore_charge" value="false"/> | |
| 3699 <param name="ignore_adduct" value="true"/> | |
| 3700 <section name="distance_RT"> | |
| 3701 <param name="max_difference" value="200.0"/> | |
| 3702 <param name="exponent" value="1.0"/> | |
| 3703 <param name="weight" value="1.0"/> | |
| 3704 </section> | |
| 3705 <section name="distance_MZ"> | |
| 3706 <param name="max_difference" value="0.3"/> | |
| 3707 <param name="unit" value="Da"/> | |
| 3708 <param name="exponent" value="2.0"/> | |
| 3709 <param name="weight" value="1.0"/> | |
| 3710 </section> | |
| 3711 <section name="distance_intensity"> | |
| 3712 <param name="exponent" value="1.0"/> | |
| 3713 <param name="weight" value="0.0"/> | |
| 3714 <param name="log_transform" value="disabled"/> | |
| 3715 </section> | |
| 3716 </section> | |
| 3717 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3718 <output name="ctd_out" ftype="xml"> | |
| 3719 <assert_contents> | |
| 3720 <is_valid_xml/> | |
| 3721 </assert_contents> | |
| 3722 </output> | |
| 3723 </test> | |
| 3724 <test expect_num_outputs="2"> | |
| 3725 <conditional name="adv_opts_cond"> | |
| 3726 <param name="adv_opts_selector" value="advanced"/> | |
| 3727 <param name="force" value="false"/> | |
| 3728 <param name="test" value="true"/> | |
| 3729 </conditional> | |
| 3730 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> | |
| 3731 <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3732 <param name="keep_subelements" value="false"/> | |
| 3733 <section name="algorithm"> | |
| 3734 <param name="use_identifications" value="true"/> | |
| 3735 <param name="nr_partitions" value="100"/> | |
| 3736 <param name="ignore_charge" value="false"/> | |
| 3737 <param name="ignore_adduct" value="true"/> | |
| 3738 <section name="distance_RT"> | |
| 3739 <param name="max_difference" value="200.0"/> | |
| 3740 <param name="exponent" value="1.0"/> | |
| 3741 <param name="weight" value="1.0"/> | |
| 3742 </section> | |
| 3743 <section name="distance_MZ"> | |
| 3744 <param name="max_difference" value="0.3"/> | |
| 3745 <param name="unit" value="Da"/> | |
| 3746 <param name="exponent" value="2.0"/> | |
| 3747 <param name="weight" value="1.0"/> | |
| 3748 </section> | |
| 3749 <section name="distance_intensity"> | |
| 3750 <param name="exponent" value="1.0"/> | |
| 3751 <param name="weight" value="0.0"/> | |
| 3752 <param name="log_transform" value="disabled"/> | |
| 3753 </section> | |
| 3754 </section> | |
| 3755 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3756 <output name="ctd_out" ftype="xml"> | |
| 3757 <assert_contents> | |
| 3758 <is_valid_xml/> | |
| 3759 </assert_contents> | |
| 3760 </output> | |
| 3761 </test> | |
| 3762 </xml> | |
| 3763 <xml name="autotest_FeatureLinkerUnlabeled"> | |
| 3764 <test expect_num_outputs="2"> | |
| 3765 <conditional name="adv_opts_cond"> | |
| 3766 <param name="adv_opts_selector" value="advanced"/> | |
| 3767 <param name="force" value="false"/> | |
| 3768 <param name="test" value="true"/> | |
| 3769 </conditional> | |
| 3770 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> | |
| 3771 <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3772 <param name="keep_subelements" value="false"/> | |
| 3773 <section name="algorithm"> | |
| 3774 <param name="second_nearest_gap" value="2.0"/> | |
| 3775 <param name="use_identifications" value="false"/> | |
| 3776 <param name="ignore_charge" value="true"/> | |
| 3777 <param name="ignore_adduct" value="true"/> | |
| 3778 <section name="distance_RT"> | |
| 3779 <param name="max_difference" value="200.0"/> | |
| 3780 <param name="exponent" value="1.0"/> | |
| 3781 <param name="weight" value="1.0"/> | |
| 3782 </section> | |
| 3783 <section name="distance_MZ"> | |
| 3784 <param name="max_difference" value="0.5"/> | |
| 3785 <param name="unit" value="Da"/> | |
| 3786 <param name="exponent" value="1.0"/> | |
| 3787 <param name="weight" value="1.0"/> | |
| 3788 </section> | |
| 3789 <section name="distance_intensity"> | |
| 3790 <param name="exponent" value="1.0"/> | |
| 3791 <param name="weight" value="0.0"/> | |
| 3792 <param name="log_transform" value="disabled"/> | |
| 3793 </section> | |
| 3794 </section> | |
| 3795 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3796 <output name="ctd_out" ftype="xml"> | |
| 3797 <assert_contents> | |
| 3798 <is_valid_xml/> | |
| 3799 </assert_contents> | |
| 3800 </output> | |
| 3801 </test> | |
| 3802 <test expect_num_outputs="2"> | |
| 3803 <conditional name="adv_opts_cond"> | |
| 3804 <param name="adv_opts_selector" value="advanced"/> | |
| 3805 <param name="force" value="false"/> | |
| 3806 <param name="test" value="true"/> | |
| 3807 </conditional> | |
| 3808 <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/> | |
| 3809 <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3810 <param name="keep_subelements" value="false"/> | |
| 3811 <section name="algorithm"> | |
| 3812 <param name="second_nearest_gap" value="2.0"/> | |
| 3813 <param name="use_identifications" value="false"/> | |
| 3814 <param name="ignore_charge" value="false"/> | |
| 3815 <param name="ignore_adduct" value="true"/> | |
| 3816 <section name="distance_RT"> | |
| 3817 <param name="max_difference" value="100.0"/> | |
| 3818 <param name="exponent" value="1.0"/> | |
| 3819 <param name="weight" value="1.0"/> | |
| 3820 </section> | |
| 3821 <section name="distance_MZ"> | |
| 3822 <param name="max_difference" value="0.3"/> | |
| 3823 <param name="unit" value="Da"/> | |
| 3824 <param name="exponent" value="2.0"/> | |
| 3825 <param name="weight" value="1.0"/> | |
| 3826 </section> | |
| 3827 <section name="distance_intensity"> | |
| 3828 <param name="exponent" value="1.0"/> | |
| 3829 <param name="weight" value="0.5"/> | |
| 3830 <param name="log_transform" value="disabled"/> | |
| 3831 </section> | |
| 3832 </section> | |
| 3833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3834 <output name="ctd_out" ftype="xml"> | |
| 3835 <assert_contents> | |
| 3836 <is_valid_xml/> | |
| 3837 </assert_contents> | |
| 3838 </output> | |
| 3839 </test> | |
| 3840 <test expect_num_outputs="2"> | |
| 3841 <conditional name="adv_opts_cond"> | |
| 3842 <param name="adv_opts_selector" value="advanced"/> | |
| 3843 <param name="force" value="false"/> | |
| 3844 <param name="test" value="true"/> | |
| 3845 </conditional> | |
| 3846 <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/> | |
| 3847 <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3848 <param name="keep_subelements" value="false"/> | |
| 3849 <section name="algorithm"> | |
| 3850 <param name="second_nearest_gap" value="1.5"/> | |
| 3851 <param name="use_identifications" value="false"/> | |
| 3852 <param name="ignore_charge" value="true"/> | |
| 3853 <param name="ignore_adduct" value="true"/> | |
| 3854 <section name="distance_RT"> | |
| 3855 <param name="max_difference" value="30.0"/> | |
| 3856 <param name="exponent" value="1.0"/> | |
| 3857 <param name="weight" value="1.0"/> | |
| 3858 </section> | |
| 3859 <section name="distance_MZ"> | |
| 3860 <param name="max_difference" value="0.3"/> | |
| 3861 <param name="unit" value="Da"/> | |
| 3862 <param name="exponent" value="2.0"/> | |
| 3863 <param name="weight" value="1.0"/> | |
| 3864 </section> | |
| 3865 <section name="distance_intensity"> | |
| 3866 <param name="exponent" value="1.0"/> | |
| 3867 <param name="weight" value="0.0"/> | |
| 3868 <param name="log_transform" value="disabled"/> | |
| 3869 </section> | |
| 3870 </section> | |
| 3871 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3872 <output name="ctd_out" ftype="xml"> | |
| 3873 <assert_contents> | |
| 3874 <is_valid_xml/> | |
| 3875 </assert_contents> | |
| 3876 </output> | |
| 3877 </test> | |
| 3878 <test expect_num_outputs="2"> | |
| 3879 <conditional name="adv_opts_cond"> | |
| 3880 <param name="adv_opts_selector" value="advanced"/> | |
| 3881 <param name="force" value="false"/> | |
| 3882 <param name="test" value="true"/> | |
| 3883 </conditional> | |
| 3884 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> | |
| 3885 <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 3886 <param name="keep_subelements" value="false"/> | |
| 3887 <section name="algorithm"> | |
| 3888 <param name="second_nearest_gap" value="2.0"/> | |
| 3889 <param name="use_identifications" value="true"/> | |
| 3890 <param name="ignore_charge" value="true"/> | |
| 3891 <param name="ignore_adduct" value="true"/> | |
| 3892 <section name="distance_RT"> | |
| 3893 <param name="max_difference" value="200.0"/> | |
| 3894 <param name="exponent" value="2.0"/> | |
| 3895 <param name="weight" value="1.0"/> | |
| 3896 </section> | |
| 3897 <section name="distance_MZ"> | |
| 3898 <param name="max_difference" value="0.5"/> | |
| 3899 <param name="unit" value="Da"/> | |
| 3900 <param name="exponent" value="2.0"/> | |
| 3901 <param name="weight" value="1.0"/> | |
| 3902 </section> | |
| 3903 <section name="distance_intensity"> | |
| 3904 <param name="exponent" value="1.0"/> | |
| 3905 <param name="weight" value="0.0"/> | |
| 3906 <param name="log_transform" value="disabled"/> | |
| 3907 </section> | |
| 3908 </section> | |
| 3909 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3910 <output name="ctd_out" ftype="xml"> | |
| 3911 <assert_contents> | |
| 3912 <is_valid_xml/> | |
| 3913 </assert_contents> | |
| 3914 </output> | |
| 3915 </test> | |
| 3916 </xml> | |
| 3917 <xml name="autotest_FFEval"> | |
| 3918 </xml> | |
| 3919 <xml name="autotest_FidoAdapter"> | |
| 3920 <test expect_num_outputs="2"> | |
| 3921 <conditional name="adv_opts_cond"> | |
| 3922 <param name="adv_opts_selector" value="advanced"/> | |
| 3923 <param name="keep_zero_group" value="false"/> | |
| 3924 <param name="accuracy" value=""/> | |
| 3925 <param name="log2_states_precalc" value="0"/> | |
| 3926 <param name="force" value="false"/> | |
| 3927 <param name="test" value="true"/> | |
| 3928 </conditional> | |
| 3929 <param name="in" value="FidoAdapter_1_input.idXML"/> | |
| 3930 <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 3931 <param name="separate_runs" value="false"/> | |
| 3932 <param name="greedy_group_resolution" value="false"/> | |
| 3933 <param name="no_cleanup" value="false"/> | |
| 3934 <param name="all_PSMs" value="false"/> | |
| 3935 <param name="group_level" value="false"/> | |
| 3936 <param name="log2_states" value="0"/> | |
| 3937 <section name="prob"> | |
| 3938 <param name="protein" value="0.0"/> | |
| 3939 <param name="peptide" value="0.0"/> | |
| 3940 <param name="spurious" value="0.0"/> | |
| 3941 </section> | |
| 3942 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3943 <output name="ctd_out" ftype="xml"> | |
| 3944 <assert_contents> | |
| 3945 <is_valid_xml/> | |
| 3946 </assert_contents> | |
| 3947 </output> | |
| 3948 </test> | |
| 3949 <test expect_num_outputs="2"> | |
| 3950 <conditional name="adv_opts_cond"> | |
| 3951 <param name="adv_opts_selector" value="advanced"/> | |
| 3952 <param name="keep_zero_group" value="false"/> | |
| 3953 <param name="accuracy" value=""/> | |
| 3954 <param name="log2_states_precalc" value="0"/> | |
| 3955 <param name="force" value="false"/> | |
| 3956 <param name="test" value="true"/> | |
| 3957 </conditional> | |
| 3958 <param name="in" value="FidoAdapter_1_input.idXML"/> | |
| 3959 <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 3960 <param name="separate_runs" value="true"/> | |
| 3961 <param name="greedy_group_resolution" value="false"/> | |
| 3962 <param name="no_cleanup" value="false"/> | |
| 3963 <param name="all_PSMs" value="false"/> | |
| 3964 <param name="group_level" value="false"/> | |
| 3965 <param name="log2_states" value="0"/> | |
| 3966 <section name="prob"> | |
| 3967 <param name="protein" value="0.0"/> | |
| 3968 <param name="peptide" value="0.0"/> | |
| 3969 <param name="spurious" value="0.0"/> | |
| 3970 </section> | |
| 3971 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 3972 <output name="ctd_out" ftype="xml"> | |
| 3973 <assert_contents> | |
| 3974 <is_valid_xml/> | |
| 3975 </assert_contents> | |
| 3976 </output> | |
| 3977 </test> | |
| 3978 <test expect_num_outputs="2"> | |
| 3979 <conditional name="adv_opts_cond"> | |
| 3980 <param name="adv_opts_selector" value="advanced"/> | |
| 3981 <param name="keep_zero_group" value="false"/> | |
| 3982 <param name="accuracy" value=""/> | |
| 3983 <param name="log2_states_precalc" value="0"/> | |
| 3984 <param name="force" value="false"/> | |
| 3985 <param name="test" value="true"/> | |
| 3986 </conditional> | |
| 3987 <param name="in" value="FidoAdapter_1_input.idXML"/> | |
| 3988 <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 3989 <param name="separate_runs" value="false"/> | |
| 3990 <param name="greedy_group_resolution" value="false"/> | |
| 3991 <param name="no_cleanup" value="false"/> | |
| 3992 <param name="all_PSMs" value="true"/> | |
| 3993 <param name="group_level" value="true"/> | |
| 3994 <param name="log2_states" value="0"/> | |
| 3995 <section name="prob"> | |
| 3996 <param name="protein" value="0.0"/> | |
| 3997 <param name="peptide" value="0.0"/> | |
| 3998 <param name="spurious" value="0.0"/> | |
| 3999 </section> | |
| 4000 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4001 <output name="ctd_out" ftype="xml"> | |
| 4002 <assert_contents> | |
| 4003 <is_valid_xml/> | |
| 4004 </assert_contents> | |
| 4005 </output> | |
| 4006 </test> | |
| 4007 <test expect_num_outputs="2"> | |
| 4008 <conditional name="adv_opts_cond"> | |
| 4009 <param name="adv_opts_selector" value="advanced"/> | |
| 4010 <param name="keep_zero_group" value="false"/> | |
| 4011 <param name="accuracy" value=""/> | |
| 4012 <param name="log2_states_precalc" value="0"/> | |
| 4013 <param name="force" value="false"/> | |
| 4014 <param name="test" value="true"/> | |
| 4015 </conditional> | |
| 4016 <param name="in" value="FidoAdapter_4_input.idXML"/> | |
| 4017 <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 4018 <param name="separate_runs" value="false"/> | |
| 4019 <param name="greedy_group_resolution" value="false"/> | |
| 4020 <param name="no_cleanup" value="false"/> | |
| 4021 <param name="all_PSMs" value="false"/> | |
| 4022 <param name="group_level" value="false"/> | |
| 4023 <param name="log2_states" value="0"/> | |
| 4024 <section name="prob"> | |
| 4025 <param name="protein" value="0.0"/> | |
| 4026 <param name="peptide" value="0.0"/> | |
| 4027 <param name="spurious" value="0.0"/> | |
| 4028 </section> | |
| 4029 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4030 <output name="ctd_out" ftype="xml"> | |
| 4031 <assert_contents> | |
| 4032 <is_valid_xml/> | |
| 4033 </assert_contents> | |
| 4034 </output> | |
| 4035 </test> | |
| 4036 <test expect_num_outputs="2"> | |
| 4037 <conditional name="adv_opts_cond"> | |
| 4038 <param name="adv_opts_selector" value="advanced"/> | |
| 4039 <param name="keep_zero_group" value="false"/> | |
| 4040 <param name="accuracy" value=""/> | |
| 4041 <param name="log2_states_precalc" value="0"/> | |
| 4042 <param name="force" value="false"/> | |
| 4043 <param name="test" value="true"/> | |
| 4044 </conditional> | |
| 4045 <param name="in" value="FidoAdapter_5_input.idXML"/> | |
| 4046 <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 4047 <param name="separate_runs" value="false"/> | |
| 4048 <param name="greedy_group_resolution" value="true"/> | |
| 4049 <param name="no_cleanup" value="false"/> | |
| 4050 <param name="all_PSMs" value="false"/> | |
| 4051 <param name="group_level" value="false"/> | |
| 4052 <param name="log2_states" value="0"/> | |
| 4053 <section name="prob"> | |
| 4054 <param name="protein" value="0.0"/> | |
| 4055 <param name="peptide" value="0.0"/> | |
| 4056 <param name="spurious" value="0.0"/> | |
| 4057 </section> | |
| 4058 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4059 <output name="ctd_out" ftype="xml"> | |
| 4060 <assert_contents> | |
| 4061 <is_valid_xml/> | |
| 4062 </assert_contents> | |
| 4063 </output> | |
| 4064 </test> | |
| 4065 <test expect_num_outputs="2"> | |
| 4066 <conditional name="adv_opts_cond"> | |
| 4067 <param name="adv_opts_selector" value="advanced"/> | |
| 4068 <param name="keep_zero_group" value="false"/> | |
| 4069 <param name="accuracy" value=""/> | |
| 4070 <param name="log2_states_precalc" value="0"/> | |
| 4071 <param name="force" value="false"/> | |
| 4072 <param name="test" value="true"/> | |
| 4073 </conditional> | |
| 4074 <param name="in" value="FidoAdapter_1_input.idXML"/> | |
| 4075 <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 4076 <param name="separate_runs" value="false"/> | |
| 4077 <param name="greedy_group_resolution" value="false"/> | |
| 4078 <param name="no_cleanup" value="false"/> | |
| 4079 <param name="all_PSMs" value="false"/> | |
| 4080 <param name="group_level" value="false"/> | |
| 4081 <param name="log2_states" value="0"/> | |
| 4082 <section name="prob"> | |
| 4083 <param name="protein" value="0.9"/> | |
| 4084 <param name="peptide" value="0.01"/> | |
| 4085 <param name="spurious" value="0.0"/> | |
| 4086 </section> | |
| 4087 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4088 <output name="ctd_out" ftype="xml"> | |
| 4089 <assert_contents> | |
| 4090 <is_valid_xml/> | |
| 4091 </assert_contents> | |
| 4092 </output> | |
| 4093 </test> | |
| 4094 </xml> | |
| 4095 <xml name="autotest_FileConverter"> | |
| 4096 <test expect_num_outputs="2"> | |
| 4097 <conditional name="adv_opts_cond"> | |
| 4098 <param name="adv_opts_selector" value="advanced"/> | |
| 4099 <param name="UID_postprocessing" value="ensure"/> | |
| 4100 <param name="TIC_DTA2D" value="false"/> | |
| 4101 <param name="MGF_compact" value="false"/> | |
| 4102 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4103 <param name="convert_to_chromatograms" value="false"/> | |
| 4104 <param name="force_TPP_compatibility" value="false"/> | |
| 4105 <param name="change_im_format" value="none"/> | |
| 4106 <param name="write_scan_index" value="true"/> | |
| 4107 <param name="lossy_compression" value="false"/> | |
| 4108 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4109 <param name="process_lowmemory" value="false"/> | |
| 4110 <param name="no_peak_picking" value="false"/> | |
| 4111 <param name="force" value="false"/> | |
| 4112 <param name="test" value="true"/> | |
| 4113 </conditional> | |
| 4114 <param name="in" value="FileConverter_1_input.mzData"/> | |
| 4115 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4116 <param name="out_type" value="mzML"/> | |
| 4117 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4118 <output name="ctd_out" ftype="xml"> | |
| 4119 <assert_contents> | |
| 4120 <is_valid_xml/> | |
| 4121 </assert_contents> | |
| 4122 </output> | |
| 4123 </test> | |
| 4124 <test expect_num_outputs="2"> | |
| 4125 <conditional name="adv_opts_cond"> | |
| 4126 <param name="adv_opts_selector" value="advanced"/> | |
| 4127 <param name="UID_postprocessing" value="ensure"/> | |
| 4128 <param name="TIC_DTA2D" value="false"/> | |
| 4129 <param name="MGF_compact" value="false"/> | |
| 4130 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4131 <param name="convert_to_chromatograms" value="false"/> | |
| 4132 <param name="force_TPP_compatibility" value="false"/> | |
| 4133 <param name="change_im_format" value="none"/> | |
| 4134 <param name="write_scan_index" value="true"/> | |
| 4135 <param name="lossy_compression" value="false"/> | |
| 4136 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4137 <param name="process_lowmemory" value="false"/> | |
| 4138 <param name="no_peak_picking" value="false"/> | |
| 4139 <param name="force" value="false"/> | |
| 4140 <param name="test" value="true"/> | |
| 4141 </conditional> | |
| 4142 <param name="in" value="FileConverter_2_input.someInputDTA2D"/> | |
| 4143 <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4144 <param name="out_type" value="mzML"/> | |
| 4145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4146 <output name="ctd_out" ftype="xml"> | |
| 4147 <assert_contents> | |
| 4148 <is_valid_xml/> | |
| 4149 </assert_contents> | |
| 4150 </output> | |
| 4151 </test> | |
| 4152 <test expect_num_outputs="2"> | |
| 4153 <conditional name="adv_opts_cond"> | |
| 4154 <param name="adv_opts_selector" value="advanced"/> | |
| 4155 <param name="UID_postprocessing" value="ensure"/> | |
| 4156 <param name="TIC_DTA2D" value="false"/> | |
| 4157 <param name="MGF_compact" value="false"/> | |
| 4158 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4159 <param name="convert_to_chromatograms" value="false"/> | |
| 4160 <param name="force_TPP_compatibility" value="false"/> | |
| 4161 <param name="change_im_format" value="none"/> | |
| 4162 <param name="write_scan_index" value="true"/> | |
| 4163 <param name="lossy_compression" value="false"/> | |
| 4164 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4165 <param name="process_lowmemory" value="false"/> | |
| 4166 <param name="no_peak_picking" value="false"/> | |
| 4167 <param name="force" value="false"/> | |
| 4168 <param name="test" value="true"/> | |
| 4169 </conditional> | |
| 4170 <param name="in" value="FileConverter_3_input.featureXML"/> | |
| 4171 <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4172 <param name="out_type" value="mzML"/> | |
| 4173 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4174 <output name="ctd_out" ftype="xml"> | |
| 4175 <assert_contents> | |
| 4176 <is_valid_xml/> | |
| 4177 </assert_contents> | |
| 4178 </output> | |
| 4179 </test> | |
| 4180 <test expect_num_outputs="2"> | |
| 4181 <conditional name="adv_opts_cond"> | |
| 4182 <param name="adv_opts_selector" value="advanced"/> | |
| 4183 <param name="UID_postprocessing" value="ensure"/> | |
| 4184 <param name="TIC_DTA2D" value="false"/> | |
| 4185 <param name="MGF_compact" value="false"/> | |
| 4186 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4187 <param name="convert_to_chromatograms" value="false"/> | |
| 4188 <param name="force_TPP_compatibility" value="false"/> | |
| 4189 <param name="change_im_format" value="none"/> | |
| 4190 <param name="write_scan_index" value="true"/> | |
| 4191 <param name="lossy_compression" value="false"/> | |
| 4192 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4193 <param name="process_lowmemory" value="false"/> | |
| 4194 <param name="no_peak_picking" value="false"/> | |
| 4195 <param name="force" value="false"/> | |
| 4196 <param name="test" value="true"/> | |
| 4197 </conditional> | |
| 4198 <param name="in" value="FileConverter_4_input.mzXML"/> | |
| 4199 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4200 <param name="out_type" value="mzML"/> | |
| 4201 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4202 <output name="ctd_out" ftype="xml"> | |
| 4203 <assert_contents> | |
| 4204 <is_valid_xml/> | |
| 4205 </assert_contents> | |
| 4206 </output> | |
| 4207 </test> | |
| 4208 <test expect_num_outputs="2"> | |
| 4209 <conditional name="adv_opts_cond"> | |
| 4210 <param name="adv_opts_selector" value="advanced"/> | |
| 4211 <param name="UID_postprocessing" value="ensure"/> | |
| 4212 <param name="TIC_DTA2D" value="false"/> | |
| 4213 <param name="MGF_compact" value="false"/> | |
| 4214 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4215 <param name="convert_to_chromatograms" value="false"/> | |
| 4216 <param name="force_TPP_compatibility" value="false"/> | |
| 4217 <param name="change_im_format" value="none"/> | |
| 4218 <param name="write_scan_index" value="true"/> | |
| 4219 <param name="lossy_compression" value="false"/> | |
| 4220 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4221 <param name="process_lowmemory" value="false"/> | |
| 4222 <param name="no_peak_picking" value="false"/> | |
| 4223 <param name="force" value="false"/> | |
| 4224 <param name="test" value="true"/> | |
| 4225 </conditional> | |
| 4226 <param name="in" value="FileConverter_5_input.mzML"/> | |
| 4227 <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> | |
| 4228 <param name="out_type" value="mzXML"/> | |
| 4229 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4230 <output name="ctd_out" ftype="xml"> | |
| 4231 <assert_contents> | |
| 4232 <is_valid_xml/> | |
| 4233 </assert_contents> | |
| 4234 </output> | |
| 4235 </test> | |
| 4236 <test expect_num_outputs="2"> | |
| 4237 <conditional name="adv_opts_cond"> | |
| 4238 <param name="adv_opts_selector" value="advanced"/> | |
| 4239 <param name="UID_postprocessing" value="ensure"/> | |
| 4240 <param name="TIC_DTA2D" value="false"/> | |
| 4241 <param name="MGF_compact" value="false"/> | |
| 4242 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4243 <param name="convert_to_chromatograms" value="false"/> | |
| 4244 <param name="force_TPP_compatibility" value="false"/> | |
| 4245 <param name="change_im_format" value="none"/> | |
| 4246 <param name="write_scan_index" value="true"/> | |
| 4247 <param name="lossy_compression" value="false"/> | |
| 4248 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4249 <param name="process_lowmemory" value="false"/> | |
| 4250 <param name="no_peak_picking" value="false"/> | |
| 4251 <param name="force" value="false"/> | |
| 4252 <param name="test" value="true"/> | |
| 4253 </conditional> | |
| 4254 <param name="in" value="FileConverter_6_input.mzML"/> | |
| 4255 <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> | |
| 4256 <param name="out_type" value="mzXML"/> | |
| 4257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4258 <output name="ctd_out" ftype="xml"> | |
| 4259 <assert_contents> | |
| 4260 <is_valid_xml/> | |
| 4261 </assert_contents> | |
| 4262 </output> | |
| 4263 </test> | |
| 4264 <test expect_num_outputs="2"> | |
| 4265 <conditional name="adv_opts_cond"> | |
| 4266 <param name="adv_opts_selector" value="advanced"/> | |
| 4267 <param name="UID_postprocessing" value="ensure"/> | |
| 4268 <param name="TIC_DTA2D" value="false"/> | |
| 4269 <param name="MGF_compact" value="false"/> | |
| 4270 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4271 <param name="convert_to_chromatograms" value="false"/> | |
| 4272 <param name="force_TPP_compatibility" value="false"/> | |
| 4273 <param name="change_im_format" value="none"/> | |
| 4274 <param name="write_scan_index" value="true"/> | |
| 4275 <param name="lossy_compression" value="false"/> | |
| 4276 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4277 <param name="process_lowmemory" value="false"/> | |
| 4278 <param name="no_peak_picking" value="false"/> | |
| 4279 <param name="force" value="false"/> | |
| 4280 <param name="test" value="true"/> | |
| 4281 </conditional> | |
| 4282 <param name="in" value="FileConverter_7_input.consensusXML"/> | |
| 4283 <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 4284 <param name="out_type" value="featureXML"/> | |
| 4285 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4286 <output name="ctd_out" ftype="xml"> | |
| 4287 <assert_contents> | |
| 4288 <is_valid_xml/> | |
| 4289 </assert_contents> | |
| 4290 </output> | |
| 4291 </test> | |
| 4292 <test expect_num_outputs="2"> | |
| 4293 <conditional name="adv_opts_cond"> | |
| 4294 <param name="adv_opts_selector" value="advanced"/> | |
| 4295 <param name="UID_postprocessing" value="ensure"/> | |
| 4296 <param name="TIC_DTA2D" value="false"/> | |
| 4297 <param name="MGF_compact" value="false"/> | |
| 4298 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4299 <param name="convert_to_chromatograms" value="false"/> | |
| 4300 <param name="force_TPP_compatibility" value="false"/> | |
| 4301 <param name="change_im_format" value="none"/> | |
| 4302 <param name="write_scan_index" value="true"/> | |
| 4303 <param name="lossy_compression" value="false"/> | |
| 4304 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4305 <param name="process_lowmemory" value="false"/> | |
| 4306 <param name="no_peak_picking" value="false"/> | |
| 4307 <param name="force" value="false"/> | |
| 4308 <param name="test" value="true"/> | |
| 4309 </conditional> | |
| 4310 <param name="in" value="FileConverter_8_input.mzML"/> | |
| 4311 <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/> | |
| 4312 <param name="out_type" value="mzData"/> | |
| 4313 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4314 <output name="ctd_out" ftype="xml"> | |
| 4315 <assert_contents> | |
| 4316 <is_valid_xml/> | |
| 4317 </assert_contents> | |
| 4318 </output> | |
| 4319 </test> | |
| 4320 <test expect_num_outputs="2"> | |
| 4321 <conditional name="adv_opts_cond"> | |
| 4322 <param name="adv_opts_selector" value="advanced"/> | |
| 4323 <param name="UID_postprocessing" value="ensure"/> | |
| 4324 <param name="TIC_DTA2D" value="false"/> | |
| 4325 <param name="MGF_compact" value="false"/> | |
| 4326 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4327 <param name="convert_to_chromatograms" value="false"/> | |
| 4328 <param name="force_TPP_compatibility" value="false"/> | |
| 4329 <param name="change_im_format" value="none"/> | |
| 4330 <param name="write_scan_index" value="true"/> | |
| 4331 <param name="lossy_compression" value="false"/> | |
| 4332 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4333 <param name="process_lowmemory" value="false"/> | |
| 4334 <param name="no_peak_picking" value="false"/> | |
| 4335 <param name="force" value="false"/> | |
| 4336 <param name="test" value="true"/> | |
| 4337 </conditional> | |
| 4338 <param name="in" value="FileConverter_9_input.consensusXML"/> | |
| 4339 <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 4340 <param name="out_type" value="featureXML"/> | |
| 4341 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4342 <output name="ctd_out" ftype="xml"> | |
| 4343 <assert_contents> | |
| 4344 <is_valid_xml/> | |
| 4345 </assert_contents> | |
| 4346 </output> | |
| 4347 </test> | |
| 4348 <test expect_num_outputs="2"> | |
| 4349 <conditional name="adv_opts_cond"> | |
| 4350 <param name="adv_opts_selector" value="advanced"/> | |
| 4351 <param name="UID_postprocessing" value="ensure"/> | |
| 4352 <param name="TIC_DTA2D" value="false"/> | |
| 4353 <param name="MGF_compact" value="false"/> | |
| 4354 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4355 <param name="convert_to_chromatograms" value="false"/> | |
| 4356 <param name="force_TPP_compatibility" value="false"/> | |
| 4357 <param name="change_im_format" value="none"/> | |
| 4358 <param name="write_scan_index" value="true"/> | |
| 4359 <param name="lossy_compression" value="false"/> | |
| 4360 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4361 <param name="process_lowmemory" value="false"/> | |
| 4362 <param name="no_peak_picking" value="false"/> | |
| 4363 <param name="force" value="false"/> | |
| 4364 <param name="test" value="true"/> | |
| 4365 </conditional> | |
| 4366 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> | |
| 4367 <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 4368 <param name="out_type" value="featureXML"/> | |
| 4369 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4370 <output name="ctd_out" ftype="xml"> | |
| 4371 <assert_contents> | |
| 4372 <is_valid_xml/> | |
| 4373 </assert_contents> | |
| 4374 </output> | |
| 4375 </test> | |
| 4376 <test expect_num_outputs="2"> | |
| 4377 <conditional name="adv_opts_cond"> | |
| 4378 <param name="adv_opts_selector" value="advanced"/> | |
| 4379 <param name="UID_postprocessing" value="ensure"/> | |
| 4380 <param name="TIC_DTA2D" value="false"/> | |
| 4381 <param name="MGF_compact" value="false"/> | |
| 4382 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4383 <param name="convert_to_chromatograms" value="false"/> | |
| 4384 <param name="force_TPP_compatibility" value="false"/> | |
| 4385 <param name="change_im_format" value="none"/> | |
| 4386 <param name="write_scan_index" value="true"/> | |
| 4387 <param name="lossy_compression" value="false"/> | |
| 4388 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4389 <param name="process_lowmemory" value="false"/> | |
| 4390 <param name="no_peak_picking" value="false"/> | |
| 4391 <param name="force" value="false"/> | |
| 4392 <param name="test" value="true"/> | |
| 4393 </conditional> | |
| 4394 <param name="in" value="FileConverter_11_input.peplist"/> | |
| 4395 <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 4396 <param name="out_type" value="featureXML"/> | |
| 4397 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4398 <output name="ctd_out" ftype="xml"> | |
| 4399 <assert_contents> | |
| 4400 <is_valid_xml/> | |
| 4401 </assert_contents> | |
| 4402 </output> | |
| 4403 </test> | |
| 4404 <test expect_num_outputs="2"> | |
| 4405 <conditional name="adv_opts_cond"> | |
| 4406 <param name="adv_opts_selector" value="advanced"/> | |
| 4407 <param name="UID_postprocessing" value="ensure"/> | |
| 4408 <param name="TIC_DTA2D" value="false"/> | |
| 4409 <param name="MGF_compact" value="false"/> | |
| 4410 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4411 <param name="convert_to_chromatograms" value="false"/> | |
| 4412 <param name="force_TPP_compatibility" value="false"/> | |
| 4413 <param name="change_im_format" value="none"/> | |
| 4414 <param name="write_scan_index" value="true"/> | |
| 4415 <param name="lossy_compression" value="false"/> | |
| 4416 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4417 <param name="process_lowmemory" value="false"/> | |
| 4418 <param name="no_peak_picking" value="false"/> | |
| 4419 <param name="force" value="false"/> | |
| 4420 <param name="test" value="true"/> | |
| 4421 </conditional> | |
| 4422 <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/> | |
| 4423 <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 4424 <param name="out_type" value="featureXML"/> | |
| 4425 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4426 <output name="ctd_out" ftype="xml"> | |
| 4427 <assert_contents> | |
| 4428 <is_valid_xml/> | |
| 4429 </assert_contents> | |
| 4430 </output> | |
| 4431 </test> | |
| 4432 <test expect_num_outputs="2"> | |
| 4433 <conditional name="adv_opts_cond"> | |
| 4434 <param name="adv_opts_selector" value="advanced"/> | |
| 4435 <param name="UID_postprocessing" value="ensure"/> | |
| 4436 <param name="TIC_DTA2D" value="false"/> | |
| 4437 <param name="MGF_compact" value="false"/> | |
| 4438 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4439 <param name="convert_to_chromatograms" value="false"/> | |
| 4440 <param name="force_TPP_compatibility" value="false"/> | |
| 4441 <param name="change_im_format" value="none"/> | |
| 4442 <param name="write_scan_index" value="true"/> | |
| 4443 <param name="lossy_compression" value="false"/> | |
| 4444 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4445 <param name="process_lowmemory" value="false"/> | |
| 4446 <param name="no_peak_picking" value="false"/> | |
| 4447 <param name="force" value="false"/> | |
| 4448 <param name="test" value="true"/> | |
| 4449 </conditional> | |
| 4450 <param name="in" value="FileConverter_13_input.peptides.kroenik"/> | |
| 4451 <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 4452 <param name="out_type" value="featureXML"/> | |
| 4453 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4454 <output name="ctd_out" ftype="xml"> | |
| 4455 <assert_contents> | |
| 4456 <is_valid_xml/> | |
| 4457 </assert_contents> | |
| 4458 </output> | |
| 4459 </test> | |
| 4460 <test expect_num_outputs="2"> | |
| 4461 <conditional name="adv_opts_cond"> | |
| 4462 <param name="adv_opts_selector" value="advanced"/> | |
| 4463 <param name="UID_postprocessing" value="ensure"/> | |
| 4464 <param name="TIC_DTA2D" value="false"/> | |
| 4465 <param name="MGF_compact" value="false"/> | |
| 4466 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4467 <param name="convert_to_chromatograms" value="false"/> | |
| 4468 <param name="force_TPP_compatibility" value="false"/> | |
| 4469 <param name="change_im_format" value="none"/> | |
| 4470 <param name="write_scan_index" value="true"/> | |
| 4471 <param name="lossy_compression" value="false"/> | |
| 4472 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4473 <param name="process_lowmemory" value="false"/> | |
| 4474 <param name="no_peak_picking" value="false"/> | |
| 4475 <param name="force" value="false"/> | |
| 4476 <param name="test" value="true"/> | |
| 4477 </conditional> | |
| 4478 <param name="in" value="FileConverter_9_output.featureXML"/> | |
| 4479 <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 4480 <param name="out_type" value="consensusXML"/> | |
| 4481 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4482 <output name="ctd_out" ftype="xml"> | |
| 4483 <assert_contents> | |
| 4484 <is_valid_xml/> | |
| 4485 </assert_contents> | |
| 4486 </output> | |
| 4487 </test> | |
| 4488 <test expect_num_outputs="2"> | |
| 4489 <conditional name="adv_opts_cond"> | |
| 4490 <param name="adv_opts_selector" value="advanced"/> | |
| 4491 <param name="UID_postprocessing" value="ensure"/> | |
| 4492 <param name="TIC_DTA2D" value="false"/> | |
| 4493 <param name="MGF_compact" value="false"/> | |
| 4494 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4495 <param name="convert_to_chromatograms" value="false"/> | |
| 4496 <param name="force_TPP_compatibility" value="false"/> | |
| 4497 <param name="change_im_format" value="none"/> | |
| 4498 <param name="write_scan_index" value="true"/> | |
| 4499 <param name="lossy_compression" value="false"/> | |
| 4500 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4501 <param name="process_lowmemory" value="false"/> | |
| 4502 <param name="no_peak_picking" value="false"/> | |
| 4503 <param name="force" value="false"/> | |
| 4504 <param name="test" value="true"/> | |
| 4505 </conditional> | |
| 4506 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> | |
| 4507 <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 4508 <param name="out_type" value="consensusXML"/> | |
| 4509 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4510 <output name="ctd_out" ftype="xml"> | |
| 4511 <assert_contents> | |
| 4512 <is_valid_xml/> | |
| 4513 </assert_contents> | |
| 4514 </output> | |
| 4515 </test> | |
| 4516 <test expect_num_outputs="2"> | |
| 4517 <conditional name="adv_opts_cond"> | |
| 4518 <param name="adv_opts_selector" value="advanced"/> | |
| 4519 <param name="UID_postprocessing" value="ensure"/> | |
| 4520 <param name="TIC_DTA2D" value="false"/> | |
| 4521 <param name="MGF_compact" value="false"/> | |
| 4522 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4523 <param name="convert_to_chromatograms" value="false"/> | |
| 4524 <param name="force_TPP_compatibility" value="false"/> | |
| 4525 <param name="change_im_format" value="none"/> | |
| 4526 <param name="write_scan_index" value="true"/> | |
| 4527 <param name="lossy_compression" value="false"/> | |
| 4528 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4529 <param name="process_lowmemory" value="false"/> | |
| 4530 <param name="no_peak_picking" value="false"/> | |
| 4531 <param name="force" value="false"/> | |
| 4532 <param name="test" value="true"/> | |
| 4533 </conditional> | |
| 4534 <param name="in" value="FileConverter_16_input.edta" ftype="edta"/> | |
| 4535 <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 4536 <param name="out_type" value="consensusXML"/> | |
| 4537 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4538 <output name="ctd_out" ftype="xml"> | |
| 4539 <assert_contents> | |
| 4540 <is_valid_xml/> | |
| 4541 </assert_contents> | |
| 4542 </output> | |
| 4543 </test> | |
| 4544 <test expect_num_outputs="2"> | |
| 4545 <conditional name="adv_opts_cond"> | |
| 4546 <param name="adv_opts_selector" value="advanced"/> | |
| 4547 <param name="UID_postprocessing" value="ensure"/> | |
| 4548 <param name="TIC_DTA2D" value="false"/> | |
| 4549 <param name="MGF_compact" value="false"/> | |
| 4550 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4551 <param name="convert_to_chromatograms" value="false"/> | |
| 4552 <param name="force_TPP_compatibility" value="false"/> | |
| 4553 <param name="change_im_format" value="none"/> | |
| 4554 <param name="write_scan_index" value="true"/> | |
| 4555 <param name="lossy_compression" value="false"/> | |
| 4556 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4557 <param name="process_lowmemory" value="false"/> | |
| 4558 <param name="no_peak_picking" value="false"/> | |
| 4559 <param name="force" value="false"/> | |
| 4560 <param name="test" value="true"/> | |
| 4561 </conditional> | |
| 4562 <param name="in" value="FileConverter_17_input.consensusXML"/> | |
| 4563 <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 4564 <param name="out_type" value="csv"/> | |
| 4565 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4566 <output name="ctd_out" ftype="xml"> | |
| 4567 <assert_contents> | |
| 4568 <is_valid_xml/> | |
| 4569 </assert_contents> | |
| 4570 </output> | |
| 4571 </test> | |
| 4572 <test expect_num_outputs="2"> | |
| 4573 <conditional name="adv_opts_cond"> | |
| 4574 <param name="adv_opts_selector" value="advanced"/> | |
| 4575 <param name="UID_postprocessing" value="ensure"/> | |
| 4576 <param name="TIC_DTA2D" value="false"/> | |
| 4577 <param name="MGF_compact" value="false"/> | |
| 4578 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4579 <param name="convert_to_chromatograms" value="false"/> | |
| 4580 <param name="force_TPP_compatibility" value="false"/> | |
| 4581 <param name="change_im_format" value="none"/> | |
| 4582 <param name="write_scan_index" value="true"/> | |
| 4583 <param name="lossy_compression" value="false"/> | |
| 4584 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4585 <param name="process_lowmemory" value="false"/> | |
| 4586 <param name="no_peak_picking" value="false"/> | |
| 4587 <param name="force" value="false"/> | |
| 4588 <param name="test" value="true"/> | |
| 4589 </conditional> | |
| 4590 <param name="in" value="FileConverter_17_input.consensusXML"/> | |
| 4591 <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 4592 <param name="out_type" value="csv"/> | |
| 4593 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4594 <output name="ctd_out" ftype="xml"> | |
| 4595 <assert_contents> | |
| 4596 <is_valid_xml/> | |
| 4597 </assert_contents> | |
| 4598 </output> | |
| 4599 </test> | |
| 4600 <test expect_num_outputs="2"> | |
| 4601 <conditional name="adv_opts_cond"> | |
| 4602 <param name="adv_opts_selector" value="advanced"/> | |
| 4603 <param name="UID_postprocessing" value="ensure"/> | |
| 4604 <param name="TIC_DTA2D" value="false"/> | |
| 4605 <param name="MGF_compact" value="false"/> | |
| 4606 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4607 <param name="convert_to_chromatograms" value="false"/> | |
| 4608 <param name="force_TPP_compatibility" value="false"/> | |
| 4609 <param name="change_im_format" value="none"/> | |
| 4610 <param name="write_scan_index" value="true"/> | |
| 4611 <param name="lossy_compression" value="false"/> | |
| 4612 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4613 <param name="process_lowmemory" value="true"/> | |
| 4614 <param name="no_peak_picking" value="false"/> | |
| 4615 <param name="force" value="false"/> | |
| 4616 <param name="test" value="true"/> | |
| 4617 </conditional> | |
| 4618 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 4619 <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4620 <param name="out_type" value="mzML"/> | |
| 4621 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4622 <output name="ctd_out" ftype="xml"> | |
| 4623 <assert_contents> | |
| 4624 <is_valid_xml/> | |
| 4625 </assert_contents> | |
| 4626 </output> | |
| 4627 </test> | |
| 4628 <test expect_num_outputs="2"> | |
| 4629 <conditional name="adv_opts_cond"> | |
| 4630 <param name="adv_opts_selector" value="advanced"/> | |
| 4631 <param name="UID_postprocessing" value="ensure"/> | |
| 4632 <param name="TIC_DTA2D" value="false"/> | |
| 4633 <param name="MGF_compact" value="false"/> | |
| 4634 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4635 <param name="convert_to_chromatograms" value="false"/> | |
| 4636 <param name="force_TPP_compatibility" value="false"/> | |
| 4637 <param name="change_im_format" value="none"/> | |
| 4638 <param name="write_scan_index" value="true"/> | |
| 4639 <param name="lossy_compression" value="false"/> | |
| 4640 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4641 <param name="process_lowmemory" value="false"/> | |
| 4642 <param name="no_peak_picking" value="false"/> | |
| 4643 <param name="force" value="false"/> | |
| 4644 <param name="test" value="true"/> | |
| 4645 </conditional> | |
| 4646 <param name="in" value="FileConverter_20_input.featureXML"/> | |
| 4647 <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 4648 <param name="out_type" value="featureXML"/> | |
| 4649 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4650 <output name="ctd_out" ftype="xml"> | |
| 4651 <assert_contents> | |
| 4652 <is_valid_xml/> | |
| 4653 </assert_contents> | |
| 4654 </output> | |
| 4655 </test> | |
| 4656 <test expect_num_outputs="2"> | |
| 4657 <conditional name="adv_opts_cond"> | |
| 4658 <param name="adv_opts_selector" value="advanced"/> | |
| 4659 <param name="UID_postprocessing" value="ensure"/> | |
| 4660 <param name="TIC_DTA2D" value="false"/> | |
| 4661 <param name="MGF_compact" value="false"/> | |
| 4662 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4663 <param name="convert_to_chromatograms" value="false"/> | |
| 4664 <param name="force_TPP_compatibility" value="false"/> | |
| 4665 <param name="change_im_format" value="none"/> | |
| 4666 <param name="write_scan_index" value="true"/> | |
| 4667 <param name="lossy_compression" value="false"/> | |
| 4668 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4669 <param name="process_lowmemory" value="true"/> | |
| 4670 <param name="no_peak_picking" value="false"/> | |
| 4671 <param name="force" value="false"/> | |
| 4672 <param name="test" value="true"/> | |
| 4673 </conditional> | |
| 4674 <param name="in" value="FileConverter_4_input.mzXML"/> | |
| 4675 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4676 <param name="out_type" value="mzML"/> | |
| 4677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4678 <output name="ctd_out" ftype="xml"> | |
| 4679 <assert_contents> | |
| 4680 <is_valid_xml/> | |
| 4681 </assert_contents> | |
| 4682 </output> | |
| 4683 </test> | |
| 4684 <test expect_num_outputs="2"> | |
| 4685 <conditional name="adv_opts_cond"> | |
| 4686 <param name="adv_opts_selector" value="advanced"/> | |
| 4687 <param name="UID_postprocessing" value="ensure"/> | |
| 4688 <param name="TIC_DTA2D" value="false"/> | |
| 4689 <param name="MGF_compact" value="false"/> | |
| 4690 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4691 <param name="convert_to_chromatograms" value="false"/> | |
| 4692 <param name="force_TPP_compatibility" value="false"/> | |
| 4693 <param name="change_im_format" value="none"/> | |
| 4694 <param name="write_scan_index" value="true"/> | |
| 4695 <param name="lossy_compression" value="false"/> | |
| 4696 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4697 <param name="process_lowmemory" value="false"/> | |
| 4698 <param name="no_peak_picking" value="false"/> | |
| 4699 <param name="force" value="false"/> | |
| 4700 <param name="test" value="true"/> | |
| 4701 </conditional> | |
| 4702 <param name="in" value="FileConverter_23_input.mzML"/> | |
| 4703 <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4704 <param name="out_type" value="mzML"/> | |
| 4705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4706 <output name="ctd_out" ftype="xml"> | |
| 4707 <assert_contents> | |
| 4708 <is_valid_xml/> | |
| 4709 </assert_contents> | |
| 4710 </output> | |
| 4711 </test> | |
| 4712 <test expect_num_outputs="2"> | |
| 4713 <conditional name="adv_opts_cond"> | |
| 4714 <param name="adv_opts_selector" value="advanced"/> | |
| 4715 <param name="UID_postprocessing" value="ensure"/> | |
| 4716 <param name="TIC_DTA2D" value="false"/> | |
| 4717 <param name="MGF_compact" value="false"/> | |
| 4718 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4719 <param name="convert_to_chromatograms" value="false"/> | |
| 4720 <param name="force_TPP_compatibility" value="false"/> | |
| 4721 <param name="change_im_format" value="none"/> | |
| 4722 <param name="write_scan_index" value="true"/> | |
| 4723 <param name="lossy_compression" value="true"/> | |
| 4724 <param name="lossy_mass_accuracy" value="0.0001"/> | |
| 4725 <param name="process_lowmemory" value="true"/> | |
| 4726 <param name="no_peak_picking" value="false"/> | |
| 4727 <param name="force" value="false"/> | |
| 4728 <param name="test" value="true"/> | |
| 4729 </conditional> | |
| 4730 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 4731 <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4732 <param name="out_type" value="mzML"/> | |
| 4733 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4734 <output name="ctd_out" ftype="xml"> | |
| 4735 <assert_contents> | |
| 4736 <is_valid_xml/> | |
| 4737 </assert_contents> | |
| 4738 </output> | |
| 4739 </test> | |
| 4740 <test expect_num_outputs="2"> | |
| 4741 <conditional name="adv_opts_cond"> | |
| 4742 <param name="adv_opts_selector" value="advanced"/> | |
| 4743 <param name="UID_postprocessing" value="ensure"/> | |
| 4744 <param name="TIC_DTA2D" value="false"/> | |
| 4745 <param name="MGF_compact" value="false"/> | |
| 4746 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4747 <param name="convert_to_chromatograms" value="false"/> | |
| 4748 <param name="force_TPP_compatibility" value="false"/> | |
| 4749 <param name="change_im_format" value="none"/> | |
| 4750 <param name="write_scan_index" value="true"/> | |
| 4751 <param name="lossy_compression" value="true"/> | |
| 4752 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4753 <param name="process_lowmemory" value="true"/> | |
| 4754 <param name="no_peak_picking" value="false"/> | |
| 4755 <param name="force" value="false"/> | |
| 4756 <param name="test" value="true"/> | |
| 4757 </conditional> | |
| 4758 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 4759 <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4760 <param name="out_type" value="mzML"/> | |
| 4761 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4762 <output name="ctd_out" ftype="xml"> | |
| 4763 <assert_contents> | |
| 4764 <is_valid_xml/> | |
| 4765 </assert_contents> | |
| 4766 </output> | |
| 4767 </test> | |
| 4768 <test expect_num_outputs="2"> | |
| 4769 <conditional name="adv_opts_cond"> | |
| 4770 <param name="adv_opts_selector" value="advanced"/> | |
| 4771 <param name="UID_postprocessing" value="ensure"/> | |
| 4772 <param name="TIC_DTA2D" value="false"/> | |
| 4773 <param name="MGF_compact" value="false"/> | |
| 4774 <param name="force_MaxQuant_compatibility" value="true"/> | |
| 4775 <param name="convert_to_chromatograms" value="false"/> | |
| 4776 <param name="force_TPP_compatibility" value="false"/> | |
| 4777 <param name="change_im_format" value="none"/> | |
| 4778 <param name="write_scan_index" value="true"/> | |
| 4779 <param name="lossy_compression" value="false"/> | |
| 4780 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4781 <param name="process_lowmemory" value="false"/> | |
| 4782 <param name="no_peak_picking" value="false"/> | |
| 4783 <param name="force" value="false"/> | |
| 4784 <param name="test" value="true"/> | |
| 4785 </conditional> | |
| 4786 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 4787 <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> | |
| 4788 <param name="out_type" value="mzXML"/> | |
| 4789 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4790 <output name="ctd_out" ftype="xml"> | |
| 4791 <assert_contents> | |
| 4792 <is_valid_xml/> | |
| 4793 </assert_contents> | |
| 4794 </output> | |
| 4795 </test> | |
| 4796 <test expect_num_outputs="2"> | |
| 4797 <conditional name="adv_opts_cond"> | |
| 4798 <param name="adv_opts_selector" value="advanced"/> | |
| 4799 <param name="UID_postprocessing" value="ensure"/> | |
| 4800 <param name="TIC_DTA2D" value="false"/> | |
| 4801 <param name="MGF_compact" value="false"/> | |
| 4802 <param name="force_MaxQuant_compatibility" value="true"/> | |
| 4803 <param name="convert_to_chromatograms" value="false"/> | |
| 4804 <param name="force_TPP_compatibility" value="false"/> | |
| 4805 <param name="change_im_format" value="none"/> | |
| 4806 <param name="write_scan_index" value="true"/> | |
| 4807 <param name="lossy_compression" value="false"/> | |
| 4808 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4809 <param name="process_lowmemory" value="false"/> | |
| 4810 <param name="no_peak_picking" value="false"/> | |
| 4811 <param name="force" value="false"/> | |
| 4812 <param name="test" value="true"/> | |
| 4813 </conditional> | |
| 4814 <param name="in" value="FileConverter_26_output.mzXML"/> | |
| 4815 <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> | |
| 4816 <param name="out_type" value="mzXML"/> | |
| 4817 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4818 <output name="ctd_out" ftype="xml"> | |
| 4819 <assert_contents> | |
| 4820 <is_valid_xml/> | |
| 4821 </assert_contents> | |
| 4822 </output> | |
| 4823 </test> | |
| 4824 <test expect_num_outputs="2"> | |
| 4825 <conditional name="adv_opts_cond"> | |
| 4826 <param name="adv_opts_selector" value="advanced"/> | |
| 4827 <param name="UID_postprocessing" value="ensure"/> | |
| 4828 <param name="TIC_DTA2D" value="false"/> | |
| 4829 <param name="MGF_compact" value="false"/> | |
| 4830 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4831 <param name="convert_to_chromatograms" value="true"/> | |
| 4832 <param name="force_TPP_compatibility" value="false"/> | |
| 4833 <param name="change_im_format" value="none"/> | |
| 4834 <param name="write_scan_index" value="true"/> | |
| 4835 <param name="lossy_compression" value="false"/> | |
| 4836 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4837 <param name="process_lowmemory" value="false"/> | |
| 4838 <param name="no_peak_picking" value="false"/> | |
| 4839 <param name="force" value="false"/> | |
| 4840 <param name="test" value="true"/> | |
| 4841 </conditional> | |
| 4842 <param name="in" value="FileConverter_27_input.mzML"/> | |
| 4843 <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4844 <param name="out_type" value="mzML"/> | |
| 4845 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4846 <output name="ctd_out" ftype="xml"> | |
| 4847 <assert_contents> | |
| 4848 <is_valid_xml/> | |
| 4849 </assert_contents> | |
| 4850 </output> | |
| 4851 </test> | |
| 4852 <test expect_num_outputs="2"> | |
| 4853 <conditional name="adv_opts_cond"> | |
| 4854 <param name="adv_opts_selector" value="advanced"/> | |
| 4855 <param name="UID_postprocessing" value="ensure"/> | |
| 4856 <param name="TIC_DTA2D" value="false"/> | |
| 4857 <param name="MGF_compact" value="false"/> | |
| 4858 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4859 <param name="convert_to_chromatograms" value="true"/> | |
| 4860 <param name="force_TPP_compatibility" value="false"/> | |
| 4861 <param name="change_im_format" value="none"/> | |
| 4862 <param name="write_scan_index" value="true"/> | |
| 4863 <param name="lossy_compression" value="false"/> | |
| 4864 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4865 <param name="process_lowmemory" value="false"/> | |
| 4866 <param name="no_peak_picking" value="false"/> | |
| 4867 <param name="force" value="false"/> | |
| 4868 <param name="test" value="true"/> | |
| 4869 </conditional> | |
| 4870 <param name="in" value="FileConverter_28_input.mzML"/> | |
| 4871 <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4872 <param name="out_type" value="mzML"/> | |
| 4873 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4874 <output name="ctd_out" ftype="xml"> | |
| 4875 <assert_contents> | |
| 4876 <is_valid_xml/> | |
| 4877 </assert_contents> | |
| 4878 </output> | |
| 4879 </test> | |
| 4880 <test expect_num_outputs="2"> | |
| 4881 <conditional name="adv_opts_cond"> | |
| 4882 <param name="adv_opts_selector" value="advanced"/> | |
| 4883 <param name="UID_postprocessing" value="ensure"/> | |
| 4884 <param name="TIC_DTA2D" value="false"/> | |
| 4885 <param name="MGF_compact" value="false"/> | |
| 4886 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4887 <param name="convert_to_chromatograms" value="false"/> | |
| 4888 <param name="force_TPP_compatibility" value="false"/> | |
| 4889 <param name="change_im_format" value="none"/> | |
| 4890 <param name="write_scan_index" value="true"/> | |
| 4891 <param name="lossy_compression" value="true"/> | |
| 4892 <param name="lossy_mass_accuracy" value="1e-05"/> | |
| 4893 <param name="process_lowmemory" value="true"/> | |
| 4894 <param name="no_peak_picking" value="false"/> | |
| 4895 <param name="force" value="false"/> | |
| 4896 <param name="test" value="true"/> | |
| 4897 </conditional> | |
| 4898 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> | |
| 4899 <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4900 <param name="out_type" value="mzML"/> | |
| 4901 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4902 <output name="ctd_out" ftype="xml"> | |
| 4903 <assert_contents> | |
| 4904 <is_valid_xml/> | |
| 4905 </assert_contents> | |
| 4906 </output> | |
| 4907 </test> | |
| 4908 <test expect_num_outputs="2"> | |
| 4909 <conditional name="adv_opts_cond"> | |
| 4910 <param name="adv_opts_selector" value="advanced"/> | |
| 4911 <param name="UID_postprocessing" value="ensure"/> | |
| 4912 <param name="TIC_DTA2D" value="false"/> | |
| 4913 <param name="MGF_compact" value="false"/> | |
| 4914 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4915 <param name="convert_to_chromatograms" value="false"/> | |
| 4916 <param name="force_TPP_compatibility" value="false"/> | |
| 4917 <param name="change_im_format" value="none"/> | |
| 4918 <param name="write_scan_index" value="true"/> | |
| 4919 <param name="lossy_compression" value="false"/> | |
| 4920 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4921 <param name="process_lowmemory" value="false"/> | |
| 4922 <param name="no_peak_picking" value="false"/> | |
| 4923 <param name="force" value="false"/> | |
| 4924 <param name="test" value="true"/> | |
| 4925 </conditional> | |
| 4926 <param name="in" value="FileConverter_29_output.mzML"/> | |
| 4927 <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/> | |
| 4928 <param name="out_type" value="mzML"/> | |
| 4929 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4930 <output name="ctd_out" ftype="xml"> | |
| 4931 <assert_contents> | |
| 4932 <is_valid_xml/> | |
| 4933 </assert_contents> | |
| 4934 </output> | |
| 4935 </test> | |
| 4936 <test expect_num_outputs="2"> | |
| 4937 <conditional name="adv_opts_cond"> | |
| 4938 <param name="adv_opts_selector" value="advanced"/> | |
| 4939 <param name="UID_postprocessing" value="ensure"/> | |
| 4940 <param name="TIC_DTA2D" value="false"/> | |
| 4941 <param name="MGF_compact" value="false"/> | |
| 4942 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4943 <param name="convert_to_chromatograms" value="false"/> | |
| 4944 <param name="force_TPP_compatibility" value="false"/> | |
| 4945 <param name="change_im_format" value="multiple"/> | |
| 4946 <param name="write_scan_index" value="true"/> | |
| 4947 <param name="lossy_compression" value="false"/> | |
| 4948 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4949 <param name="process_lowmemory" value="false"/> | |
| 4950 <param name="no_peak_picking" value="false"/> | |
| 4951 <param name="force" value="false"/> | |
| 4952 <param name="test" value="true"/> | |
| 4953 </conditional> | |
| 4954 <param name="in" value="FileConverter_30_input.mzML"/> | |
| 4955 <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4956 <param name="out_type" value="mzML"/> | |
| 4957 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4958 <output name="ctd_out" ftype="xml"> | |
| 4959 <assert_contents> | |
| 4960 <is_valid_xml/> | |
| 4961 </assert_contents> | |
| 4962 </output> | |
| 4963 </test> | |
| 4964 <test expect_num_outputs="2"> | |
| 4965 <conditional name="adv_opts_cond"> | |
| 4966 <param name="adv_opts_selector" value="advanced"/> | |
| 4967 <param name="UID_postprocessing" value="ensure"/> | |
| 4968 <param name="TIC_DTA2D" value="false"/> | |
| 4969 <param name="MGF_compact" value="false"/> | |
| 4970 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4971 <param name="convert_to_chromatograms" value="false"/> | |
| 4972 <param name="force_TPP_compatibility" value="false"/> | |
| 4973 <param name="change_im_format" value="single"/> | |
| 4974 <param name="write_scan_index" value="true"/> | |
| 4975 <param name="lossy_compression" value="false"/> | |
| 4976 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 4977 <param name="process_lowmemory" value="false"/> | |
| 4978 <param name="no_peak_picking" value="false"/> | |
| 4979 <param name="force" value="false"/> | |
| 4980 <param name="test" value="true"/> | |
| 4981 </conditional> | |
| 4982 <param name="in" value="FileConverter_30_output.mzML"/> | |
| 4983 <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 4984 <param name="out_type" value="mzML"/> | |
| 4985 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 4986 <output name="ctd_out" ftype="xml"> | |
| 4987 <assert_contents> | |
| 4988 <is_valid_xml/> | |
| 4989 </assert_contents> | |
| 4990 </output> | |
| 4991 </test> | |
| 4992 <test expect_num_outputs="2"> | |
| 4993 <conditional name="adv_opts_cond"> | |
| 4994 <param name="adv_opts_selector" value="advanced"/> | |
| 4995 <param name="UID_postprocessing" value="ensure"/> | |
| 4996 <param name="TIC_DTA2D" value="false"/> | |
| 4997 <param name="MGF_compact" value="false"/> | |
| 4998 <param name="force_MaxQuant_compatibility" value="false"/> | |
| 4999 <param name="convert_to_chromatograms" value="false"/> | |
| 5000 <param name="force_TPP_compatibility" value="false"/> | |
| 5001 <param name="change_im_format" value="none"/> | |
| 5002 <param name="write_scan_index" value="true"/> | |
| 5003 <param name="lossy_compression" value="false"/> | |
| 5004 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5005 <param name="process_lowmemory" value="false"/> | |
| 5006 <param name="no_peak_picking" value="false"/> | |
| 5007 <param name="force" value="false"/> | |
| 5008 <param name="test" value="true"/> | |
| 5009 </conditional> | |
| 5010 <param name="in" value="ginkgotoxin-ms-switching.raw"/> | |
| 5011 <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5012 <param name="out_type" value="mzml"/> | |
| 5013 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5014 <output name="ctd_out" ftype="xml"> | |
| 5015 <assert_contents> | |
| 5016 <is_valid_xml/> | |
| 5017 </assert_contents> | |
| 5018 </output> | |
| 5019 </test> | |
| 5020 </xml> | |
| 5021 <xml name="autotest_FileFilter"> | |
| 5022 <test expect_num_outputs="2"> | |
| 5023 <conditional name="adv_opts_cond"> | |
| 5024 <param name="adv_opts_selector" value="advanced"/> | |
| 5025 <param name="force" value="false"/> | |
| 5026 <param name="test" value="true"/> | |
| 5027 </conditional> | |
| 5028 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 5029 <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5030 <param name="out_type" value="mzML"/> | |
| 5031 <param name="rt" value=":30"/> | |
| 5032 <param name="mz" value=":1000"/> | |
| 5033 <param name="int" value=":20000"/> | |
| 5034 <param name="sort" value="false"/> | |
| 5035 <section name="peak_options"> | |
| 5036 <param name="sn" value="0.0"/> | |
| 5037 <param name="rm_pc_charge" value=""/> | |
| 5038 <param name="pc_mz_range" value=":"/> | |
| 5039 <param name="pc_mz_list" value=""/> | |
| 5040 <param name="level" value="1 2 3"/> | |
| 5041 <param name="sort_peaks" value="false"/> | |
| 5042 <param name="no_chromatograms" value="false"/> | |
| 5043 <param name="remove_chromatograms" value="false"/> | |
| 5044 <param name="remove_empty" value="false"/> | |
| 5045 <param name="mz_precision" value="64"/> | |
| 5046 <param name="int_precision" value="32"/> | |
| 5047 <param name="indexed_file" value="true"/> | |
| 5048 <param name="zlib_compression" value="false"/> | |
| 5049 <section name="numpress"> | |
| 5050 <param name="masstime" value="none"/> | |
| 5051 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5052 <param name="intensity" value="none"/> | |
| 5053 <param name="float_da" value="none"/> | |
| 5054 </section> | |
| 5055 </section> | |
| 5056 <section name="spectra"> | |
| 5057 <param name="remove_zoom" value="false"/> | |
| 5058 <param name="remove_mode" value=""/> | |
| 5059 <param name="remove_activation" value=""/> | |
| 5060 <param name="remove_collision_energy" value=":"/> | |
| 5061 <param name="remove_isolation_window_width" value=":"/> | |
| 5062 <param name="select_zoom" value="false"/> | |
| 5063 <param name="select_mode" value=""/> | |
| 5064 <param name="select_activation" value=""/> | |
| 5065 <param name="select_collision_energy" value=":"/> | |
| 5066 <param name="select_isolation_window_width" value=":"/> | |
| 5067 <param name="select_polarity" value=""/> | |
| 5068 <section name="blackorwhitelist"> | |
| 5069 <param name="similarity_threshold" value="-1.0"/> | |
| 5070 <param name="rt" value="0.01"/> | |
| 5071 <param name="mz" value="0.01"/> | |
| 5072 <param name="use_ppm_tolerance" value="false"/> | |
| 5073 <param name="blacklist" value="true"/> | |
| 5074 </section> | |
| 5075 </section> | |
| 5076 <section name="feature"> | |
| 5077 <param name="q" value=":"/> | |
| 5078 </section> | |
| 5079 <section name="consensus"> | |
| 5080 <param name="map" value=""/> | |
| 5081 <param name="map_and" value="false"/> | |
| 5082 <section name="blackorwhitelist"> | |
| 5083 <param name="blacklist" value="true"/> | |
| 5084 <param name="maps" value=""/> | |
| 5085 <param name="rt" value="60.0"/> | |
| 5086 <param name="mz" value="0.01"/> | |
| 5087 <param name="use_ppm_tolerance" value="false"/> | |
| 5088 </section> | |
| 5089 </section> | |
| 5090 <section name="f_and_c"> | |
| 5091 <param name="charge" value=":"/> | |
| 5092 <param name="size" value=":"/> | |
| 5093 <param name="remove_meta" value=""/> | |
| 5094 </section> | |
| 5095 <section name="id"> | |
| 5096 <param name="remove_clashes" value="false"/> | |
| 5097 <param name="keep_best_score_id" value="false"/> | |
| 5098 <param name="sequences_whitelist" value=""/> | |
| 5099 <param name="sequence_comparison_method" value="substring"/> | |
| 5100 <param name="accessions_whitelist" value=""/> | |
| 5101 <param name="remove_annotated_features" value="false"/> | |
| 5102 <param name="remove_unannotated_features" value="false"/> | |
| 5103 <param name="remove_unassigned_ids" value="false"/> | |
| 5104 <param name="rt" value="0.1"/> | |
| 5105 <param name="mz" value="0.001"/> | |
| 5106 <param name="blacklist_imperfect" value="false"/> | |
| 5107 </section> | |
| 5108 <section name="algorithm"> | |
| 5109 <section name="SignalToNoise"> | |
| 5110 <param name="max_intensity" value="-1"/> | |
| 5111 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5112 <param name="auto_max_percentile" value="95"/> | |
| 5113 <param name="auto_mode" value="0"/> | |
| 5114 <param name="win_len" value="200.0"/> | |
| 5115 <param name="bin_count" value="30"/> | |
| 5116 <param name="min_required_elements" value="10"/> | |
| 5117 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5118 <param name="write_log_messages" value="true"/> | |
| 5119 </section> | |
| 5120 </section> | |
| 5121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5122 <output name="ctd_out" ftype="xml"> | |
| 5123 <assert_contents> | |
| 5124 <is_valid_xml/> | |
| 5125 </assert_contents> | |
| 5126 </output> | |
| 5127 </test> | |
| 5128 <test expect_num_outputs="2"> | |
| 5129 <conditional name="adv_opts_cond"> | |
| 5130 <param name="adv_opts_selector" value="advanced"/> | |
| 5131 <param name="force" value="false"/> | |
| 5132 <param name="test" value="true"/> | |
| 5133 </conditional> | |
| 5134 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 5135 <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5136 <param name="out_type" value="mzML"/> | |
| 5137 <param name="rt" value="30:"/> | |
| 5138 <param name="mz" value="1000:"/> | |
| 5139 <param name="int" value="100:"/> | |
| 5140 <param name="sort" value="false"/> | |
| 5141 <section name="peak_options"> | |
| 5142 <param name="sn" value="0.0"/> | |
| 5143 <param name="rm_pc_charge" value=""/> | |
| 5144 <param name="pc_mz_range" value=":"/> | |
| 5145 <param name="pc_mz_list" value=""/> | |
| 5146 <param name="level" value="1 2 3"/> | |
| 5147 <param name="sort_peaks" value="false"/> | |
| 5148 <param name="no_chromatograms" value="false"/> | |
| 5149 <param name="remove_chromatograms" value="false"/> | |
| 5150 <param name="remove_empty" value="false"/> | |
| 5151 <param name="mz_precision" value="64"/> | |
| 5152 <param name="int_precision" value="32"/> | |
| 5153 <param name="indexed_file" value="true"/> | |
| 5154 <param name="zlib_compression" value="false"/> | |
| 5155 <section name="numpress"> | |
| 5156 <param name="masstime" value="none"/> | |
| 5157 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5158 <param name="intensity" value="none"/> | |
| 5159 <param name="float_da" value="none"/> | |
| 5160 </section> | |
| 5161 </section> | |
| 5162 <section name="spectra"> | |
| 5163 <param name="remove_zoom" value="false"/> | |
| 5164 <param name="remove_mode" value=""/> | |
| 5165 <param name="remove_activation" value=""/> | |
| 5166 <param name="remove_collision_energy" value=":"/> | |
| 5167 <param name="remove_isolation_window_width" value=":"/> | |
| 5168 <param name="select_zoom" value="false"/> | |
| 5169 <param name="select_mode" value=""/> | |
| 5170 <param name="select_activation" value=""/> | |
| 5171 <param name="select_collision_energy" value=":"/> | |
| 5172 <param name="select_isolation_window_width" value=":"/> | |
| 5173 <param name="select_polarity" value=""/> | |
| 5174 <section name="blackorwhitelist"> | |
| 5175 <param name="similarity_threshold" value="-1.0"/> | |
| 5176 <param name="rt" value="0.01"/> | |
| 5177 <param name="mz" value="0.01"/> | |
| 5178 <param name="use_ppm_tolerance" value="false"/> | |
| 5179 <param name="blacklist" value="true"/> | |
| 5180 </section> | |
| 5181 </section> | |
| 5182 <section name="feature"> | |
| 5183 <param name="q" value=":"/> | |
| 5184 </section> | |
| 5185 <section name="consensus"> | |
| 5186 <param name="map" value=""/> | |
| 5187 <param name="map_and" value="false"/> | |
| 5188 <section name="blackorwhitelist"> | |
| 5189 <param name="blacklist" value="true"/> | |
| 5190 <param name="maps" value=""/> | |
| 5191 <param name="rt" value="60.0"/> | |
| 5192 <param name="mz" value="0.01"/> | |
| 5193 <param name="use_ppm_tolerance" value="false"/> | |
| 5194 </section> | |
| 5195 </section> | |
| 5196 <section name="f_and_c"> | |
| 5197 <param name="charge" value=":"/> | |
| 5198 <param name="size" value=":"/> | |
| 5199 <param name="remove_meta" value=""/> | |
| 5200 </section> | |
| 5201 <section name="id"> | |
| 5202 <param name="remove_clashes" value="false"/> | |
| 5203 <param name="keep_best_score_id" value="false"/> | |
| 5204 <param name="sequences_whitelist" value=""/> | |
| 5205 <param name="sequence_comparison_method" value="substring"/> | |
| 5206 <param name="accessions_whitelist" value=""/> | |
| 5207 <param name="remove_annotated_features" value="false"/> | |
| 5208 <param name="remove_unannotated_features" value="false"/> | |
| 5209 <param name="remove_unassigned_ids" value="false"/> | |
| 5210 <param name="rt" value="0.1"/> | |
| 5211 <param name="mz" value="0.001"/> | |
| 5212 <param name="blacklist_imperfect" value="false"/> | |
| 5213 </section> | |
| 5214 <section name="algorithm"> | |
| 5215 <section name="SignalToNoise"> | |
| 5216 <param name="max_intensity" value="-1"/> | |
| 5217 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5218 <param name="auto_max_percentile" value="95"/> | |
| 5219 <param name="auto_mode" value="0"/> | |
| 5220 <param name="win_len" value="200.0"/> | |
| 5221 <param name="bin_count" value="30"/> | |
| 5222 <param name="min_required_elements" value="10"/> | |
| 5223 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5224 <param name="write_log_messages" value="true"/> | |
| 5225 </section> | |
| 5226 </section> | |
| 5227 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5228 <output name="ctd_out" ftype="xml"> | |
| 5229 <assert_contents> | |
| 5230 <is_valid_xml/> | |
| 5231 </assert_contents> | |
| 5232 </output> | |
| 5233 </test> | |
| 5234 <test expect_num_outputs="2"> | |
| 5235 <conditional name="adv_opts_cond"> | |
| 5236 <param name="adv_opts_selector" value="advanced"/> | |
| 5237 <param name="force" value="false"/> | |
| 5238 <param name="test" value="true"/> | |
| 5239 </conditional> | |
| 5240 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 5241 <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5242 <param name="out_type" value="mzML"/> | |
| 5243 <param name="rt" value=":"/> | |
| 5244 <param name="mz" value=":"/> | |
| 5245 <param name="int" value=":"/> | |
| 5246 <param name="sort" value="false"/> | |
| 5247 <section name="peak_options"> | |
| 5248 <param name="sn" value="0.0"/> | |
| 5249 <param name="rm_pc_charge" value=""/> | |
| 5250 <param name="pc_mz_range" value=":"/> | |
| 5251 <param name="pc_mz_list" value=""/> | |
| 5252 <param name="level" value="2"/> | |
| 5253 <param name="sort_peaks" value="false"/> | |
| 5254 <param name="no_chromatograms" value="false"/> | |
| 5255 <param name="remove_chromatograms" value="false"/> | |
| 5256 <param name="remove_empty" value="false"/> | |
| 5257 <param name="mz_precision" value="64"/> | |
| 5258 <param name="int_precision" value="32"/> | |
| 5259 <param name="indexed_file" value="true"/> | |
| 5260 <param name="zlib_compression" value="false"/> | |
| 5261 <section name="numpress"> | |
| 5262 <param name="masstime" value="none"/> | |
| 5263 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5264 <param name="intensity" value="none"/> | |
| 5265 <param name="float_da" value="none"/> | |
| 5266 </section> | |
| 5267 </section> | |
| 5268 <section name="spectra"> | |
| 5269 <param name="remove_zoom" value="false"/> | |
| 5270 <param name="remove_mode" value=""/> | |
| 5271 <param name="remove_activation" value=""/> | |
| 5272 <param name="remove_collision_energy" value=":"/> | |
| 5273 <param name="remove_isolation_window_width" value=":"/> | |
| 5274 <param name="select_zoom" value="false"/> | |
| 5275 <param name="select_mode" value=""/> | |
| 5276 <param name="select_activation" value=""/> | |
| 5277 <param name="select_collision_energy" value=":"/> | |
| 5278 <param name="select_isolation_window_width" value=":"/> | |
| 5279 <param name="select_polarity" value=""/> | |
| 5280 <section name="blackorwhitelist"> | |
| 5281 <param name="similarity_threshold" value="-1.0"/> | |
| 5282 <param name="rt" value="0.01"/> | |
| 5283 <param name="mz" value="0.01"/> | |
| 5284 <param name="use_ppm_tolerance" value="false"/> | |
| 5285 <param name="blacklist" value="true"/> | |
| 5286 </section> | |
| 5287 </section> | |
| 5288 <section name="feature"> | |
| 5289 <param name="q" value=":"/> | |
| 5290 </section> | |
| 5291 <section name="consensus"> | |
| 5292 <param name="map" value=""/> | |
| 5293 <param name="map_and" value="false"/> | |
| 5294 <section name="blackorwhitelist"> | |
| 5295 <param name="blacklist" value="true"/> | |
| 5296 <param name="maps" value=""/> | |
| 5297 <param name="rt" value="60.0"/> | |
| 5298 <param name="mz" value="0.01"/> | |
| 5299 <param name="use_ppm_tolerance" value="false"/> | |
| 5300 </section> | |
| 5301 </section> | |
| 5302 <section name="f_and_c"> | |
| 5303 <param name="charge" value=":"/> | |
| 5304 <param name="size" value=":"/> | |
| 5305 <param name="remove_meta" value=""/> | |
| 5306 </section> | |
| 5307 <section name="id"> | |
| 5308 <param name="remove_clashes" value="false"/> | |
| 5309 <param name="keep_best_score_id" value="false"/> | |
| 5310 <param name="sequences_whitelist" value=""/> | |
| 5311 <param name="sequence_comparison_method" value="substring"/> | |
| 5312 <param name="accessions_whitelist" value=""/> | |
| 5313 <param name="remove_annotated_features" value="false"/> | |
| 5314 <param name="remove_unannotated_features" value="false"/> | |
| 5315 <param name="remove_unassigned_ids" value="false"/> | |
| 5316 <param name="rt" value="0.1"/> | |
| 5317 <param name="mz" value="0.001"/> | |
| 5318 <param name="blacklist_imperfect" value="false"/> | |
| 5319 </section> | |
| 5320 <section name="algorithm"> | |
| 5321 <section name="SignalToNoise"> | |
| 5322 <param name="max_intensity" value="-1"/> | |
| 5323 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5324 <param name="auto_max_percentile" value="95"/> | |
| 5325 <param name="auto_mode" value="0"/> | |
| 5326 <param name="win_len" value="200.0"/> | |
| 5327 <param name="bin_count" value="30"/> | |
| 5328 <param name="min_required_elements" value="10"/> | |
| 5329 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5330 <param name="write_log_messages" value="true"/> | |
| 5331 </section> | |
| 5332 </section> | |
| 5333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5334 <output name="ctd_out" ftype="xml"> | |
| 5335 <assert_contents> | |
| 5336 <is_valid_xml/> | |
| 5337 </assert_contents> | |
| 5338 </output> | |
| 5339 </test> | |
| 5340 <test expect_num_outputs="2"> | |
| 5341 <conditional name="adv_opts_cond"> | |
| 5342 <param name="adv_opts_selector" value="advanced"/> | |
| 5343 <param name="force" value="false"/> | |
| 5344 <param name="test" value="true"/> | |
| 5345 </conditional> | |
| 5346 <param name="in" value="FileFilter_4_input.mzML"/> | |
| 5347 <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5348 <param name="out_type" value="mzML"/> | |
| 5349 <param name="rt" value=":"/> | |
| 5350 <param name="mz" value=":"/> | |
| 5351 <param name="int" value=":"/> | |
| 5352 <param name="sort" value="false"/> | |
| 5353 <section name="peak_options"> | |
| 5354 <param name="sn" value="0.0"/> | |
| 5355 <param name="rm_pc_charge" value=""/> | |
| 5356 <param name="pc_mz_range" value=":"/> | |
| 5357 <param name="pc_mz_list" value=""/> | |
| 5358 <param name="level" value="1 2 3"/> | |
| 5359 <param name="sort_peaks" value="false"/> | |
| 5360 <param name="no_chromatograms" value="false"/> | |
| 5361 <param name="remove_chromatograms" value="false"/> | |
| 5362 <param name="remove_empty" value="false"/> | |
| 5363 <param name="mz_precision" value="64"/> | |
| 5364 <param name="int_precision" value="32"/> | |
| 5365 <param name="indexed_file" value="true"/> | |
| 5366 <param name="zlib_compression" value="false"/> | |
| 5367 <section name="numpress"> | |
| 5368 <param name="masstime" value="none"/> | |
| 5369 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5370 <param name="intensity" value="none"/> | |
| 5371 <param name="float_da" value="none"/> | |
| 5372 </section> | |
| 5373 </section> | |
| 5374 <section name="spectra"> | |
| 5375 <param name="remove_zoom" value="true"/> | |
| 5376 <param name="remove_mode" value=""/> | |
| 5377 <param name="remove_activation" value=""/> | |
| 5378 <param name="remove_collision_energy" value=":"/> | |
| 5379 <param name="remove_isolation_window_width" value=":"/> | |
| 5380 <param name="select_zoom" value="false"/> | |
| 5381 <param name="select_mode" value=""/> | |
| 5382 <param name="select_activation" value=""/> | |
| 5383 <param name="select_collision_energy" value=":"/> | |
| 5384 <param name="select_isolation_window_width" value=":"/> | |
| 5385 <param name="select_polarity" value=""/> | |
| 5386 <section name="blackorwhitelist"> | |
| 5387 <param name="similarity_threshold" value="-1.0"/> | |
| 5388 <param name="rt" value="0.01"/> | |
| 5389 <param name="mz" value="0.01"/> | |
| 5390 <param name="use_ppm_tolerance" value="false"/> | |
| 5391 <param name="blacklist" value="true"/> | |
| 5392 </section> | |
| 5393 </section> | |
| 5394 <section name="feature"> | |
| 5395 <param name="q" value=":"/> | |
| 5396 </section> | |
| 5397 <section name="consensus"> | |
| 5398 <param name="map" value=""/> | |
| 5399 <param name="map_and" value="false"/> | |
| 5400 <section name="blackorwhitelist"> | |
| 5401 <param name="blacklist" value="true"/> | |
| 5402 <param name="maps" value=""/> | |
| 5403 <param name="rt" value="60.0"/> | |
| 5404 <param name="mz" value="0.01"/> | |
| 5405 <param name="use_ppm_tolerance" value="false"/> | |
| 5406 </section> | |
| 5407 </section> | |
| 5408 <section name="f_and_c"> | |
| 5409 <param name="charge" value=":"/> | |
| 5410 <param name="size" value=":"/> | |
| 5411 <param name="remove_meta" value=""/> | |
| 5412 </section> | |
| 5413 <section name="id"> | |
| 5414 <param name="remove_clashes" value="false"/> | |
| 5415 <param name="keep_best_score_id" value="false"/> | |
| 5416 <param name="sequences_whitelist" value=""/> | |
| 5417 <param name="sequence_comparison_method" value="substring"/> | |
| 5418 <param name="accessions_whitelist" value=""/> | |
| 5419 <param name="remove_annotated_features" value="false"/> | |
| 5420 <param name="remove_unannotated_features" value="false"/> | |
| 5421 <param name="remove_unassigned_ids" value="false"/> | |
| 5422 <param name="rt" value="0.1"/> | |
| 5423 <param name="mz" value="0.001"/> | |
| 5424 <param name="blacklist_imperfect" value="false"/> | |
| 5425 </section> | |
| 5426 <section name="algorithm"> | |
| 5427 <section name="SignalToNoise"> | |
| 5428 <param name="max_intensity" value="-1"/> | |
| 5429 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5430 <param name="auto_max_percentile" value="95"/> | |
| 5431 <param name="auto_mode" value="0"/> | |
| 5432 <param name="win_len" value="200.0"/> | |
| 5433 <param name="bin_count" value="30"/> | |
| 5434 <param name="min_required_elements" value="10"/> | |
| 5435 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5436 <param name="write_log_messages" value="true"/> | |
| 5437 </section> | |
| 5438 </section> | |
| 5439 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5440 <output name="ctd_out" ftype="xml"> | |
| 5441 <assert_contents> | |
| 5442 <is_valid_xml/> | |
| 5443 </assert_contents> | |
| 5444 </output> | |
| 5445 </test> | |
| 5446 <test expect_num_outputs="2"> | |
| 5447 <conditional name="adv_opts_cond"> | |
| 5448 <param name="adv_opts_selector" value="advanced"/> | |
| 5449 <param name="force" value="false"/> | |
| 5450 <param name="test" value="true"/> | |
| 5451 </conditional> | |
| 5452 <param name="in" value="FileFilter_5_input.featureXML"/> | |
| 5453 <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 5454 <param name="out_type" value="featureXML"/> | |
| 5455 <param name="rt" value=":1000"/> | |
| 5456 <param name="mz" value=":480"/> | |
| 5457 <param name="int" value=":79000"/> | |
| 5458 <param name="sort" value="false"/> | |
| 5459 <section name="peak_options"> | |
| 5460 <param name="sn" value="0.0"/> | |
| 5461 <param name="rm_pc_charge" value=""/> | |
| 5462 <param name="pc_mz_range" value=":"/> | |
| 5463 <param name="pc_mz_list" value=""/> | |
| 5464 <param name="level" value="1 2 3"/> | |
| 5465 <param name="sort_peaks" value="false"/> | |
| 5466 <param name="no_chromatograms" value="false"/> | |
| 5467 <param name="remove_chromatograms" value="false"/> | |
| 5468 <param name="remove_empty" value="false"/> | |
| 5469 <param name="mz_precision" value="64"/> | |
| 5470 <param name="int_precision" value="32"/> | |
| 5471 <param name="indexed_file" value="true"/> | |
| 5472 <param name="zlib_compression" value="false"/> | |
| 5473 <section name="numpress"> | |
| 5474 <param name="masstime" value="none"/> | |
| 5475 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5476 <param name="intensity" value="none"/> | |
| 5477 <param name="float_da" value="none"/> | |
| 5478 </section> | |
| 5479 </section> | |
| 5480 <section name="spectra"> | |
| 5481 <param name="remove_zoom" value="false"/> | |
| 5482 <param name="remove_mode" value=""/> | |
| 5483 <param name="remove_activation" value=""/> | |
| 5484 <param name="remove_collision_energy" value=":"/> | |
| 5485 <param name="remove_isolation_window_width" value=":"/> | |
| 5486 <param name="select_zoom" value="false"/> | |
| 5487 <param name="select_mode" value=""/> | |
| 5488 <param name="select_activation" value=""/> | |
| 5489 <param name="select_collision_energy" value=":"/> | |
| 5490 <param name="select_isolation_window_width" value=":"/> | |
| 5491 <param name="select_polarity" value=""/> | |
| 5492 <section name="blackorwhitelist"> | |
| 5493 <param name="similarity_threshold" value="-1.0"/> | |
| 5494 <param name="rt" value="0.01"/> | |
| 5495 <param name="mz" value="0.01"/> | |
| 5496 <param name="use_ppm_tolerance" value="false"/> | |
| 5497 <param name="blacklist" value="true"/> | |
| 5498 </section> | |
| 5499 </section> | |
| 5500 <section name="feature"> | |
| 5501 <param name="q" value=":0.6"/> | |
| 5502 </section> | |
| 5503 <section name="consensus"> | |
| 5504 <param name="map" value=""/> | |
| 5505 <param name="map_and" value="false"/> | |
| 5506 <section name="blackorwhitelist"> | |
| 5507 <param name="blacklist" value="true"/> | |
| 5508 <param name="maps" value=""/> | |
| 5509 <param name="rt" value="60.0"/> | |
| 5510 <param name="mz" value="0.01"/> | |
| 5511 <param name="use_ppm_tolerance" value="false"/> | |
| 5512 </section> | |
| 5513 </section> | |
| 5514 <section name="f_and_c"> | |
| 5515 <param name="charge" value=":3"/> | |
| 5516 <param name="size" value=":"/> | |
| 5517 <param name="remove_meta" value=""/> | |
| 5518 </section> | |
| 5519 <section name="id"> | |
| 5520 <param name="remove_clashes" value="false"/> | |
| 5521 <param name="keep_best_score_id" value="false"/> | |
| 5522 <param name="sequences_whitelist" value=""/> | |
| 5523 <param name="sequence_comparison_method" value="substring"/> | |
| 5524 <param name="accessions_whitelist" value=""/> | |
| 5525 <param name="remove_annotated_features" value="false"/> | |
| 5526 <param name="remove_unannotated_features" value="false"/> | |
| 5527 <param name="remove_unassigned_ids" value="false"/> | |
| 5528 <param name="rt" value="0.1"/> | |
| 5529 <param name="mz" value="0.001"/> | |
| 5530 <param name="blacklist_imperfect" value="false"/> | |
| 5531 </section> | |
| 5532 <section name="algorithm"> | |
| 5533 <section name="SignalToNoise"> | |
| 5534 <param name="max_intensity" value="-1"/> | |
| 5535 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5536 <param name="auto_max_percentile" value="95"/> | |
| 5537 <param name="auto_mode" value="0"/> | |
| 5538 <param name="win_len" value="200.0"/> | |
| 5539 <param name="bin_count" value="30"/> | |
| 5540 <param name="min_required_elements" value="10"/> | |
| 5541 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5542 <param name="write_log_messages" value="true"/> | |
| 5543 </section> | |
| 5544 </section> | |
| 5545 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5546 <output name="ctd_out" ftype="xml"> | |
| 5547 <assert_contents> | |
| 5548 <is_valid_xml/> | |
| 5549 </assert_contents> | |
| 5550 </output> | |
| 5551 </test> | |
| 5552 <test expect_num_outputs="2"> | |
| 5553 <conditional name="adv_opts_cond"> | |
| 5554 <param name="adv_opts_selector" value="advanced"/> | |
| 5555 <param name="force" value="false"/> | |
| 5556 <param name="test" value="true"/> | |
| 5557 </conditional> | |
| 5558 <param name="in" value="FileFilter_5_input.featureXML"/> | |
| 5559 <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 5560 <param name="out_type" value="featureXML"/> | |
| 5561 <param name="rt" value="1000:"/> | |
| 5562 <param name="mz" value="440:"/> | |
| 5563 <param name="int" value="70000:"/> | |
| 5564 <param name="sort" value="false"/> | |
| 5565 <section name="peak_options"> | |
| 5566 <param name="sn" value="0.0"/> | |
| 5567 <param name="rm_pc_charge" value=""/> | |
| 5568 <param name="pc_mz_range" value=":"/> | |
| 5569 <param name="pc_mz_list" value=""/> | |
| 5570 <param name="level" value="1 2 3"/> | |
| 5571 <param name="sort_peaks" value="false"/> | |
| 5572 <param name="no_chromatograms" value="false"/> | |
| 5573 <param name="remove_chromatograms" value="false"/> | |
| 5574 <param name="remove_empty" value="false"/> | |
| 5575 <param name="mz_precision" value="64"/> | |
| 5576 <param name="int_precision" value="32"/> | |
| 5577 <param name="indexed_file" value="true"/> | |
| 5578 <param name="zlib_compression" value="false"/> | |
| 5579 <section name="numpress"> | |
| 5580 <param name="masstime" value="none"/> | |
| 5581 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5582 <param name="intensity" value="none"/> | |
| 5583 <param name="float_da" value="none"/> | |
| 5584 </section> | |
| 5585 </section> | |
| 5586 <section name="spectra"> | |
| 5587 <param name="remove_zoom" value="false"/> | |
| 5588 <param name="remove_mode" value=""/> | |
| 5589 <param name="remove_activation" value=""/> | |
| 5590 <param name="remove_collision_energy" value=":"/> | |
| 5591 <param name="remove_isolation_window_width" value=":"/> | |
| 5592 <param name="select_zoom" value="false"/> | |
| 5593 <param name="select_mode" value=""/> | |
| 5594 <param name="select_activation" value=""/> | |
| 5595 <param name="select_collision_energy" value=":"/> | |
| 5596 <param name="select_isolation_window_width" value=":"/> | |
| 5597 <param name="select_polarity" value=""/> | |
| 5598 <section name="blackorwhitelist"> | |
| 5599 <param name="similarity_threshold" value="-1.0"/> | |
| 5600 <param name="rt" value="0.01"/> | |
| 5601 <param name="mz" value="0.01"/> | |
| 5602 <param name="use_ppm_tolerance" value="false"/> | |
| 5603 <param name="blacklist" value="true"/> | |
| 5604 </section> | |
| 5605 </section> | |
| 5606 <section name="feature"> | |
| 5607 <param name="q" value="0.51:"/> | |
| 5608 </section> | |
| 5609 <section name="consensus"> | |
| 5610 <param name="map" value=""/> | |
| 5611 <param name="map_and" value="false"/> | |
| 5612 <section name="blackorwhitelist"> | |
| 5613 <param name="blacklist" value="true"/> | |
| 5614 <param name="maps" value=""/> | |
| 5615 <param name="rt" value="60.0"/> | |
| 5616 <param name="mz" value="0.01"/> | |
| 5617 <param name="use_ppm_tolerance" value="false"/> | |
| 5618 </section> | |
| 5619 </section> | |
| 5620 <section name="f_and_c"> | |
| 5621 <param name="charge" value="3:"/> | |
| 5622 <param name="size" value=":"/> | |
| 5623 <param name="remove_meta" value=""/> | |
| 5624 </section> | |
| 5625 <section name="id"> | |
| 5626 <param name="remove_clashes" value="false"/> | |
| 5627 <param name="keep_best_score_id" value="false"/> | |
| 5628 <param name="sequences_whitelist" value=""/> | |
| 5629 <param name="sequence_comparison_method" value="substring"/> | |
| 5630 <param name="accessions_whitelist" value=""/> | |
| 5631 <param name="remove_annotated_features" value="false"/> | |
| 5632 <param name="remove_unannotated_features" value="false"/> | |
| 5633 <param name="remove_unassigned_ids" value="false"/> | |
| 5634 <param name="rt" value="0.1"/> | |
| 5635 <param name="mz" value="0.001"/> | |
| 5636 <param name="blacklist_imperfect" value="false"/> | |
| 5637 </section> | |
| 5638 <section name="algorithm"> | |
| 5639 <section name="SignalToNoise"> | |
| 5640 <param name="max_intensity" value="-1"/> | |
| 5641 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5642 <param name="auto_max_percentile" value="95"/> | |
| 5643 <param name="auto_mode" value="0"/> | |
| 5644 <param name="win_len" value="200.0"/> | |
| 5645 <param name="bin_count" value="30"/> | |
| 5646 <param name="min_required_elements" value="10"/> | |
| 5647 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5648 <param name="write_log_messages" value="true"/> | |
| 5649 </section> | |
| 5650 </section> | |
| 5651 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5652 <output name="ctd_out" ftype="xml"> | |
| 5653 <assert_contents> | |
| 5654 <is_valid_xml/> | |
| 5655 </assert_contents> | |
| 5656 </output> | |
| 5657 </test> | |
| 5658 <test expect_num_outputs="2"> | |
| 5659 <conditional name="adv_opts_cond"> | |
| 5660 <param name="adv_opts_selector" value="advanced"/> | |
| 5661 <param name="force" value="false"/> | |
| 5662 <param name="test" value="true"/> | |
| 5663 </conditional> | |
| 5664 <param name="in" value="FileFilter_7_input.mzML"/> | |
| 5665 <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5666 <param name="out_type" value="mzML"/> | |
| 5667 <param name="rt" value=":"/> | |
| 5668 <param name="mz" value=":"/> | |
| 5669 <param name="int" value="7000:"/> | |
| 5670 <param name="sort" value="false"/> | |
| 5671 <section name="peak_options"> | |
| 5672 <param name="sn" value="0.0"/> | |
| 5673 <param name="rm_pc_charge" value=""/> | |
| 5674 <param name="pc_mz_range" value=":"/> | |
| 5675 <param name="pc_mz_list" value=""/> | |
| 5676 <param name="level" value="1 2 3"/> | |
| 5677 <param name="sort_peaks" value="false"/> | |
| 5678 <param name="no_chromatograms" value="false"/> | |
| 5679 <param name="remove_chromatograms" value="false"/> | |
| 5680 <param name="remove_empty" value="false"/> | |
| 5681 <param name="mz_precision" value="64"/> | |
| 5682 <param name="int_precision" value="32"/> | |
| 5683 <param name="indexed_file" value="true"/> | |
| 5684 <param name="zlib_compression" value="false"/> | |
| 5685 <section name="numpress"> | |
| 5686 <param name="masstime" value="none"/> | |
| 5687 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5688 <param name="intensity" value="none"/> | |
| 5689 <param name="float_da" value="none"/> | |
| 5690 </section> | |
| 5691 </section> | |
| 5692 <section name="spectra"> | |
| 5693 <param name="remove_zoom" value="false"/> | |
| 5694 <param name="remove_mode" value=""/> | |
| 5695 <param name="remove_activation" value=""/> | |
| 5696 <param name="remove_collision_energy" value=":"/> | |
| 5697 <param name="remove_isolation_window_width" value=":"/> | |
| 5698 <param name="select_zoom" value="false"/> | |
| 5699 <param name="select_mode" value=""/> | |
| 5700 <param name="select_activation" value=""/> | |
| 5701 <param name="select_collision_energy" value=":"/> | |
| 5702 <param name="select_isolation_window_width" value=":"/> | |
| 5703 <param name="select_polarity" value=""/> | |
| 5704 <section name="blackorwhitelist"> | |
| 5705 <param name="similarity_threshold" value="-1.0"/> | |
| 5706 <param name="rt" value="0.01"/> | |
| 5707 <param name="mz" value="0.01"/> | |
| 5708 <param name="use_ppm_tolerance" value="false"/> | |
| 5709 <param name="blacklist" value="true"/> | |
| 5710 </section> | |
| 5711 </section> | |
| 5712 <section name="feature"> | |
| 5713 <param name="q" value=":"/> | |
| 5714 </section> | |
| 5715 <section name="consensus"> | |
| 5716 <param name="map" value=""/> | |
| 5717 <param name="map_and" value="false"/> | |
| 5718 <section name="blackorwhitelist"> | |
| 5719 <param name="blacklist" value="true"/> | |
| 5720 <param name="maps" value=""/> | |
| 5721 <param name="rt" value="60.0"/> | |
| 5722 <param name="mz" value="0.01"/> | |
| 5723 <param name="use_ppm_tolerance" value="false"/> | |
| 5724 </section> | |
| 5725 </section> | |
| 5726 <section name="f_and_c"> | |
| 5727 <param name="charge" value=":"/> | |
| 5728 <param name="size" value=":"/> | |
| 5729 <param name="remove_meta" value=""/> | |
| 5730 </section> | |
| 5731 <section name="id"> | |
| 5732 <param name="remove_clashes" value="false"/> | |
| 5733 <param name="keep_best_score_id" value="false"/> | |
| 5734 <param name="sequences_whitelist" value=""/> | |
| 5735 <param name="sequence_comparison_method" value="substring"/> | |
| 5736 <param name="accessions_whitelist" value=""/> | |
| 5737 <param name="remove_annotated_features" value="false"/> | |
| 5738 <param name="remove_unannotated_features" value="false"/> | |
| 5739 <param name="remove_unassigned_ids" value="false"/> | |
| 5740 <param name="rt" value="0.1"/> | |
| 5741 <param name="mz" value="0.001"/> | |
| 5742 <param name="blacklist_imperfect" value="false"/> | |
| 5743 </section> | |
| 5744 <section name="algorithm"> | |
| 5745 <section name="SignalToNoise"> | |
| 5746 <param name="max_intensity" value="-1"/> | |
| 5747 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5748 <param name="auto_max_percentile" value="95"/> | |
| 5749 <param name="auto_mode" value="0"/> | |
| 5750 <param name="win_len" value="200.0"/> | |
| 5751 <param name="bin_count" value="30"/> | |
| 5752 <param name="min_required_elements" value="10"/> | |
| 5753 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5754 <param name="write_log_messages" value="true"/> | |
| 5755 </section> | |
| 5756 </section> | |
| 5757 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5758 <output name="ctd_out" ftype="xml"> | |
| 5759 <assert_contents> | |
| 5760 <is_valid_xml/> | |
| 5761 </assert_contents> | |
| 5762 </output> | |
| 5763 </test> | |
| 5764 <test expect_num_outputs="2"> | |
| 5765 <conditional name="adv_opts_cond"> | |
| 5766 <param name="adv_opts_selector" value="advanced"/> | |
| 5767 <param name="force" value="false"/> | |
| 5768 <param name="test" value="true"/> | |
| 5769 </conditional> | |
| 5770 <param name="in" value="FileFilter_8_input.consensusXML"/> | |
| 5771 <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 5772 <param name="out_type" value="consensusXML"/> | |
| 5773 <param name="rt" value="600:1400"/> | |
| 5774 <param name="mz" value="700:2300"/> | |
| 5775 <param name="int" value="1100:6000"/> | |
| 5776 <param name="sort" value="false"/> | |
| 5777 <section name="peak_options"> | |
| 5778 <param name="sn" value="0.0"/> | |
| 5779 <param name="rm_pc_charge" value=""/> | |
| 5780 <param name="pc_mz_range" value=":"/> | |
| 5781 <param name="pc_mz_list" value=""/> | |
| 5782 <param name="level" value="1 2 3"/> | |
| 5783 <param name="sort_peaks" value="false"/> | |
| 5784 <param name="no_chromatograms" value="false"/> | |
| 5785 <param name="remove_chromatograms" value="false"/> | |
| 5786 <param name="remove_empty" value="false"/> | |
| 5787 <param name="mz_precision" value="64"/> | |
| 5788 <param name="int_precision" value="32"/> | |
| 5789 <param name="indexed_file" value="true"/> | |
| 5790 <param name="zlib_compression" value="false"/> | |
| 5791 <section name="numpress"> | |
| 5792 <param name="masstime" value="none"/> | |
| 5793 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5794 <param name="intensity" value="none"/> | |
| 5795 <param name="float_da" value="none"/> | |
| 5796 </section> | |
| 5797 </section> | |
| 5798 <section name="spectra"> | |
| 5799 <param name="remove_zoom" value="false"/> | |
| 5800 <param name="remove_mode" value=""/> | |
| 5801 <param name="remove_activation" value=""/> | |
| 5802 <param name="remove_collision_energy" value=":"/> | |
| 5803 <param name="remove_isolation_window_width" value=":"/> | |
| 5804 <param name="select_zoom" value="false"/> | |
| 5805 <param name="select_mode" value=""/> | |
| 5806 <param name="select_activation" value=""/> | |
| 5807 <param name="select_collision_energy" value=":"/> | |
| 5808 <param name="select_isolation_window_width" value=":"/> | |
| 5809 <param name="select_polarity" value=""/> | |
| 5810 <section name="blackorwhitelist"> | |
| 5811 <param name="similarity_threshold" value="-1.0"/> | |
| 5812 <param name="rt" value="0.01"/> | |
| 5813 <param name="mz" value="0.01"/> | |
| 5814 <param name="use_ppm_tolerance" value="false"/> | |
| 5815 <param name="blacklist" value="true"/> | |
| 5816 </section> | |
| 5817 </section> | |
| 5818 <section name="feature"> | |
| 5819 <param name="q" value=":"/> | |
| 5820 </section> | |
| 5821 <section name="consensus"> | |
| 5822 <param name="map" value=""/> | |
| 5823 <param name="map_and" value="false"/> | |
| 5824 <section name="blackorwhitelist"> | |
| 5825 <param name="blacklist" value="true"/> | |
| 5826 <param name="maps" value=""/> | |
| 5827 <param name="rt" value="60.0"/> | |
| 5828 <param name="mz" value="0.01"/> | |
| 5829 <param name="use_ppm_tolerance" value="false"/> | |
| 5830 </section> | |
| 5831 </section> | |
| 5832 <section name="f_and_c"> | |
| 5833 <param name="charge" value=":"/> | |
| 5834 <param name="size" value=":"/> | |
| 5835 <param name="remove_meta" value=""/> | |
| 5836 </section> | |
| 5837 <section name="id"> | |
| 5838 <param name="remove_clashes" value="false"/> | |
| 5839 <param name="keep_best_score_id" value="false"/> | |
| 5840 <param name="sequences_whitelist" value=""/> | |
| 5841 <param name="sequence_comparison_method" value="substring"/> | |
| 5842 <param name="accessions_whitelist" value=""/> | |
| 5843 <param name="remove_annotated_features" value="false"/> | |
| 5844 <param name="remove_unannotated_features" value="false"/> | |
| 5845 <param name="remove_unassigned_ids" value="false"/> | |
| 5846 <param name="rt" value="0.1"/> | |
| 5847 <param name="mz" value="0.001"/> | |
| 5848 <param name="blacklist_imperfect" value="false"/> | |
| 5849 </section> | |
| 5850 <section name="algorithm"> | |
| 5851 <section name="SignalToNoise"> | |
| 5852 <param name="max_intensity" value="-1"/> | |
| 5853 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5854 <param name="auto_max_percentile" value="95"/> | |
| 5855 <param name="auto_mode" value="0"/> | |
| 5856 <param name="win_len" value="200.0"/> | |
| 5857 <param name="bin_count" value="30"/> | |
| 5858 <param name="min_required_elements" value="10"/> | |
| 5859 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5860 <param name="write_log_messages" value="true"/> | |
| 5861 </section> | |
| 5862 </section> | |
| 5863 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5864 <output name="ctd_out" ftype="xml"> | |
| 5865 <assert_contents> | |
| 5866 <is_valid_xml/> | |
| 5867 </assert_contents> | |
| 5868 </output> | |
| 5869 </test> | |
| 5870 <test expect_num_outputs="2"> | |
| 5871 <conditional name="adv_opts_cond"> | |
| 5872 <param name="adv_opts_selector" value="advanced"/> | |
| 5873 <param name="force" value="false"/> | |
| 5874 <param name="test" value="true"/> | |
| 5875 </conditional> | |
| 5876 <param name="in" value="FileFilter_9_input.mzML"/> | |
| 5877 <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5878 <param name="out_type" value="mzML"/> | |
| 5879 <param name="rt" value=":"/> | |
| 5880 <param name="mz" value=":"/> | |
| 5881 <param name="int" value=":"/> | |
| 5882 <param name="sort" value="false"/> | |
| 5883 <section name="peak_options"> | |
| 5884 <param name="sn" value="0.0"/> | |
| 5885 <param name="rm_pc_charge" value=""/> | |
| 5886 <param name="pc_mz_range" value=":"/> | |
| 5887 <param name="pc_mz_list" value=""/> | |
| 5888 <param name="level" value="1 2 3"/> | |
| 5889 <param name="sort_peaks" value="false"/> | |
| 5890 <param name="no_chromatograms" value="false"/> | |
| 5891 <param name="remove_chromatograms" value="false"/> | |
| 5892 <param name="remove_empty" value="false"/> | |
| 5893 <param name="mz_precision" value="64"/> | |
| 5894 <param name="int_precision" value="32"/> | |
| 5895 <param name="indexed_file" value="true"/> | |
| 5896 <param name="zlib_compression" value="false"/> | |
| 5897 <section name="numpress"> | |
| 5898 <param name="masstime" value="none"/> | |
| 5899 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 5900 <param name="intensity" value="none"/> | |
| 5901 <param name="float_da" value="none"/> | |
| 5902 </section> | |
| 5903 </section> | |
| 5904 <section name="spectra"> | |
| 5905 <param name="remove_zoom" value="false"/> | |
| 5906 <param name="remove_mode" value="SelectedIonMonitoring"/> | |
| 5907 <param name="remove_activation" value=""/> | |
| 5908 <param name="remove_collision_energy" value=":"/> | |
| 5909 <param name="remove_isolation_window_width" value=":"/> | |
| 5910 <param name="select_zoom" value="false"/> | |
| 5911 <param name="select_mode" value=""/> | |
| 5912 <param name="select_activation" value=""/> | |
| 5913 <param name="select_collision_energy" value=":"/> | |
| 5914 <param name="select_isolation_window_width" value=":"/> | |
| 5915 <param name="select_polarity" value=""/> | |
| 5916 <section name="blackorwhitelist"> | |
| 5917 <param name="similarity_threshold" value="-1.0"/> | |
| 5918 <param name="rt" value="0.01"/> | |
| 5919 <param name="mz" value="0.01"/> | |
| 5920 <param name="use_ppm_tolerance" value="false"/> | |
| 5921 <param name="blacklist" value="true"/> | |
| 5922 </section> | |
| 5923 </section> | |
| 5924 <section name="feature"> | |
| 5925 <param name="q" value=":"/> | |
| 5926 </section> | |
| 5927 <section name="consensus"> | |
| 5928 <param name="map" value=""/> | |
| 5929 <param name="map_and" value="false"/> | |
| 5930 <section name="blackorwhitelist"> | |
| 5931 <param name="blacklist" value="true"/> | |
| 5932 <param name="maps" value=""/> | |
| 5933 <param name="rt" value="60.0"/> | |
| 5934 <param name="mz" value="0.01"/> | |
| 5935 <param name="use_ppm_tolerance" value="false"/> | |
| 5936 </section> | |
| 5937 </section> | |
| 5938 <section name="f_and_c"> | |
| 5939 <param name="charge" value=":"/> | |
| 5940 <param name="size" value=":"/> | |
| 5941 <param name="remove_meta" value=""/> | |
| 5942 </section> | |
| 5943 <section name="id"> | |
| 5944 <param name="remove_clashes" value="false"/> | |
| 5945 <param name="keep_best_score_id" value="false"/> | |
| 5946 <param name="sequences_whitelist" value=""/> | |
| 5947 <param name="sequence_comparison_method" value="substring"/> | |
| 5948 <param name="accessions_whitelist" value=""/> | |
| 5949 <param name="remove_annotated_features" value="false"/> | |
| 5950 <param name="remove_unannotated_features" value="false"/> | |
| 5951 <param name="remove_unassigned_ids" value="false"/> | |
| 5952 <param name="rt" value="0.1"/> | |
| 5953 <param name="mz" value="0.001"/> | |
| 5954 <param name="blacklist_imperfect" value="false"/> | |
| 5955 </section> | |
| 5956 <section name="algorithm"> | |
| 5957 <section name="SignalToNoise"> | |
| 5958 <param name="max_intensity" value="-1"/> | |
| 5959 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 5960 <param name="auto_max_percentile" value="95"/> | |
| 5961 <param name="auto_mode" value="0"/> | |
| 5962 <param name="win_len" value="200.0"/> | |
| 5963 <param name="bin_count" value="30"/> | |
| 5964 <param name="min_required_elements" value="10"/> | |
| 5965 <param name="noise_for_empty_window" value="1e+20"/> | |
| 5966 <param name="write_log_messages" value="true"/> | |
| 5967 </section> | |
| 5968 </section> | |
| 5969 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 5970 <output name="ctd_out" ftype="xml"> | |
| 5971 <assert_contents> | |
| 5972 <is_valid_xml/> | |
| 5973 </assert_contents> | |
| 5974 </output> | |
| 5975 </test> | |
| 5976 <test expect_num_outputs="2"> | |
| 5977 <conditional name="adv_opts_cond"> | |
| 5978 <param name="adv_opts_selector" value="advanced"/> | |
| 5979 <param name="force" value="false"/> | |
| 5980 <param name="test" value="true"/> | |
| 5981 </conditional> | |
| 5982 <param name="in" value="FileFilter_10_input.mzML"/> | |
| 5983 <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 5984 <param name="out_type" value="mzML"/> | |
| 5985 <param name="rt" value=":"/> | |
| 5986 <param name="mz" value=":"/> | |
| 5987 <param name="int" value=":"/> | |
| 5988 <param name="sort" value="false"/> | |
| 5989 <section name="peak_options"> | |
| 5990 <param name="sn" value="0.0"/> | |
| 5991 <param name="rm_pc_charge" value=""/> | |
| 5992 <param name="pc_mz_range" value=":"/> | |
| 5993 <param name="pc_mz_list" value=""/> | |
| 5994 <param name="level" value="1 2 3"/> | |
| 5995 <param name="sort_peaks" value="false"/> | |
| 5996 <param name="no_chromatograms" value="false"/> | |
| 5997 <param name="remove_chromatograms" value="false"/> | |
| 5998 <param name="remove_empty" value="false"/> | |
| 5999 <param name="mz_precision" value="64"/> | |
| 6000 <param name="int_precision" value="32"/> | |
| 6001 <param name="indexed_file" value="true"/> | |
| 6002 <param name="zlib_compression" value="false"/> | |
| 6003 <section name="numpress"> | |
| 6004 <param name="masstime" value="none"/> | |
| 6005 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6006 <param name="intensity" value="none"/> | |
| 6007 <param name="float_da" value="none"/> | |
| 6008 </section> | |
| 6009 </section> | |
| 6010 <section name="spectra"> | |
| 6011 <param name="remove_zoom" value="false"/> | |
| 6012 <param name="remove_mode" value=""/> | |
| 6013 <param name="remove_activation" value="Collision-induced dissociation"/> | |
| 6014 <param name="remove_collision_energy" value=":"/> | |
| 6015 <param name="remove_isolation_window_width" value=":"/> | |
| 6016 <param name="select_zoom" value="false"/> | |
| 6017 <param name="select_mode" value=""/> | |
| 6018 <param name="select_activation" value=""/> | |
| 6019 <param name="select_collision_energy" value=":"/> | |
| 6020 <param name="select_isolation_window_width" value=":"/> | |
| 6021 <param name="select_polarity" value=""/> | |
| 6022 <section name="blackorwhitelist"> | |
| 6023 <param name="similarity_threshold" value="-1.0"/> | |
| 6024 <param name="rt" value="0.01"/> | |
| 6025 <param name="mz" value="0.01"/> | |
| 6026 <param name="use_ppm_tolerance" value="false"/> | |
| 6027 <param name="blacklist" value="true"/> | |
| 6028 </section> | |
| 6029 </section> | |
| 6030 <section name="feature"> | |
| 6031 <param name="q" value=":"/> | |
| 6032 </section> | |
| 6033 <section name="consensus"> | |
| 6034 <param name="map" value=""/> | |
| 6035 <param name="map_and" value="false"/> | |
| 6036 <section name="blackorwhitelist"> | |
| 6037 <param name="blacklist" value="true"/> | |
| 6038 <param name="maps" value=""/> | |
| 6039 <param name="rt" value="60.0"/> | |
| 6040 <param name="mz" value="0.01"/> | |
| 6041 <param name="use_ppm_tolerance" value="false"/> | |
| 6042 </section> | |
| 6043 </section> | |
| 6044 <section name="f_and_c"> | |
| 6045 <param name="charge" value=":"/> | |
| 6046 <param name="size" value=":"/> | |
| 6047 <param name="remove_meta" value=""/> | |
| 6048 </section> | |
| 6049 <section name="id"> | |
| 6050 <param name="remove_clashes" value="false"/> | |
| 6051 <param name="keep_best_score_id" value="false"/> | |
| 6052 <param name="sequences_whitelist" value=""/> | |
| 6053 <param name="sequence_comparison_method" value="substring"/> | |
| 6054 <param name="accessions_whitelist" value=""/> | |
| 6055 <param name="remove_annotated_features" value="false"/> | |
| 6056 <param name="remove_unannotated_features" value="false"/> | |
| 6057 <param name="remove_unassigned_ids" value="false"/> | |
| 6058 <param name="rt" value="0.1"/> | |
| 6059 <param name="mz" value="0.001"/> | |
| 6060 <param name="blacklist_imperfect" value="false"/> | |
| 6061 </section> | |
| 6062 <section name="algorithm"> | |
| 6063 <section name="SignalToNoise"> | |
| 6064 <param name="max_intensity" value="-1"/> | |
| 6065 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6066 <param name="auto_max_percentile" value="95"/> | |
| 6067 <param name="auto_mode" value="0"/> | |
| 6068 <param name="win_len" value="200.0"/> | |
| 6069 <param name="bin_count" value="30"/> | |
| 6070 <param name="min_required_elements" value="10"/> | |
| 6071 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6072 <param name="write_log_messages" value="true"/> | |
| 6073 </section> | |
| 6074 </section> | |
| 6075 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6076 <output name="ctd_out" ftype="xml"> | |
| 6077 <assert_contents> | |
| 6078 <is_valid_xml/> | |
| 6079 </assert_contents> | |
| 6080 </output> | |
| 6081 </test> | |
| 6082 <test expect_num_outputs="2"> | |
| 6083 <conditional name="adv_opts_cond"> | |
| 6084 <param name="adv_opts_selector" value="advanced"/> | |
| 6085 <param name="force" value="false"/> | |
| 6086 <param name="test" value="true"/> | |
| 6087 </conditional> | |
| 6088 <param name="in" value="FileFilter_11_input.mzML"/> | |
| 6089 <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 6090 <param name="out_type" value="mzML"/> | |
| 6091 <param name="rt" value=":"/> | |
| 6092 <param name="mz" value=":"/> | |
| 6093 <param name="int" value=":"/> | |
| 6094 <param name="sort" value="false"/> | |
| 6095 <section name="peak_options"> | |
| 6096 <param name="sn" value="0.0"/> | |
| 6097 <param name="rm_pc_charge" value=""/> | |
| 6098 <param name="pc_mz_range" value=":"/> | |
| 6099 <param name="pc_mz_list" value=""/> | |
| 6100 <param name="level" value="1 2 3"/> | |
| 6101 <param name="sort_peaks" value="false"/> | |
| 6102 <param name="no_chromatograms" value="false"/> | |
| 6103 <param name="remove_chromatograms" value="false"/> | |
| 6104 <param name="remove_empty" value="false"/> | |
| 6105 <param name="mz_precision" value="64"/> | |
| 6106 <param name="int_precision" value="32"/> | |
| 6107 <param name="indexed_file" value="true"/> | |
| 6108 <param name="zlib_compression" value="false"/> | |
| 6109 <section name="numpress"> | |
| 6110 <param name="masstime" value="none"/> | |
| 6111 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6112 <param name="intensity" value="none"/> | |
| 6113 <param name="float_da" value="none"/> | |
| 6114 </section> | |
| 6115 </section> | |
| 6116 <section name="spectra"> | |
| 6117 <param name="remove_zoom" value="false"/> | |
| 6118 <param name="remove_mode" value=""/> | |
| 6119 <param name="remove_activation" value="Plasma desorption"/> | |
| 6120 <param name="remove_collision_energy" value=":"/> | |
| 6121 <param name="remove_isolation_window_width" value=":"/> | |
| 6122 <param name="select_zoom" value="false"/> | |
| 6123 <param name="select_mode" value=""/> | |
| 6124 <param name="select_activation" value=""/> | |
| 6125 <param name="select_collision_energy" value=":"/> | |
| 6126 <param name="select_isolation_window_width" value=":"/> | |
| 6127 <param name="select_polarity" value=""/> | |
| 6128 <section name="blackorwhitelist"> | |
| 6129 <param name="similarity_threshold" value="-1.0"/> | |
| 6130 <param name="rt" value="0.01"/> | |
| 6131 <param name="mz" value="0.01"/> | |
| 6132 <param name="use_ppm_tolerance" value="false"/> | |
| 6133 <param name="blacklist" value="true"/> | |
| 6134 </section> | |
| 6135 </section> | |
| 6136 <section name="feature"> | |
| 6137 <param name="q" value=":"/> | |
| 6138 </section> | |
| 6139 <section name="consensus"> | |
| 6140 <param name="map" value=""/> | |
| 6141 <param name="map_and" value="false"/> | |
| 6142 <section name="blackorwhitelist"> | |
| 6143 <param name="blacklist" value="true"/> | |
| 6144 <param name="maps" value=""/> | |
| 6145 <param name="rt" value="60.0"/> | |
| 6146 <param name="mz" value="0.01"/> | |
| 6147 <param name="use_ppm_tolerance" value="false"/> | |
| 6148 </section> | |
| 6149 </section> | |
| 6150 <section name="f_and_c"> | |
| 6151 <param name="charge" value=":"/> | |
| 6152 <param name="size" value=":"/> | |
| 6153 <param name="remove_meta" value=""/> | |
| 6154 </section> | |
| 6155 <section name="id"> | |
| 6156 <param name="remove_clashes" value="false"/> | |
| 6157 <param name="keep_best_score_id" value="false"/> | |
| 6158 <param name="sequences_whitelist" value=""/> | |
| 6159 <param name="sequence_comparison_method" value="substring"/> | |
| 6160 <param name="accessions_whitelist" value=""/> | |
| 6161 <param name="remove_annotated_features" value="false"/> | |
| 6162 <param name="remove_unannotated_features" value="false"/> | |
| 6163 <param name="remove_unassigned_ids" value="false"/> | |
| 6164 <param name="rt" value="0.1"/> | |
| 6165 <param name="mz" value="0.001"/> | |
| 6166 <param name="blacklist_imperfect" value="false"/> | |
| 6167 </section> | |
| 6168 <section name="algorithm"> | |
| 6169 <section name="SignalToNoise"> | |
| 6170 <param name="max_intensity" value="-1"/> | |
| 6171 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6172 <param name="auto_max_percentile" value="95"/> | |
| 6173 <param name="auto_mode" value="0"/> | |
| 6174 <param name="win_len" value="200.0"/> | |
| 6175 <param name="bin_count" value="30"/> | |
| 6176 <param name="min_required_elements" value="10"/> | |
| 6177 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6178 <param name="write_log_messages" value="true"/> | |
| 6179 </section> | |
| 6180 </section> | |
| 6181 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6182 <output name="ctd_out" ftype="xml"> | |
| 6183 <assert_contents> | |
| 6184 <is_valid_xml/> | |
| 6185 </assert_contents> | |
| 6186 </output> | |
| 6187 </test> | |
| 6188 <test expect_num_outputs="2"> | |
| 6189 <conditional name="adv_opts_cond"> | |
| 6190 <param name="adv_opts_selector" value="advanced"/> | |
| 6191 <param name="force" value="false"/> | |
| 6192 <param name="test" value="true"/> | |
| 6193 </conditional> | |
| 6194 <param name="in" value="FileFilter_12_input.mzML"/> | |
| 6195 <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 6196 <param name="out_type" value="mzML"/> | |
| 6197 <param name="rt" value=":"/> | |
| 6198 <param name="mz" value=":"/> | |
| 6199 <param name="int" value=":"/> | |
| 6200 <param name="sort" value="false"/> | |
| 6201 <section name="peak_options"> | |
| 6202 <param name="sn" value="0.0"/> | |
| 6203 <param name="rm_pc_charge" value=""/> | |
| 6204 <param name="pc_mz_range" value=":"/> | |
| 6205 <param name="pc_mz_list" value=""/> | |
| 6206 <param name="level" value="1 2 3"/> | |
| 6207 <param name="sort_peaks" value="false"/> | |
| 6208 <param name="no_chromatograms" value="false"/> | |
| 6209 <param name="remove_chromatograms" value="true"/> | |
| 6210 <param name="remove_empty" value="false"/> | |
| 6211 <param name="mz_precision" value="64"/> | |
| 6212 <param name="int_precision" value="32"/> | |
| 6213 <param name="indexed_file" value="true"/> | |
| 6214 <param name="zlib_compression" value="false"/> | |
| 6215 <section name="numpress"> | |
| 6216 <param name="masstime" value="none"/> | |
| 6217 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6218 <param name="intensity" value="none"/> | |
| 6219 <param name="float_da" value="none"/> | |
| 6220 </section> | |
| 6221 </section> | |
| 6222 <section name="spectra"> | |
| 6223 <param name="remove_zoom" value="false"/> | |
| 6224 <param name="remove_mode" value=""/> | |
| 6225 <param name="remove_activation" value=""/> | |
| 6226 <param name="remove_collision_energy" value=":"/> | |
| 6227 <param name="remove_isolation_window_width" value=":"/> | |
| 6228 <param name="select_zoom" value="false"/> | |
| 6229 <param name="select_mode" value=""/> | |
| 6230 <param name="select_activation" value=""/> | |
| 6231 <param name="select_collision_energy" value=":"/> | |
| 6232 <param name="select_isolation_window_width" value=":"/> | |
| 6233 <param name="select_polarity" value=""/> | |
| 6234 <section name="blackorwhitelist"> | |
| 6235 <param name="similarity_threshold" value="-1.0"/> | |
| 6236 <param name="rt" value="0.01"/> | |
| 6237 <param name="mz" value="0.01"/> | |
| 6238 <param name="use_ppm_tolerance" value="false"/> | |
| 6239 <param name="blacklist" value="true"/> | |
| 6240 </section> | |
| 6241 </section> | |
| 6242 <section name="feature"> | |
| 6243 <param name="q" value=":"/> | |
| 6244 </section> | |
| 6245 <section name="consensus"> | |
| 6246 <param name="map" value=""/> | |
| 6247 <param name="map_and" value="false"/> | |
| 6248 <section name="blackorwhitelist"> | |
| 6249 <param name="blacklist" value="true"/> | |
| 6250 <param name="maps" value=""/> | |
| 6251 <param name="rt" value="60.0"/> | |
| 6252 <param name="mz" value="0.01"/> | |
| 6253 <param name="use_ppm_tolerance" value="false"/> | |
| 6254 </section> | |
| 6255 </section> | |
| 6256 <section name="f_and_c"> | |
| 6257 <param name="charge" value=":"/> | |
| 6258 <param name="size" value=":"/> | |
| 6259 <param name="remove_meta" value=""/> | |
| 6260 </section> | |
| 6261 <section name="id"> | |
| 6262 <param name="remove_clashes" value="false"/> | |
| 6263 <param name="keep_best_score_id" value="false"/> | |
| 6264 <param name="sequences_whitelist" value=""/> | |
| 6265 <param name="sequence_comparison_method" value="substring"/> | |
| 6266 <param name="accessions_whitelist" value=""/> | |
| 6267 <param name="remove_annotated_features" value="false"/> | |
| 6268 <param name="remove_unannotated_features" value="false"/> | |
| 6269 <param name="remove_unassigned_ids" value="false"/> | |
| 6270 <param name="rt" value="0.1"/> | |
| 6271 <param name="mz" value="0.001"/> | |
| 6272 <param name="blacklist_imperfect" value="false"/> | |
| 6273 </section> | |
| 6274 <section name="algorithm"> | |
| 6275 <section name="SignalToNoise"> | |
| 6276 <param name="max_intensity" value="-1"/> | |
| 6277 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6278 <param name="auto_max_percentile" value="95"/> | |
| 6279 <param name="auto_mode" value="0"/> | |
| 6280 <param name="win_len" value="200.0"/> | |
| 6281 <param name="bin_count" value="30"/> | |
| 6282 <param name="min_required_elements" value="10"/> | |
| 6283 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6284 <param name="write_log_messages" value="true"/> | |
| 6285 </section> | |
| 6286 </section> | |
| 6287 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6288 <output name="ctd_out" ftype="xml"> | |
| 6289 <assert_contents> | |
| 6290 <is_valid_xml/> | |
| 6291 </assert_contents> | |
| 6292 </output> | |
| 6293 </test> | |
| 6294 <test expect_num_outputs="2"> | |
| 6295 <conditional name="adv_opts_cond"> | |
| 6296 <param name="adv_opts_selector" value="advanced"/> | |
| 6297 <param name="force" value="false"/> | |
| 6298 <param name="test" value="true"/> | |
| 6299 </conditional> | |
| 6300 <param name="in" value="FileFilter_13_input.consensusXML"/> | |
| 6301 <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 6302 <param name="out_type" value="featureXML"/> | |
| 6303 <param name="rt" value=":"/> | |
| 6304 <param name="mz" value=":"/> | |
| 6305 <param name="int" value=":"/> | |
| 6306 <param name="sort" value="false"/> | |
| 6307 <section name="peak_options"> | |
| 6308 <param name="sn" value="0.0"/> | |
| 6309 <param name="rm_pc_charge" value=""/> | |
| 6310 <param name="pc_mz_range" value=":"/> | |
| 6311 <param name="pc_mz_list" value=""/> | |
| 6312 <param name="level" value="1 2 3"/> | |
| 6313 <param name="sort_peaks" value="false"/> | |
| 6314 <param name="no_chromatograms" value="false"/> | |
| 6315 <param name="remove_chromatograms" value="false"/> | |
| 6316 <param name="remove_empty" value="false"/> | |
| 6317 <param name="mz_precision" value="64"/> | |
| 6318 <param name="int_precision" value="32"/> | |
| 6319 <param name="indexed_file" value="true"/> | |
| 6320 <param name="zlib_compression" value="false"/> | |
| 6321 <section name="numpress"> | |
| 6322 <param name="masstime" value="none"/> | |
| 6323 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6324 <param name="intensity" value="none"/> | |
| 6325 <param name="float_da" value="none"/> | |
| 6326 </section> | |
| 6327 </section> | |
| 6328 <section name="spectra"> | |
| 6329 <param name="remove_zoom" value="false"/> | |
| 6330 <param name="remove_mode" value=""/> | |
| 6331 <param name="remove_activation" value=""/> | |
| 6332 <param name="remove_collision_energy" value=":"/> | |
| 6333 <param name="remove_isolation_window_width" value=":"/> | |
| 6334 <param name="select_zoom" value="false"/> | |
| 6335 <param name="select_mode" value=""/> | |
| 6336 <param name="select_activation" value=""/> | |
| 6337 <param name="select_collision_energy" value=":"/> | |
| 6338 <param name="select_isolation_window_width" value=":"/> | |
| 6339 <param name="select_polarity" value=""/> | |
| 6340 <section name="blackorwhitelist"> | |
| 6341 <param name="similarity_threshold" value="-1.0"/> | |
| 6342 <param name="rt" value="0.01"/> | |
| 6343 <param name="mz" value="0.01"/> | |
| 6344 <param name="use_ppm_tolerance" value="false"/> | |
| 6345 <param name="blacklist" value="true"/> | |
| 6346 </section> | |
| 6347 </section> | |
| 6348 <section name="feature"> | |
| 6349 <param name="q" value=":"/> | |
| 6350 </section> | |
| 6351 <section name="consensus"> | |
| 6352 <param name="map" value="2"/> | |
| 6353 <param name="map_and" value="false"/> | |
| 6354 <section name="blackorwhitelist"> | |
| 6355 <param name="blacklist" value="true"/> | |
| 6356 <param name="maps" value=""/> | |
| 6357 <param name="rt" value="60.0"/> | |
| 6358 <param name="mz" value="0.01"/> | |
| 6359 <param name="use_ppm_tolerance" value="false"/> | |
| 6360 </section> | |
| 6361 </section> | |
| 6362 <section name="f_and_c"> | |
| 6363 <param name="charge" value=":"/> | |
| 6364 <param name="size" value=":"/> | |
| 6365 <param name="remove_meta" value=""/> | |
| 6366 </section> | |
| 6367 <section name="id"> | |
| 6368 <param name="remove_clashes" value="false"/> | |
| 6369 <param name="keep_best_score_id" value="false"/> | |
| 6370 <param name="sequences_whitelist" value=""/> | |
| 6371 <param name="sequence_comparison_method" value="substring"/> | |
| 6372 <param name="accessions_whitelist" value=""/> | |
| 6373 <param name="remove_annotated_features" value="false"/> | |
| 6374 <param name="remove_unannotated_features" value="false"/> | |
| 6375 <param name="remove_unassigned_ids" value="false"/> | |
| 6376 <param name="rt" value="0.1"/> | |
| 6377 <param name="mz" value="0.001"/> | |
| 6378 <param name="blacklist_imperfect" value="false"/> | |
| 6379 </section> | |
| 6380 <section name="algorithm"> | |
| 6381 <section name="SignalToNoise"> | |
| 6382 <param name="max_intensity" value="-1"/> | |
| 6383 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6384 <param name="auto_max_percentile" value="95"/> | |
| 6385 <param name="auto_mode" value="0"/> | |
| 6386 <param name="win_len" value="200.0"/> | |
| 6387 <param name="bin_count" value="30"/> | |
| 6388 <param name="min_required_elements" value="10"/> | |
| 6389 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6390 <param name="write_log_messages" value="true"/> | |
| 6391 </section> | |
| 6392 </section> | |
| 6393 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6394 <output name="ctd_out" ftype="xml"> | |
| 6395 <assert_contents> | |
| 6396 <is_valid_xml/> | |
| 6397 </assert_contents> | |
| 6398 </output> | |
| 6399 </test> | |
| 6400 <test expect_num_outputs="2"> | |
| 6401 <conditional name="adv_opts_cond"> | |
| 6402 <param name="adv_opts_selector" value="advanced"/> | |
| 6403 <param name="force" value="false"/> | |
| 6404 <param name="test" value="true"/> | |
| 6405 </conditional> | |
| 6406 <param name="in" value="FileFilter_14_input.consensusXML"/> | |
| 6407 <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 6408 <param name="out_type" value="consensusXML"/> | |
| 6409 <param name="rt" value=":"/> | |
| 6410 <param name="mz" value=":"/> | |
| 6411 <param name="int" value=":"/> | |
| 6412 <param name="sort" value="false"/> | |
| 6413 <section name="peak_options"> | |
| 6414 <param name="sn" value="0.0"/> | |
| 6415 <param name="rm_pc_charge" value=""/> | |
| 6416 <param name="pc_mz_range" value=":"/> | |
| 6417 <param name="pc_mz_list" value=""/> | |
| 6418 <param name="level" value="1 2 3"/> | |
| 6419 <param name="sort_peaks" value="false"/> | |
| 6420 <param name="no_chromatograms" value="false"/> | |
| 6421 <param name="remove_chromatograms" value="false"/> | |
| 6422 <param name="remove_empty" value="false"/> | |
| 6423 <param name="mz_precision" value="64"/> | |
| 6424 <param name="int_precision" value="32"/> | |
| 6425 <param name="indexed_file" value="true"/> | |
| 6426 <param name="zlib_compression" value="false"/> | |
| 6427 <section name="numpress"> | |
| 6428 <param name="masstime" value="none"/> | |
| 6429 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6430 <param name="intensity" value="none"/> | |
| 6431 <param name="float_da" value="none"/> | |
| 6432 </section> | |
| 6433 </section> | |
| 6434 <section name="spectra"> | |
| 6435 <param name="remove_zoom" value="false"/> | |
| 6436 <param name="remove_mode" value=""/> | |
| 6437 <param name="remove_activation" value=""/> | |
| 6438 <param name="remove_collision_energy" value=":"/> | |
| 6439 <param name="remove_isolation_window_width" value=":"/> | |
| 6440 <param name="select_zoom" value="false"/> | |
| 6441 <param name="select_mode" value=""/> | |
| 6442 <param name="select_activation" value=""/> | |
| 6443 <param name="select_collision_energy" value=":"/> | |
| 6444 <param name="select_isolation_window_width" value=":"/> | |
| 6445 <param name="select_polarity" value=""/> | |
| 6446 <section name="blackorwhitelist"> | |
| 6447 <param name="similarity_threshold" value="-1.0"/> | |
| 6448 <param name="rt" value="0.01"/> | |
| 6449 <param name="mz" value="0.01"/> | |
| 6450 <param name="use_ppm_tolerance" value="false"/> | |
| 6451 <param name="blacklist" value="true"/> | |
| 6452 </section> | |
| 6453 </section> | |
| 6454 <section name="feature"> | |
| 6455 <param name="q" value=":"/> | |
| 6456 </section> | |
| 6457 <section name="consensus"> | |
| 6458 <param name="map" value="0 2"/> | |
| 6459 <param name="map_and" value="false"/> | |
| 6460 <section name="blackorwhitelist"> | |
| 6461 <param name="blacklist" value="true"/> | |
| 6462 <param name="maps" value=""/> | |
| 6463 <param name="rt" value="60.0"/> | |
| 6464 <param name="mz" value="0.01"/> | |
| 6465 <param name="use_ppm_tolerance" value="false"/> | |
| 6466 </section> | |
| 6467 </section> | |
| 6468 <section name="f_and_c"> | |
| 6469 <param name="charge" value=":"/> | |
| 6470 <param name="size" value=":"/> | |
| 6471 <param name="remove_meta" value=""/> | |
| 6472 </section> | |
| 6473 <section name="id"> | |
| 6474 <param name="remove_clashes" value="false"/> | |
| 6475 <param name="keep_best_score_id" value="false"/> | |
| 6476 <param name="sequences_whitelist" value=""/> | |
| 6477 <param name="sequence_comparison_method" value="substring"/> | |
| 6478 <param name="accessions_whitelist" value=""/> | |
| 6479 <param name="remove_annotated_features" value="false"/> | |
| 6480 <param name="remove_unannotated_features" value="false"/> | |
| 6481 <param name="remove_unassigned_ids" value="false"/> | |
| 6482 <param name="rt" value="0.1"/> | |
| 6483 <param name="mz" value="0.001"/> | |
| 6484 <param name="blacklist_imperfect" value="false"/> | |
| 6485 </section> | |
| 6486 <section name="algorithm"> | |
| 6487 <section name="SignalToNoise"> | |
| 6488 <param name="max_intensity" value="-1"/> | |
| 6489 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6490 <param name="auto_max_percentile" value="95"/> | |
| 6491 <param name="auto_mode" value="0"/> | |
| 6492 <param name="win_len" value="200.0"/> | |
| 6493 <param name="bin_count" value="30"/> | |
| 6494 <param name="min_required_elements" value="10"/> | |
| 6495 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6496 <param name="write_log_messages" value="true"/> | |
| 6497 </section> | |
| 6498 </section> | |
| 6499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6500 <output name="ctd_out" ftype="xml"> | |
| 6501 <assert_contents> | |
| 6502 <is_valid_xml/> | |
| 6503 </assert_contents> | |
| 6504 </output> | |
| 6505 </test> | |
| 6506 <test expect_num_outputs="2"> | |
| 6507 <conditional name="adv_opts_cond"> | |
| 6508 <param name="adv_opts_selector" value="advanced"/> | |
| 6509 <param name="force" value="false"/> | |
| 6510 <param name="test" value="true"/> | |
| 6511 </conditional> | |
| 6512 <param name="in" value="FileFilter_15_input.featureXML"/> | |
| 6513 <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 6514 <param name="out_type" value="featurexml"/> | |
| 6515 <param name="rt" value=":"/> | |
| 6516 <param name="mz" value=":"/> | |
| 6517 <param name="int" value=":"/> | |
| 6518 <param name="sort" value="false"/> | |
| 6519 <section name="peak_options"> | |
| 6520 <param name="sn" value="0.0"/> | |
| 6521 <param name="rm_pc_charge" value=""/> | |
| 6522 <param name="pc_mz_range" value=":"/> | |
| 6523 <param name="pc_mz_list" value=""/> | |
| 6524 <param name="level" value="1 2 3"/> | |
| 6525 <param name="sort_peaks" value="false"/> | |
| 6526 <param name="no_chromatograms" value="false"/> | |
| 6527 <param name="remove_chromatograms" value="false"/> | |
| 6528 <param name="remove_empty" value="false"/> | |
| 6529 <param name="mz_precision" value="64"/> | |
| 6530 <param name="int_precision" value="32"/> | |
| 6531 <param name="indexed_file" value="true"/> | |
| 6532 <param name="zlib_compression" value="false"/> | |
| 6533 <section name="numpress"> | |
| 6534 <param name="masstime" value="none"/> | |
| 6535 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6536 <param name="intensity" value="none"/> | |
| 6537 <param name="float_da" value="none"/> | |
| 6538 </section> | |
| 6539 </section> | |
| 6540 <section name="spectra"> | |
| 6541 <param name="remove_zoom" value="false"/> | |
| 6542 <param name="remove_mode" value=""/> | |
| 6543 <param name="remove_activation" value=""/> | |
| 6544 <param name="remove_collision_energy" value=":"/> | |
| 6545 <param name="remove_isolation_window_width" value=":"/> | |
| 6546 <param name="select_zoom" value="false"/> | |
| 6547 <param name="select_mode" value=""/> | |
| 6548 <param name="select_activation" value=""/> | |
| 6549 <param name="select_collision_energy" value=":"/> | |
| 6550 <param name="select_isolation_window_width" value=":"/> | |
| 6551 <param name="select_polarity" value=""/> | |
| 6552 <section name="blackorwhitelist"> | |
| 6553 <param name="similarity_threshold" value="-1.0"/> | |
| 6554 <param name="rt" value="0.01"/> | |
| 6555 <param name="mz" value="0.01"/> | |
| 6556 <param name="use_ppm_tolerance" value="false"/> | |
| 6557 <param name="blacklist" value="true"/> | |
| 6558 </section> | |
| 6559 </section> | |
| 6560 <section name="feature"> | |
| 6561 <param name="q" value=":"/> | |
| 6562 </section> | |
| 6563 <section name="consensus"> | |
| 6564 <param name="map" value=""/> | |
| 6565 <param name="map_and" value="false"/> | |
| 6566 <section name="blackorwhitelist"> | |
| 6567 <param name="blacklist" value="true"/> | |
| 6568 <param name="maps" value=""/> | |
| 6569 <param name="rt" value="60.0"/> | |
| 6570 <param name="mz" value="0.01"/> | |
| 6571 <param name="use_ppm_tolerance" value="false"/> | |
| 6572 </section> | |
| 6573 </section> | |
| 6574 <section name="f_and_c"> | |
| 6575 <param name="charge" value=":"/> | |
| 6576 <param name="size" value=":"/> | |
| 6577 <param name="remove_meta" value=""/> | |
| 6578 </section> | |
| 6579 <section name="id"> | |
| 6580 <param name="remove_clashes" value="false"/> | |
| 6581 <param name="keep_best_score_id" value="false"/> | |
| 6582 <param name="sequences_whitelist" value=""Oxidation""/> | |
| 6583 <param name="sequence_comparison_method" value="substring"/> | |
| 6584 <param name="accessions_whitelist" value=""/> | |
| 6585 <param name="remove_annotated_features" value="false"/> | |
| 6586 <param name="remove_unannotated_features" value="false"/> | |
| 6587 <param name="remove_unassigned_ids" value="true"/> | |
| 6588 <param name="rt" value="0.1"/> | |
| 6589 <param name="mz" value="0.001"/> | |
| 6590 <param name="blacklist_imperfect" value="false"/> | |
| 6591 </section> | |
| 6592 <section name="algorithm"> | |
| 6593 <section name="SignalToNoise"> | |
| 6594 <param name="max_intensity" value="-1"/> | |
| 6595 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6596 <param name="auto_max_percentile" value="95"/> | |
| 6597 <param name="auto_mode" value="0"/> | |
| 6598 <param name="win_len" value="200.0"/> | |
| 6599 <param name="bin_count" value="30"/> | |
| 6600 <param name="min_required_elements" value="10"/> | |
| 6601 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6602 <param name="write_log_messages" value="true"/> | |
| 6603 </section> | |
| 6604 </section> | |
| 6605 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6606 <output name="ctd_out" ftype="xml"> | |
| 6607 <assert_contents> | |
| 6608 <is_valid_xml/> | |
| 6609 </assert_contents> | |
| 6610 </output> | |
| 6611 </test> | |
| 6612 <test expect_num_outputs="2"> | |
| 6613 <conditional name="adv_opts_cond"> | |
| 6614 <param name="adv_opts_selector" value="advanced"/> | |
| 6615 <param name="force" value="false"/> | |
| 6616 <param name="test" value="true"/> | |
| 6617 </conditional> | |
| 6618 <param name="in" value="FileFilter_15_input.featureXML"/> | |
| 6619 <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 6620 <param name="out_type" value="featurexml"/> | |
| 6621 <param name="rt" value="3000:4000"/> | |
| 6622 <param name="mz" value="400:600"/> | |
| 6623 <param name="int" value=":"/> | |
| 6624 <param name="sort" value="false"/> | |
| 6625 <section name="peak_options"> | |
| 6626 <param name="sn" value="0.0"/> | |
| 6627 <param name="rm_pc_charge" value=""/> | |
| 6628 <param name="pc_mz_range" value=":"/> | |
| 6629 <param name="pc_mz_list" value=""/> | |
| 6630 <param name="level" value="1 2 3"/> | |
| 6631 <param name="sort_peaks" value="false"/> | |
| 6632 <param name="no_chromatograms" value="false"/> | |
| 6633 <param name="remove_chromatograms" value="false"/> | |
| 6634 <param name="remove_empty" value="false"/> | |
| 6635 <param name="mz_precision" value="64"/> | |
| 6636 <param name="int_precision" value="32"/> | |
| 6637 <param name="indexed_file" value="true"/> | |
| 6638 <param name="zlib_compression" value="false"/> | |
| 6639 <section name="numpress"> | |
| 6640 <param name="masstime" value="none"/> | |
| 6641 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6642 <param name="intensity" value="none"/> | |
| 6643 <param name="float_da" value="none"/> | |
| 6644 </section> | |
| 6645 </section> | |
| 6646 <section name="spectra"> | |
| 6647 <param name="remove_zoom" value="false"/> | |
| 6648 <param name="remove_mode" value=""/> | |
| 6649 <param name="remove_activation" value=""/> | |
| 6650 <param name="remove_collision_energy" value=":"/> | |
| 6651 <param name="remove_isolation_window_width" value=":"/> | |
| 6652 <param name="select_zoom" value="false"/> | |
| 6653 <param name="select_mode" value=""/> | |
| 6654 <param name="select_activation" value=""/> | |
| 6655 <param name="select_collision_energy" value=":"/> | |
| 6656 <param name="select_isolation_window_width" value=":"/> | |
| 6657 <param name="select_polarity" value=""/> | |
| 6658 <section name="blackorwhitelist"> | |
| 6659 <param name="similarity_threshold" value="-1.0"/> | |
| 6660 <param name="rt" value="0.01"/> | |
| 6661 <param name="mz" value="0.01"/> | |
| 6662 <param name="use_ppm_tolerance" value="false"/> | |
| 6663 <param name="blacklist" value="true"/> | |
| 6664 </section> | |
| 6665 </section> | |
| 6666 <section name="feature"> | |
| 6667 <param name="q" value=":"/> | |
| 6668 </section> | |
| 6669 <section name="consensus"> | |
| 6670 <param name="map" value=""/> | |
| 6671 <param name="map_and" value="false"/> | |
| 6672 <section name="blackorwhitelist"> | |
| 6673 <param name="blacklist" value="true"/> | |
| 6674 <param name="maps" value=""/> | |
| 6675 <param name="rt" value="60.0"/> | |
| 6676 <param name="mz" value="0.01"/> | |
| 6677 <param name="use_ppm_tolerance" value="false"/> | |
| 6678 </section> | |
| 6679 </section> | |
| 6680 <section name="f_and_c"> | |
| 6681 <param name="charge" value=":"/> | |
| 6682 <param name="size" value=":"/> | |
| 6683 <param name="remove_meta" value=""/> | |
| 6684 </section> | |
| 6685 <section name="id"> | |
| 6686 <param name="remove_clashes" value="false"/> | |
| 6687 <param name="keep_best_score_id" value="false"/> | |
| 6688 <param name="sequences_whitelist" value=""Oxidation""/> | |
| 6689 <param name="sequence_comparison_method" value="substring"/> | |
| 6690 <param name="accessions_whitelist" value=""/> | |
| 6691 <param name="remove_annotated_features" value="false"/> | |
| 6692 <param name="remove_unannotated_features" value="false"/> | |
| 6693 <param name="remove_unassigned_ids" value="true"/> | |
| 6694 <param name="rt" value="0.1"/> | |
| 6695 <param name="mz" value="0.001"/> | |
| 6696 <param name="blacklist_imperfect" value="false"/> | |
| 6697 </section> | |
| 6698 <section name="algorithm"> | |
| 6699 <section name="SignalToNoise"> | |
| 6700 <param name="max_intensity" value="-1"/> | |
| 6701 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6702 <param name="auto_max_percentile" value="95"/> | |
| 6703 <param name="auto_mode" value="0"/> | |
| 6704 <param name="win_len" value="200.0"/> | |
| 6705 <param name="bin_count" value="30"/> | |
| 6706 <param name="min_required_elements" value="10"/> | |
| 6707 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6708 <param name="write_log_messages" value="true"/> | |
| 6709 </section> | |
| 6710 </section> | |
| 6711 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6712 <output name="ctd_out" ftype="xml"> | |
| 6713 <assert_contents> | |
| 6714 <is_valid_xml/> | |
| 6715 </assert_contents> | |
| 6716 </output> | |
| 6717 </test> | |
| 6718 <test expect_num_outputs="2"> | |
| 6719 <conditional name="adv_opts_cond"> | |
| 6720 <param name="adv_opts_selector" value="advanced"/> | |
| 6721 <param name="force" value="false"/> | |
| 6722 <param name="test" value="true"/> | |
| 6723 </conditional> | |
| 6724 <param name="in" value="FileFilter_15_input.featureXML"/> | |
| 6725 <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 6726 <param name="out_type" value="featurexml"/> | |
| 6727 <param name="rt" value="3000:4000"/> | |
| 6728 <param name="mz" value="400:600"/> | |
| 6729 <param name="int" value=":"/> | |
| 6730 <param name="sort" value="false"/> | |
| 6731 <section name="peak_options"> | |
| 6732 <param name="sn" value="0.0"/> | |
| 6733 <param name="rm_pc_charge" value=""/> | |
| 6734 <param name="pc_mz_range" value=":"/> | |
| 6735 <param name="pc_mz_list" value=""/> | |
| 6736 <param name="level" value="1 2 3"/> | |
| 6737 <param name="sort_peaks" value="false"/> | |
| 6738 <param name="no_chromatograms" value="false"/> | |
| 6739 <param name="remove_chromatograms" value="false"/> | |
| 6740 <param name="remove_empty" value="false"/> | |
| 6741 <param name="mz_precision" value="64"/> | |
| 6742 <param name="int_precision" value="32"/> | |
| 6743 <param name="indexed_file" value="true"/> | |
| 6744 <param name="zlib_compression" value="false"/> | |
| 6745 <section name="numpress"> | |
| 6746 <param name="masstime" value="none"/> | |
| 6747 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6748 <param name="intensity" value="none"/> | |
| 6749 <param name="float_da" value="none"/> | |
| 6750 </section> | |
| 6751 </section> | |
| 6752 <section name="spectra"> | |
| 6753 <param name="remove_zoom" value="false"/> | |
| 6754 <param name="remove_mode" value=""/> | |
| 6755 <param name="remove_activation" value=""/> | |
| 6756 <param name="remove_collision_energy" value=":"/> | |
| 6757 <param name="remove_isolation_window_width" value=":"/> | |
| 6758 <param name="select_zoom" value="false"/> | |
| 6759 <param name="select_mode" value=""/> | |
| 6760 <param name="select_activation" value=""/> | |
| 6761 <param name="select_collision_energy" value=":"/> | |
| 6762 <param name="select_isolation_window_width" value=":"/> | |
| 6763 <param name="select_polarity" value=""/> | |
| 6764 <section name="blackorwhitelist"> | |
| 6765 <param name="similarity_threshold" value="-1.0"/> | |
| 6766 <param name="rt" value="0.01"/> | |
| 6767 <param name="mz" value="0.01"/> | |
| 6768 <param name="use_ppm_tolerance" value="false"/> | |
| 6769 <param name="blacklist" value="true"/> | |
| 6770 </section> | |
| 6771 </section> | |
| 6772 <section name="feature"> | |
| 6773 <param name="q" value=":"/> | |
| 6774 </section> | |
| 6775 <section name="consensus"> | |
| 6776 <param name="map" value=""/> | |
| 6777 <param name="map_and" value="false"/> | |
| 6778 <section name="blackorwhitelist"> | |
| 6779 <param name="blacklist" value="true"/> | |
| 6780 <param name="maps" value=""/> | |
| 6781 <param name="rt" value="60.0"/> | |
| 6782 <param name="mz" value="0.01"/> | |
| 6783 <param name="use_ppm_tolerance" value="false"/> | |
| 6784 </section> | |
| 6785 </section> | |
| 6786 <section name="f_and_c"> | |
| 6787 <param name="charge" value=":"/> | |
| 6788 <param name="size" value=":"/> | |
| 6789 <param name="remove_meta" value=""/> | |
| 6790 </section> | |
| 6791 <section name="id"> | |
| 6792 <param name="remove_clashes" value="false"/> | |
| 6793 <param name="keep_best_score_id" value="false"/> | |
| 6794 <param name="sequences_whitelist" value=""/> | |
| 6795 <param name="sequence_comparison_method" value="substring"/> | |
| 6796 <param name="accessions_whitelist" value=""/> | |
| 6797 <param name="remove_annotated_features" value="true"/> | |
| 6798 <param name="remove_unannotated_features" value="false"/> | |
| 6799 <param name="remove_unassigned_ids" value="false"/> | |
| 6800 <param name="rt" value="0.1"/> | |
| 6801 <param name="mz" value="0.001"/> | |
| 6802 <param name="blacklist_imperfect" value="false"/> | |
| 6803 </section> | |
| 6804 <section name="algorithm"> | |
| 6805 <section name="SignalToNoise"> | |
| 6806 <param name="max_intensity" value="-1"/> | |
| 6807 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6808 <param name="auto_max_percentile" value="95"/> | |
| 6809 <param name="auto_mode" value="0"/> | |
| 6810 <param name="win_len" value="200.0"/> | |
| 6811 <param name="bin_count" value="30"/> | |
| 6812 <param name="min_required_elements" value="10"/> | |
| 6813 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6814 <param name="write_log_messages" value="true"/> | |
| 6815 </section> | |
| 6816 </section> | |
| 6817 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6818 <output name="ctd_out" ftype="xml"> | |
| 6819 <assert_contents> | |
| 6820 <is_valid_xml/> | |
| 6821 </assert_contents> | |
| 6822 </output> | |
| 6823 </test> | |
| 6824 <test expect_num_outputs="2"> | |
| 6825 <conditional name="adv_opts_cond"> | |
| 6826 <param name="adv_opts_selector" value="advanced"/> | |
| 6827 <param name="force" value="false"/> | |
| 6828 <param name="test" value="true"/> | |
| 6829 </conditional> | |
| 6830 <param name="in" value="FileFilter_18_input.consensusXML"/> | |
| 6831 <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 6832 <param name="out_type" value="consensusxml"/> | |
| 6833 <param name="rt" value=":"/> | |
| 6834 <param name="mz" value=":"/> | |
| 6835 <param name="int" value=":"/> | |
| 6836 <param name="sort" value="false"/> | |
| 6837 <section name="peak_options"> | |
| 6838 <param name="sn" value="0.0"/> | |
| 6839 <param name="rm_pc_charge" value=""/> | |
| 6840 <param name="pc_mz_range" value=":"/> | |
| 6841 <param name="pc_mz_list" value=""/> | |
| 6842 <param name="level" value="1 2 3"/> | |
| 6843 <param name="sort_peaks" value="false"/> | |
| 6844 <param name="no_chromatograms" value="false"/> | |
| 6845 <param name="remove_chromatograms" value="false"/> | |
| 6846 <param name="remove_empty" value="false"/> | |
| 6847 <param name="mz_precision" value="64"/> | |
| 6848 <param name="int_precision" value="32"/> | |
| 6849 <param name="indexed_file" value="true"/> | |
| 6850 <param name="zlib_compression" value="false"/> | |
| 6851 <section name="numpress"> | |
| 6852 <param name="masstime" value="none"/> | |
| 6853 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6854 <param name="intensity" value="none"/> | |
| 6855 <param name="float_da" value="none"/> | |
| 6856 </section> | |
| 6857 </section> | |
| 6858 <section name="spectra"> | |
| 6859 <param name="remove_zoom" value="false"/> | |
| 6860 <param name="remove_mode" value=""/> | |
| 6861 <param name="remove_activation" value=""/> | |
| 6862 <param name="remove_collision_energy" value=":"/> | |
| 6863 <param name="remove_isolation_window_width" value=":"/> | |
| 6864 <param name="select_zoom" value="false"/> | |
| 6865 <param name="select_mode" value=""/> | |
| 6866 <param name="select_activation" value=""/> | |
| 6867 <param name="select_collision_energy" value=":"/> | |
| 6868 <param name="select_isolation_window_width" value=":"/> | |
| 6869 <param name="select_polarity" value=""/> | |
| 6870 <section name="blackorwhitelist"> | |
| 6871 <param name="similarity_threshold" value="-1.0"/> | |
| 6872 <param name="rt" value="0.01"/> | |
| 6873 <param name="mz" value="0.01"/> | |
| 6874 <param name="use_ppm_tolerance" value="false"/> | |
| 6875 <param name="blacklist" value="true"/> | |
| 6876 </section> | |
| 6877 </section> | |
| 6878 <section name="feature"> | |
| 6879 <param name="q" value=":"/> | |
| 6880 </section> | |
| 6881 <section name="consensus"> | |
| 6882 <param name="map" value=""/> | |
| 6883 <param name="map_and" value="false"/> | |
| 6884 <section name="blackorwhitelist"> | |
| 6885 <param name="blacklist" value="true"/> | |
| 6886 <param name="maps" value=""/> | |
| 6887 <param name="rt" value="60.0"/> | |
| 6888 <param name="mz" value="0.01"/> | |
| 6889 <param name="use_ppm_tolerance" value="false"/> | |
| 6890 </section> | |
| 6891 </section> | |
| 6892 <section name="f_and_c"> | |
| 6893 <param name="charge" value=":"/> | |
| 6894 <param name="size" value=":"/> | |
| 6895 <param name="remove_meta" value=""/> | |
| 6896 </section> | |
| 6897 <section name="id"> | |
| 6898 <param name="remove_clashes" value="false"/> | |
| 6899 <param name="keep_best_score_id" value="false"/> | |
| 6900 <param name="sequences_whitelist" value=""Oxidation""/> | |
| 6901 <param name="sequence_comparison_method" value="substring"/> | |
| 6902 <param name="accessions_whitelist" value=""/> | |
| 6903 <param name="remove_annotated_features" value="false"/> | |
| 6904 <param name="remove_unannotated_features" value="false"/> | |
| 6905 <param name="remove_unassigned_ids" value="true"/> | |
| 6906 <param name="rt" value="0.1"/> | |
| 6907 <param name="mz" value="0.001"/> | |
| 6908 <param name="blacklist_imperfect" value="false"/> | |
| 6909 </section> | |
| 6910 <section name="algorithm"> | |
| 6911 <section name="SignalToNoise"> | |
| 6912 <param name="max_intensity" value="-1"/> | |
| 6913 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 6914 <param name="auto_max_percentile" value="95"/> | |
| 6915 <param name="auto_mode" value="0"/> | |
| 6916 <param name="win_len" value="200.0"/> | |
| 6917 <param name="bin_count" value="30"/> | |
| 6918 <param name="min_required_elements" value="10"/> | |
| 6919 <param name="noise_for_empty_window" value="1e+20"/> | |
| 6920 <param name="write_log_messages" value="true"/> | |
| 6921 </section> | |
| 6922 </section> | |
| 6923 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 6924 <output name="ctd_out" ftype="xml"> | |
| 6925 <assert_contents> | |
| 6926 <is_valid_xml/> | |
| 6927 </assert_contents> | |
| 6928 </output> | |
| 6929 </test> | |
| 6930 <test expect_num_outputs="2"> | |
| 6931 <conditional name="adv_opts_cond"> | |
| 6932 <param name="adv_opts_selector" value="advanced"/> | |
| 6933 <param name="force" value="false"/> | |
| 6934 <param name="test" value="true"/> | |
| 6935 </conditional> | |
| 6936 <param name="in" value="FileFilter_18_input.consensusXML"/> | |
| 6937 <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 6938 <param name="out_type" value="consensusxml"/> | |
| 6939 <param name="rt" value="3000:4000"/> | |
| 6940 <param name="mz" value="400:600"/> | |
| 6941 <param name="int" value=":"/> | |
| 6942 <param name="sort" value="false"/> | |
| 6943 <section name="peak_options"> | |
| 6944 <param name="sn" value="0.0"/> | |
| 6945 <param name="rm_pc_charge" value=""/> | |
| 6946 <param name="pc_mz_range" value=":"/> | |
| 6947 <param name="pc_mz_list" value=""/> | |
| 6948 <param name="level" value="1 2 3"/> | |
| 6949 <param name="sort_peaks" value="false"/> | |
| 6950 <param name="no_chromatograms" value="false"/> | |
| 6951 <param name="remove_chromatograms" value="false"/> | |
| 6952 <param name="remove_empty" value="false"/> | |
| 6953 <param name="mz_precision" value="64"/> | |
| 6954 <param name="int_precision" value="32"/> | |
| 6955 <param name="indexed_file" value="true"/> | |
| 6956 <param name="zlib_compression" value="false"/> | |
| 6957 <section name="numpress"> | |
| 6958 <param name="masstime" value="none"/> | |
| 6959 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 6960 <param name="intensity" value="none"/> | |
| 6961 <param name="float_da" value="none"/> | |
| 6962 </section> | |
| 6963 </section> | |
| 6964 <section name="spectra"> | |
| 6965 <param name="remove_zoom" value="false"/> | |
| 6966 <param name="remove_mode" value=""/> | |
| 6967 <param name="remove_activation" value=""/> | |
| 6968 <param name="remove_collision_energy" value=":"/> | |
| 6969 <param name="remove_isolation_window_width" value=":"/> | |
| 6970 <param name="select_zoom" value="false"/> | |
| 6971 <param name="select_mode" value=""/> | |
| 6972 <param name="select_activation" value=""/> | |
| 6973 <param name="select_collision_energy" value=":"/> | |
| 6974 <param name="select_isolation_window_width" value=":"/> | |
| 6975 <param name="select_polarity" value=""/> | |
| 6976 <section name="blackorwhitelist"> | |
| 6977 <param name="similarity_threshold" value="-1.0"/> | |
| 6978 <param name="rt" value="0.01"/> | |
| 6979 <param name="mz" value="0.01"/> | |
| 6980 <param name="use_ppm_tolerance" value="false"/> | |
| 6981 <param name="blacklist" value="true"/> | |
| 6982 </section> | |
| 6983 </section> | |
| 6984 <section name="feature"> | |
| 6985 <param name="q" value=":"/> | |
| 6986 </section> | |
| 6987 <section name="consensus"> | |
| 6988 <param name="map" value=""/> | |
| 6989 <param name="map_and" value="false"/> | |
| 6990 <section name="blackorwhitelist"> | |
| 6991 <param name="blacklist" value="true"/> | |
| 6992 <param name="maps" value=""/> | |
| 6993 <param name="rt" value="60.0"/> | |
| 6994 <param name="mz" value="0.01"/> | |
| 6995 <param name="use_ppm_tolerance" value="false"/> | |
| 6996 </section> | |
| 6997 </section> | |
| 6998 <section name="f_and_c"> | |
| 6999 <param name="charge" value=":"/> | |
| 7000 <param name="size" value=":"/> | |
| 7001 <param name="remove_meta" value=""/> | |
| 7002 </section> | |
| 7003 <section name="id"> | |
| 7004 <param name="remove_clashes" value="false"/> | |
| 7005 <param name="keep_best_score_id" value="false"/> | |
| 7006 <param name="sequences_whitelist" value=""/> | |
| 7007 <param name="sequence_comparison_method" value="substring"/> | |
| 7008 <param name="accessions_whitelist" value=""/> | |
| 7009 <param name="remove_annotated_features" value="false"/> | |
| 7010 <param name="remove_unannotated_features" value="true"/> | |
| 7011 <param name="remove_unassigned_ids" value="false"/> | |
| 7012 <param name="rt" value="0.1"/> | |
| 7013 <param name="mz" value="0.001"/> | |
| 7014 <param name="blacklist_imperfect" value="false"/> | |
| 7015 </section> | |
| 7016 <section name="algorithm"> | |
| 7017 <section name="SignalToNoise"> | |
| 7018 <param name="max_intensity" value="-1"/> | |
| 7019 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7020 <param name="auto_max_percentile" value="95"/> | |
| 7021 <param name="auto_mode" value="0"/> | |
| 7022 <param name="win_len" value="200.0"/> | |
| 7023 <param name="bin_count" value="30"/> | |
| 7024 <param name="min_required_elements" value="10"/> | |
| 7025 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7026 <param name="write_log_messages" value="true"/> | |
| 7027 </section> | |
| 7028 </section> | |
| 7029 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7030 <output name="ctd_out" ftype="xml"> | |
| 7031 <assert_contents> | |
| 7032 <is_valid_xml/> | |
| 7033 </assert_contents> | |
| 7034 </output> | |
| 7035 </test> | |
| 7036 <test expect_num_outputs="2"> | |
| 7037 <conditional name="adv_opts_cond"> | |
| 7038 <param name="adv_opts_selector" value="advanced"/> | |
| 7039 <param name="force" value="false"/> | |
| 7040 <param name="test" value="true"/> | |
| 7041 </conditional> | |
| 7042 <param name="in" value="FileFilter_15_input.featureXML"/> | |
| 7043 <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 7044 <param name="out_type" value="featurexml"/> | |
| 7045 <param name="rt" value=":"/> | |
| 7046 <param name="mz" value=":"/> | |
| 7047 <param name="int" value=":"/> | |
| 7048 <param name="sort" value="false"/> | |
| 7049 <section name="peak_options"> | |
| 7050 <param name="sn" value="0.0"/> | |
| 7051 <param name="rm_pc_charge" value=""/> | |
| 7052 <param name="pc_mz_range" value=":"/> | |
| 7053 <param name="pc_mz_list" value=""/> | |
| 7054 <param name="level" value="1 2 3"/> | |
| 7055 <param name="sort_peaks" value="false"/> | |
| 7056 <param name="no_chromatograms" value="false"/> | |
| 7057 <param name="remove_chromatograms" value="false"/> | |
| 7058 <param name="remove_empty" value="false"/> | |
| 7059 <param name="mz_precision" value="64"/> | |
| 7060 <param name="int_precision" value="32"/> | |
| 7061 <param name="indexed_file" value="true"/> | |
| 7062 <param name="zlib_compression" value="false"/> | |
| 7063 <section name="numpress"> | |
| 7064 <param name="masstime" value="none"/> | |
| 7065 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7066 <param name="intensity" value="none"/> | |
| 7067 <param name="float_da" value="none"/> | |
| 7068 </section> | |
| 7069 </section> | |
| 7070 <section name="spectra"> | |
| 7071 <param name="remove_zoom" value="false"/> | |
| 7072 <param name="remove_mode" value=""/> | |
| 7073 <param name="remove_activation" value=""/> | |
| 7074 <param name="remove_collision_energy" value=":"/> | |
| 7075 <param name="remove_isolation_window_width" value=":"/> | |
| 7076 <param name="select_zoom" value="false"/> | |
| 7077 <param name="select_mode" value=""/> | |
| 7078 <param name="select_activation" value=""/> | |
| 7079 <param name="select_collision_energy" value=":"/> | |
| 7080 <param name="select_isolation_window_width" value=":"/> | |
| 7081 <param name="select_polarity" value=""/> | |
| 7082 <section name="blackorwhitelist"> | |
| 7083 <param name="similarity_threshold" value="-1.0"/> | |
| 7084 <param name="rt" value="0.01"/> | |
| 7085 <param name="mz" value="0.01"/> | |
| 7086 <param name="use_ppm_tolerance" value="false"/> | |
| 7087 <param name="blacklist" value="true"/> | |
| 7088 </section> | |
| 7089 </section> | |
| 7090 <section name="feature"> | |
| 7091 <param name="q" value=":"/> | |
| 7092 </section> | |
| 7093 <section name="consensus"> | |
| 7094 <param name="map" value=""/> | |
| 7095 <param name="map_and" value="false"/> | |
| 7096 <section name="blackorwhitelist"> | |
| 7097 <param name="blacklist" value="true"/> | |
| 7098 <param name="maps" value=""/> | |
| 7099 <param name="rt" value="60.0"/> | |
| 7100 <param name="mz" value="0.01"/> | |
| 7101 <param name="use_ppm_tolerance" value="false"/> | |
| 7102 </section> | |
| 7103 </section> | |
| 7104 <section name="f_and_c"> | |
| 7105 <param name="charge" value=":"/> | |
| 7106 <param name="size" value=":"/> | |
| 7107 <param name="remove_meta" value=""/> | |
| 7108 </section> | |
| 7109 <section name="id"> | |
| 7110 <param name="remove_clashes" value="false"/> | |
| 7111 <param name="keep_best_score_id" value="false"/> | |
| 7112 <param name="sequences_whitelist" value=""/> | |
| 7113 <param name="sequence_comparison_method" value="substring"/> | |
| 7114 <param name="accessions_whitelist" value=""YDL217C""/> | |
| 7115 <param name="remove_annotated_features" value="false"/> | |
| 7116 <param name="remove_unannotated_features" value="false"/> | |
| 7117 <param name="remove_unassigned_ids" value="true"/> | |
| 7118 <param name="rt" value="0.1"/> | |
| 7119 <param name="mz" value="0.001"/> | |
| 7120 <param name="blacklist_imperfect" value="false"/> | |
| 7121 </section> | |
| 7122 <section name="algorithm"> | |
| 7123 <section name="SignalToNoise"> | |
| 7124 <param name="max_intensity" value="-1"/> | |
| 7125 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7126 <param name="auto_max_percentile" value="95"/> | |
| 7127 <param name="auto_mode" value="0"/> | |
| 7128 <param name="win_len" value="200.0"/> | |
| 7129 <param name="bin_count" value="30"/> | |
| 7130 <param name="min_required_elements" value="10"/> | |
| 7131 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7132 <param name="write_log_messages" value="true"/> | |
| 7133 </section> | |
| 7134 </section> | |
| 7135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7136 <output name="ctd_out" ftype="xml"> | |
| 7137 <assert_contents> | |
| 7138 <is_valid_xml/> | |
| 7139 </assert_contents> | |
| 7140 </output> | |
| 7141 </test> | |
| 7142 <test expect_num_outputs="2"> | |
| 7143 <conditional name="adv_opts_cond"> | |
| 7144 <param name="adv_opts_selector" value="advanced"/> | |
| 7145 <param name="force" value="false"/> | |
| 7146 <param name="test" value="true"/> | |
| 7147 </conditional> | |
| 7148 <param name="in" value="FileFilter_15_input.featureXML"/> | |
| 7149 <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 7150 <param name="out_type" value="featurexml"/> | |
| 7151 <param name="rt" value=":"/> | |
| 7152 <param name="mz" value=":"/> | |
| 7153 <param name="int" value=":"/> | |
| 7154 <param name="sort" value="false"/> | |
| 7155 <section name="peak_options"> | |
| 7156 <param name="sn" value="0.0"/> | |
| 7157 <param name="rm_pc_charge" value=""/> | |
| 7158 <param name="pc_mz_range" value=":"/> | |
| 7159 <param name="pc_mz_list" value=""/> | |
| 7160 <param name="level" value="1 2 3"/> | |
| 7161 <param name="sort_peaks" value="false"/> | |
| 7162 <param name="no_chromatograms" value="false"/> | |
| 7163 <param name="remove_chromatograms" value="false"/> | |
| 7164 <param name="remove_empty" value="false"/> | |
| 7165 <param name="mz_precision" value="64"/> | |
| 7166 <param name="int_precision" value="32"/> | |
| 7167 <param name="indexed_file" value="true"/> | |
| 7168 <param name="zlib_compression" value="false"/> | |
| 7169 <section name="numpress"> | |
| 7170 <param name="masstime" value="none"/> | |
| 7171 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7172 <param name="intensity" value="none"/> | |
| 7173 <param name="float_da" value="none"/> | |
| 7174 </section> | |
| 7175 </section> | |
| 7176 <section name="spectra"> | |
| 7177 <param name="remove_zoom" value="false"/> | |
| 7178 <param name="remove_mode" value=""/> | |
| 7179 <param name="remove_activation" value=""/> | |
| 7180 <param name="remove_collision_energy" value=":"/> | |
| 7181 <param name="remove_isolation_window_width" value=":"/> | |
| 7182 <param name="select_zoom" value="false"/> | |
| 7183 <param name="select_mode" value=""/> | |
| 7184 <param name="select_activation" value=""/> | |
| 7185 <param name="select_collision_energy" value=":"/> | |
| 7186 <param name="select_isolation_window_width" value=":"/> | |
| 7187 <param name="select_polarity" value=""/> | |
| 7188 <section name="blackorwhitelist"> | |
| 7189 <param name="similarity_threshold" value="-1.0"/> | |
| 7190 <param name="rt" value="0.01"/> | |
| 7191 <param name="mz" value="0.01"/> | |
| 7192 <param name="use_ppm_tolerance" value="false"/> | |
| 7193 <param name="blacklist" value="true"/> | |
| 7194 </section> | |
| 7195 </section> | |
| 7196 <section name="feature"> | |
| 7197 <param name="q" value=":"/> | |
| 7198 </section> | |
| 7199 <section name="consensus"> | |
| 7200 <param name="map" value=""/> | |
| 7201 <param name="map_and" value="false"/> | |
| 7202 <section name="blackorwhitelist"> | |
| 7203 <param name="blacklist" value="true"/> | |
| 7204 <param name="maps" value=""/> | |
| 7205 <param name="rt" value="60.0"/> | |
| 7206 <param name="mz" value="0.01"/> | |
| 7207 <param name="use_ppm_tolerance" value="false"/> | |
| 7208 </section> | |
| 7209 </section> | |
| 7210 <section name="f_and_c"> | |
| 7211 <param name="charge" value=":"/> | |
| 7212 <param name="size" value=":"/> | |
| 7213 <param name="remove_meta" value=""/> | |
| 7214 </section> | |
| 7215 <section name="id"> | |
| 7216 <param name="remove_clashes" value="false"/> | |
| 7217 <param name="keep_best_score_id" value="true"/> | |
| 7218 <param name="sequences_whitelist" value=""/> | |
| 7219 <param name="sequence_comparison_method" value="substring"/> | |
| 7220 <param name="accessions_whitelist" value=""/> | |
| 7221 <param name="remove_annotated_features" value="false"/> | |
| 7222 <param name="remove_unannotated_features" value="true"/> | |
| 7223 <param name="remove_unassigned_ids" value="true"/> | |
| 7224 <param name="rt" value="0.1"/> | |
| 7225 <param name="mz" value="0.001"/> | |
| 7226 <param name="blacklist_imperfect" value="false"/> | |
| 7227 </section> | |
| 7228 <section name="algorithm"> | |
| 7229 <section name="SignalToNoise"> | |
| 7230 <param name="max_intensity" value="-1"/> | |
| 7231 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7232 <param name="auto_max_percentile" value="95"/> | |
| 7233 <param name="auto_mode" value="0"/> | |
| 7234 <param name="win_len" value="200.0"/> | |
| 7235 <param name="bin_count" value="30"/> | |
| 7236 <param name="min_required_elements" value="10"/> | |
| 7237 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7238 <param name="write_log_messages" value="true"/> | |
| 7239 </section> | |
| 7240 </section> | |
| 7241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7242 <output name="ctd_out" ftype="xml"> | |
| 7243 <assert_contents> | |
| 7244 <is_valid_xml/> | |
| 7245 </assert_contents> | |
| 7246 </output> | |
| 7247 </test> | |
| 7248 <test expect_num_outputs="2"> | |
| 7249 <conditional name="adv_opts_cond"> | |
| 7250 <param name="adv_opts_selector" value="advanced"/> | |
| 7251 <param name="force" value="false"/> | |
| 7252 <param name="test" value="true"/> | |
| 7253 </conditional> | |
| 7254 <param name="in" value="FileFilter_22_input.consensusXML"/> | |
| 7255 <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 7256 <param name="out_type" value="consensusxml"/> | |
| 7257 <param name="rt" value=":"/> | |
| 7258 <param name="mz" value=":"/> | |
| 7259 <param name="int" value=":"/> | |
| 7260 <param name="sort" value="false"/> | |
| 7261 <section name="peak_options"> | |
| 7262 <param name="sn" value="0.0"/> | |
| 7263 <param name="rm_pc_charge" value=""/> | |
| 7264 <param name="pc_mz_range" value=":"/> | |
| 7265 <param name="pc_mz_list" value=""/> | |
| 7266 <param name="level" value="1 2 3"/> | |
| 7267 <param name="sort_peaks" value="false"/> | |
| 7268 <param name="no_chromatograms" value="false"/> | |
| 7269 <param name="remove_chromatograms" value="false"/> | |
| 7270 <param name="remove_empty" value="false"/> | |
| 7271 <param name="mz_precision" value="64"/> | |
| 7272 <param name="int_precision" value="32"/> | |
| 7273 <param name="indexed_file" value="true"/> | |
| 7274 <param name="zlib_compression" value="false"/> | |
| 7275 <section name="numpress"> | |
| 7276 <param name="masstime" value="none"/> | |
| 7277 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7278 <param name="intensity" value="none"/> | |
| 7279 <param name="float_da" value="none"/> | |
| 7280 </section> | |
| 7281 </section> | |
| 7282 <section name="spectra"> | |
| 7283 <param name="remove_zoom" value="false"/> | |
| 7284 <param name="remove_mode" value=""/> | |
| 7285 <param name="remove_activation" value=""/> | |
| 7286 <param name="remove_collision_energy" value=":"/> | |
| 7287 <param name="remove_isolation_window_width" value=":"/> | |
| 7288 <param name="select_zoom" value="false"/> | |
| 7289 <param name="select_mode" value=""/> | |
| 7290 <param name="select_activation" value=""/> | |
| 7291 <param name="select_collision_energy" value=":"/> | |
| 7292 <param name="select_isolation_window_width" value=":"/> | |
| 7293 <param name="select_polarity" value=""/> | |
| 7294 <section name="blackorwhitelist"> | |
| 7295 <param name="similarity_threshold" value="-1.0"/> | |
| 7296 <param name="rt" value="0.01"/> | |
| 7297 <param name="mz" value="0.01"/> | |
| 7298 <param name="use_ppm_tolerance" value="false"/> | |
| 7299 <param name="blacklist" value="true"/> | |
| 7300 </section> | |
| 7301 </section> | |
| 7302 <section name="feature"> | |
| 7303 <param name="q" value=":"/> | |
| 7304 </section> | |
| 7305 <section name="consensus"> | |
| 7306 <param name="map" value=""/> | |
| 7307 <param name="map_and" value="false"/> | |
| 7308 <section name="blackorwhitelist"> | |
| 7309 <param name="blacklist" value="true"/> | |
| 7310 <param name="maps" value=""/> | |
| 7311 <param name="rt" value="60.0"/> | |
| 7312 <param name="mz" value="0.01"/> | |
| 7313 <param name="use_ppm_tolerance" value="false"/> | |
| 7314 </section> | |
| 7315 </section> | |
| 7316 <section name="f_and_c"> | |
| 7317 <param name="charge" value=":"/> | |
| 7318 <param name="size" value=":"/> | |
| 7319 <param name="remove_meta" value=""distinct_charges" "gt" "1,2""/> | |
| 7320 </section> | |
| 7321 <section name="id"> | |
| 7322 <param name="remove_clashes" value="false"/> | |
| 7323 <param name="keep_best_score_id" value="false"/> | |
| 7324 <param name="sequences_whitelist" value=""/> | |
| 7325 <param name="sequence_comparison_method" value="substring"/> | |
| 7326 <param name="accessions_whitelist" value=""/> | |
| 7327 <param name="remove_annotated_features" value="false"/> | |
| 7328 <param name="remove_unannotated_features" value="false"/> | |
| 7329 <param name="remove_unassigned_ids" value="false"/> | |
| 7330 <param name="rt" value="0.1"/> | |
| 7331 <param name="mz" value="0.001"/> | |
| 7332 <param name="blacklist_imperfect" value="false"/> | |
| 7333 </section> | |
| 7334 <section name="algorithm"> | |
| 7335 <section name="SignalToNoise"> | |
| 7336 <param name="max_intensity" value="-1"/> | |
| 7337 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7338 <param name="auto_max_percentile" value="95"/> | |
| 7339 <param name="auto_mode" value="0"/> | |
| 7340 <param name="win_len" value="200.0"/> | |
| 7341 <param name="bin_count" value="30"/> | |
| 7342 <param name="min_required_elements" value="10"/> | |
| 7343 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7344 <param name="write_log_messages" value="true"/> | |
| 7345 </section> | |
| 7346 </section> | |
| 7347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7348 <output name="ctd_out" ftype="xml"> | |
| 7349 <assert_contents> | |
| 7350 <is_valid_xml/> | |
| 7351 </assert_contents> | |
| 7352 </output> | |
| 7353 </test> | |
| 7354 <test expect_num_outputs="2"> | |
| 7355 <conditional name="adv_opts_cond"> | |
| 7356 <param name="adv_opts_selector" value="advanced"/> | |
| 7357 <param name="force" value="false"/> | |
| 7358 <param name="test" value="true"/> | |
| 7359 </conditional> | |
| 7360 <param name="in" value="FileFilter_22_input.consensusXML"/> | |
| 7361 <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 7362 <param name="out_type" value="consensusxml"/> | |
| 7363 <param name="rt" value=":"/> | |
| 7364 <param name="mz" value=":"/> | |
| 7365 <param name="int" value=":"/> | |
| 7366 <param name="sort" value="false"/> | |
| 7367 <section name="peak_options"> | |
| 7368 <param name="sn" value="0.0"/> | |
| 7369 <param name="rm_pc_charge" value=""/> | |
| 7370 <param name="pc_mz_range" value=":"/> | |
| 7371 <param name="pc_mz_list" value=""/> | |
| 7372 <param name="level" value="1 2 3"/> | |
| 7373 <param name="sort_peaks" value="false"/> | |
| 7374 <param name="no_chromatograms" value="false"/> | |
| 7375 <param name="remove_chromatograms" value="false"/> | |
| 7376 <param name="remove_empty" value="false"/> | |
| 7377 <param name="mz_precision" value="64"/> | |
| 7378 <param name="int_precision" value="32"/> | |
| 7379 <param name="indexed_file" value="true"/> | |
| 7380 <param name="zlib_compression" value="false"/> | |
| 7381 <section name="numpress"> | |
| 7382 <param name="masstime" value="none"/> | |
| 7383 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7384 <param name="intensity" value="none"/> | |
| 7385 <param name="float_da" value="none"/> | |
| 7386 </section> | |
| 7387 </section> | |
| 7388 <section name="spectra"> | |
| 7389 <param name="remove_zoom" value="false"/> | |
| 7390 <param name="remove_mode" value=""/> | |
| 7391 <param name="remove_activation" value=""/> | |
| 7392 <param name="remove_collision_energy" value=":"/> | |
| 7393 <param name="remove_isolation_window_width" value=":"/> | |
| 7394 <param name="select_zoom" value="false"/> | |
| 7395 <param name="select_mode" value=""/> | |
| 7396 <param name="select_activation" value=""/> | |
| 7397 <param name="select_collision_energy" value=":"/> | |
| 7398 <param name="select_isolation_window_width" value=":"/> | |
| 7399 <param name="select_polarity" value=""/> | |
| 7400 <section name="blackorwhitelist"> | |
| 7401 <param name="similarity_threshold" value="-1.0"/> | |
| 7402 <param name="rt" value="0.01"/> | |
| 7403 <param name="mz" value="0.01"/> | |
| 7404 <param name="use_ppm_tolerance" value="false"/> | |
| 7405 <param name="blacklist" value="true"/> | |
| 7406 </section> | |
| 7407 </section> | |
| 7408 <section name="feature"> | |
| 7409 <param name="q" value=":"/> | |
| 7410 </section> | |
| 7411 <section name="consensus"> | |
| 7412 <param name="map" value=""/> | |
| 7413 <param name="map_and" value="false"/> | |
| 7414 <section name="blackorwhitelist"> | |
| 7415 <param name="blacklist" value="true"/> | |
| 7416 <param name="maps" value=""/> | |
| 7417 <param name="rt" value="60.0"/> | |
| 7418 <param name="mz" value="0.01"/> | |
| 7419 <param name="use_ppm_tolerance" value="false"/> | |
| 7420 </section> | |
| 7421 </section> | |
| 7422 <section name="f_and_c"> | |
| 7423 <param name="charge" value=":"/> | |
| 7424 <param name="size" value=":"/> | |
| 7425 <param name="remove_meta" value=""distinct_charges_size" "gt" "2""/> | |
| 7426 </section> | |
| 7427 <section name="id"> | |
| 7428 <param name="remove_clashes" value="false"/> | |
| 7429 <param name="keep_best_score_id" value="false"/> | |
| 7430 <param name="sequences_whitelist" value=""/> | |
| 7431 <param name="sequence_comparison_method" value="substring"/> | |
| 7432 <param name="accessions_whitelist" value=""/> | |
| 7433 <param name="remove_annotated_features" value="false"/> | |
| 7434 <param name="remove_unannotated_features" value="false"/> | |
| 7435 <param name="remove_unassigned_ids" value="false"/> | |
| 7436 <param name="rt" value="0.1"/> | |
| 7437 <param name="mz" value="0.001"/> | |
| 7438 <param name="blacklist_imperfect" value="false"/> | |
| 7439 </section> | |
| 7440 <section name="algorithm"> | |
| 7441 <section name="SignalToNoise"> | |
| 7442 <param name="max_intensity" value="-1"/> | |
| 7443 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7444 <param name="auto_max_percentile" value="95"/> | |
| 7445 <param name="auto_mode" value="0"/> | |
| 7446 <param name="win_len" value="200.0"/> | |
| 7447 <param name="bin_count" value="30"/> | |
| 7448 <param name="min_required_elements" value="10"/> | |
| 7449 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7450 <param name="write_log_messages" value="true"/> | |
| 7451 </section> | |
| 7452 </section> | |
| 7453 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7454 <output name="ctd_out" ftype="xml"> | |
| 7455 <assert_contents> | |
| 7456 <is_valid_xml/> | |
| 7457 </assert_contents> | |
| 7458 </output> | |
| 7459 </test> | |
| 7460 <test expect_num_outputs="2"> | |
| 7461 <conditional name="adv_opts_cond"> | |
| 7462 <param name="adv_opts_selector" value="advanced"/> | |
| 7463 <param name="force" value="false"/> | |
| 7464 <param name="test" value="true"/> | |
| 7465 </conditional> | |
| 7466 <param name="in" value="FileFilter_22_input.consensusXML"/> | |
| 7467 <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 7468 <param name="out_type" value="consensusxml"/> | |
| 7469 <param name="rt" value=":"/> | |
| 7470 <param name="mz" value=":"/> | |
| 7471 <param name="int" value=":"/> | |
| 7472 <param name="sort" value="false"/> | |
| 7473 <section name="peak_options"> | |
| 7474 <param name="sn" value="0.0"/> | |
| 7475 <param name="rm_pc_charge" value=""/> | |
| 7476 <param name="pc_mz_range" value=":"/> | |
| 7477 <param name="pc_mz_list" value=""/> | |
| 7478 <param name="level" value="1 2 3"/> | |
| 7479 <param name="sort_peaks" value="false"/> | |
| 7480 <param name="no_chromatograms" value="false"/> | |
| 7481 <param name="remove_chromatograms" value="false"/> | |
| 7482 <param name="remove_empty" value="false"/> | |
| 7483 <param name="mz_precision" value="64"/> | |
| 7484 <param name="int_precision" value="32"/> | |
| 7485 <param name="indexed_file" value="true"/> | |
| 7486 <param name="zlib_compression" value="false"/> | |
| 7487 <section name="numpress"> | |
| 7488 <param name="masstime" value="none"/> | |
| 7489 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7490 <param name="intensity" value="none"/> | |
| 7491 <param name="float_da" value="none"/> | |
| 7492 </section> | |
| 7493 </section> | |
| 7494 <section name="spectra"> | |
| 7495 <param name="remove_zoom" value="false"/> | |
| 7496 <param name="remove_mode" value=""/> | |
| 7497 <param name="remove_activation" value=""/> | |
| 7498 <param name="remove_collision_energy" value=":"/> | |
| 7499 <param name="remove_isolation_window_width" value=":"/> | |
| 7500 <param name="select_zoom" value="false"/> | |
| 7501 <param name="select_mode" value=""/> | |
| 7502 <param name="select_activation" value=""/> | |
| 7503 <param name="select_collision_energy" value=":"/> | |
| 7504 <param name="select_isolation_window_width" value=":"/> | |
| 7505 <param name="select_polarity" value=""/> | |
| 7506 <section name="blackorwhitelist"> | |
| 7507 <param name="similarity_threshold" value="-1.0"/> | |
| 7508 <param name="rt" value="0.01"/> | |
| 7509 <param name="mz" value="0.01"/> | |
| 7510 <param name="use_ppm_tolerance" value="false"/> | |
| 7511 <param name="blacklist" value="true"/> | |
| 7512 </section> | |
| 7513 </section> | |
| 7514 <section name="feature"> | |
| 7515 <param name="q" value=":"/> | |
| 7516 </section> | |
| 7517 <section name="consensus"> | |
| 7518 <param name="map" value=""/> | |
| 7519 <param name="map_and" value="false"/> | |
| 7520 <section name="blackorwhitelist"> | |
| 7521 <param name="blacklist" value="true"/> | |
| 7522 <param name="maps" value=""/> | |
| 7523 <param name="rt" value="60.0"/> | |
| 7524 <param name="mz" value="0.01"/> | |
| 7525 <param name="use_ppm_tolerance" value="false"/> | |
| 7526 </section> | |
| 7527 </section> | |
| 7528 <section name="f_and_c"> | |
| 7529 <param name="charge" value=":"/> | |
| 7530 <param name="size" value=":"/> | |
| 7531 <param name="remove_meta" value=""DOESNOTEXIST" "lt" "whatever""/> | |
| 7532 </section> | |
| 7533 <section name="id"> | |
| 7534 <param name="remove_clashes" value="false"/> | |
| 7535 <param name="keep_best_score_id" value="false"/> | |
| 7536 <param name="sequences_whitelist" value=""/> | |
| 7537 <param name="sequence_comparison_method" value="substring"/> | |
| 7538 <param name="accessions_whitelist" value=""/> | |
| 7539 <param name="remove_annotated_features" value="false"/> | |
| 7540 <param name="remove_unannotated_features" value="false"/> | |
| 7541 <param name="remove_unassigned_ids" value="false"/> | |
| 7542 <param name="rt" value="0.1"/> | |
| 7543 <param name="mz" value="0.001"/> | |
| 7544 <param name="blacklist_imperfect" value="false"/> | |
| 7545 </section> | |
| 7546 <section name="algorithm"> | |
| 7547 <section name="SignalToNoise"> | |
| 7548 <param name="max_intensity" value="-1"/> | |
| 7549 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7550 <param name="auto_max_percentile" value="95"/> | |
| 7551 <param name="auto_mode" value="0"/> | |
| 7552 <param name="win_len" value="200.0"/> | |
| 7553 <param name="bin_count" value="30"/> | |
| 7554 <param name="min_required_elements" value="10"/> | |
| 7555 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7556 <param name="write_log_messages" value="true"/> | |
| 7557 </section> | |
| 7558 </section> | |
| 7559 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7560 <output name="ctd_out" ftype="xml"> | |
| 7561 <assert_contents> | |
| 7562 <is_valid_xml/> | |
| 7563 </assert_contents> | |
| 7564 </output> | |
| 7565 </test> | |
| 7566 <test expect_num_outputs="2"> | |
| 7567 <conditional name="adv_opts_cond"> | |
| 7568 <param name="adv_opts_selector" value="advanced"/> | |
| 7569 <param name="force" value="false"/> | |
| 7570 <param name="test" value="true"/> | |
| 7571 </conditional> | |
| 7572 <param name="in" value="FileFilter_25_input.mzML.gz"/> | |
| 7573 <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 7574 <param name="out_type" value="mzml"/> | |
| 7575 <param name="rt" value=":"/> | |
| 7576 <param name="mz" value=":"/> | |
| 7577 <param name="int" value=":"/> | |
| 7578 <param name="sort" value="false"/> | |
| 7579 <section name="peak_options"> | |
| 7580 <param name="sn" value="0.0"/> | |
| 7581 <param name="rm_pc_charge" value=""/> | |
| 7582 <param name="pc_mz_range" value=":"/> | |
| 7583 <param name="pc_mz_list" value=""/> | |
| 7584 <param name="level" value="1 2 3"/> | |
| 7585 <param name="sort_peaks" value="false"/> | |
| 7586 <param name="no_chromatograms" value="false"/> | |
| 7587 <param name="remove_chromatograms" value="false"/> | |
| 7588 <param name="remove_empty" value="false"/> | |
| 7589 <param name="mz_precision" value="64"/> | |
| 7590 <param name="int_precision" value="32"/> | |
| 7591 <param name="indexed_file" value="true"/> | |
| 7592 <param name="zlib_compression" value="false"/> | |
| 7593 <section name="numpress"> | |
| 7594 <param name="masstime" value="none"/> | |
| 7595 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7596 <param name="intensity" value="none"/> | |
| 7597 <param name="float_da" value="none"/> | |
| 7598 </section> | |
| 7599 </section> | |
| 7600 <section name="spectra"> | |
| 7601 <param name="remove_zoom" value="false"/> | |
| 7602 <param name="remove_mode" value=""/> | |
| 7603 <param name="remove_activation" value=""/> | |
| 7604 <param name="remove_collision_energy" value=":"/> | |
| 7605 <param name="remove_isolation_window_width" value=":"/> | |
| 7606 <param name="select_zoom" value="false"/> | |
| 7607 <param name="select_mode" value=""/> | |
| 7608 <param name="select_activation" value=""/> | |
| 7609 <param name="select_collision_energy" value=":"/> | |
| 7610 <param name="select_isolation_window_width" value=":"/> | |
| 7611 <param name="select_polarity" value=""/> | |
| 7612 <section name="blackorwhitelist"> | |
| 7613 <param name="similarity_threshold" value="-1.0"/> | |
| 7614 <param name="rt" value="0.01"/> | |
| 7615 <param name="mz" value="0.01"/> | |
| 7616 <param name="use_ppm_tolerance" value="false"/> | |
| 7617 <param name="blacklist" value="true"/> | |
| 7618 </section> | |
| 7619 </section> | |
| 7620 <section name="feature"> | |
| 7621 <param name="q" value=":"/> | |
| 7622 </section> | |
| 7623 <section name="consensus"> | |
| 7624 <param name="map" value=""/> | |
| 7625 <param name="map_and" value="false"/> | |
| 7626 <section name="blackorwhitelist"> | |
| 7627 <param name="blacklist" value="true"/> | |
| 7628 <param name="maps" value=""/> | |
| 7629 <param name="rt" value="60.0"/> | |
| 7630 <param name="mz" value="0.01"/> | |
| 7631 <param name="use_ppm_tolerance" value="false"/> | |
| 7632 </section> | |
| 7633 </section> | |
| 7634 <section name="f_and_c"> | |
| 7635 <param name="charge" value=":"/> | |
| 7636 <param name="size" value=":"/> | |
| 7637 <param name="remove_meta" value=""/> | |
| 7638 </section> | |
| 7639 <section name="id"> | |
| 7640 <param name="remove_clashes" value="false"/> | |
| 7641 <param name="keep_best_score_id" value="false"/> | |
| 7642 <param name="sequences_whitelist" value=""/> | |
| 7643 <param name="sequence_comparison_method" value="substring"/> | |
| 7644 <param name="accessions_whitelist" value=""/> | |
| 7645 <param name="remove_annotated_features" value="false"/> | |
| 7646 <param name="remove_unannotated_features" value="false"/> | |
| 7647 <param name="remove_unassigned_ids" value="false"/> | |
| 7648 <param name="blacklist" value="FileFilter_25_input.idXML"/> | |
| 7649 <param name="rt" value="1.0"/> | |
| 7650 <param name="mz" value="0.05"/> | |
| 7651 <param name="blacklist_imperfect" value="true"/> | |
| 7652 </section> | |
| 7653 <section name="algorithm"> | |
| 7654 <section name="SignalToNoise"> | |
| 7655 <param name="max_intensity" value="-1"/> | |
| 7656 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7657 <param name="auto_max_percentile" value="95"/> | |
| 7658 <param name="auto_mode" value="0"/> | |
| 7659 <param name="win_len" value="200.0"/> | |
| 7660 <param name="bin_count" value="30"/> | |
| 7661 <param name="min_required_elements" value="10"/> | |
| 7662 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7663 <param name="write_log_messages" value="true"/> | |
| 7664 </section> | |
| 7665 </section> | |
| 7666 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7667 <output name="ctd_out" ftype="xml"> | |
| 7668 <assert_contents> | |
| 7669 <is_valid_xml/> | |
| 7670 </assert_contents> | |
| 7671 </output> | |
| 7672 </test> | |
| 7673 <test expect_num_outputs="2"> | |
| 7674 <conditional name="adv_opts_cond"> | |
| 7675 <param name="adv_opts_selector" value="advanced"/> | |
| 7676 <param name="force" value="false"/> | |
| 7677 <param name="test" value="true"/> | |
| 7678 </conditional> | |
| 7679 <param name="in" value="FileFilter_25_input.mzML.gz"/> | |
| 7680 <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 7681 <param name="out_type" value="mzml"/> | |
| 7682 <param name="rt" value=":"/> | |
| 7683 <param name="mz" value=":"/> | |
| 7684 <param name="int" value=":"/> | |
| 7685 <param name="sort" value="false"/> | |
| 7686 <section name="peak_options"> | |
| 7687 <param name="sn" value="0.0"/> | |
| 7688 <param name="rm_pc_charge" value=""/> | |
| 7689 <param name="pc_mz_range" value=":"/> | |
| 7690 <param name="pc_mz_list" value=""/> | |
| 7691 <param name="level" value="1 2 3"/> | |
| 7692 <param name="sort_peaks" value="false"/> | |
| 7693 <param name="no_chromatograms" value="false"/> | |
| 7694 <param name="remove_chromatograms" value="false"/> | |
| 7695 <param name="remove_empty" value="false"/> | |
| 7696 <param name="mz_precision" value="64"/> | |
| 7697 <param name="int_precision" value="32"/> | |
| 7698 <param name="indexed_file" value="true"/> | |
| 7699 <param name="zlib_compression" value="false"/> | |
| 7700 <section name="numpress"> | |
| 7701 <param name="masstime" value="none"/> | |
| 7702 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7703 <param name="intensity" value="none"/> | |
| 7704 <param name="float_da" value="none"/> | |
| 7705 </section> | |
| 7706 </section> | |
| 7707 <section name="spectra"> | |
| 7708 <param name="remove_zoom" value="false"/> | |
| 7709 <param name="remove_mode" value=""/> | |
| 7710 <param name="remove_activation" value=""/> | |
| 7711 <param name="remove_collision_energy" value=":"/> | |
| 7712 <param name="remove_isolation_window_width" value=":"/> | |
| 7713 <param name="select_zoom" value="false"/> | |
| 7714 <param name="select_mode" value=""/> | |
| 7715 <param name="select_activation" value=""/> | |
| 7716 <param name="select_collision_energy" value=":"/> | |
| 7717 <param name="select_isolation_window_width" value=":"/> | |
| 7718 <param name="select_polarity" value=""/> | |
| 7719 <section name="blackorwhitelist"> | |
| 7720 <param name="similarity_threshold" value="-1.0"/> | |
| 7721 <param name="rt" value="0.01"/> | |
| 7722 <param name="mz" value="0.01"/> | |
| 7723 <param name="use_ppm_tolerance" value="false"/> | |
| 7724 <param name="blacklist" value="true"/> | |
| 7725 </section> | |
| 7726 </section> | |
| 7727 <section name="feature"> | |
| 7728 <param name="q" value=":"/> | |
| 7729 </section> | |
| 7730 <section name="consensus"> | |
| 7731 <param name="map" value=""/> | |
| 7732 <param name="map_and" value="false"/> | |
| 7733 <section name="blackorwhitelist"> | |
| 7734 <param name="blacklist" value="true"/> | |
| 7735 <param name="maps" value=""/> | |
| 7736 <param name="rt" value="60.0"/> | |
| 7737 <param name="mz" value="0.01"/> | |
| 7738 <param name="use_ppm_tolerance" value="false"/> | |
| 7739 </section> | |
| 7740 </section> | |
| 7741 <section name="f_and_c"> | |
| 7742 <param name="charge" value=":"/> | |
| 7743 <param name="size" value=":"/> | |
| 7744 <param name="remove_meta" value=""/> | |
| 7745 </section> | |
| 7746 <section name="id"> | |
| 7747 <param name="remove_clashes" value="false"/> | |
| 7748 <param name="keep_best_score_id" value="false"/> | |
| 7749 <param name="sequences_whitelist" value=""/> | |
| 7750 <param name="sequence_comparison_method" value="substring"/> | |
| 7751 <param name="accessions_whitelist" value=""/> | |
| 7752 <param name="remove_annotated_features" value="false"/> | |
| 7753 <param name="remove_unannotated_features" value="false"/> | |
| 7754 <param name="remove_unassigned_ids" value="false"/> | |
| 7755 <param name="blacklist" value="FileFilter_25_input.idXML"/> | |
| 7756 <param name="rt" value="0.1"/> | |
| 7757 <param name="mz" value="0.001"/> | |
| 7758 <param name="blacklist_imperfect" value="true"/> | |
| 7759 </section> | |
| 7760 <section name="algorithm"> | |
| 7761 <section name="SignalToNoise"> | |
| 7762 <param name="max_intensity" value="-1"/> | |
| 7763 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7764 <param name="auto_max_percentile" value="95"/> | |
| 7765 <param name="auto_mode" value="0"/> | |
| 7766 <param name="win_len" value="200.0"/> | |
| 7767 <param name="bin_count" value="30"/> | |
| 7768 <param name="min_required_elements" value="10"/> | |
| 7769 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7770 <param name="write_log_messages" value="true"/> | |
| 7771 </section> | |
| 7772 </section> | |
| 7773 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7774 <output name="ctd_out" ftype="xml"> | |
| 7775 <assert_contents> | |
| 7776 <is_valid_xml/> | |
| 7777 </assert_contents> | |
| 7778 </output> | |
| 7779 </test> | |
| 7780 <test expect_num_outputs="2"> | |
| 7781 <conditional name="adv_opts_cond"> | |
| 7782 <param name="adv_opts_selector" value="advanced"/> | |
| 7783 <param name="force" value="false"/> | |
| 7784 <param name="test" value="true"/> | |
| 7785 </conditional> | |
| 7786 <param name="in" value="FileFilter_28_input.mzML.gz"/> | |
| 7787 <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 7788 <param name="out_type" value="mzml"/> | |
| 7789 <param name="rt" value=":"/> | |
| 7790 <param name="mz" value=":"/> | |
| 7791 <param name="int" value=":"/> | |
| 7792 <param name="sort" value="false"/> | |
| 7793 <section name="peak_options"> | |
| 7794 <param name="sn" value="0.0"/> | |
| 7795 <param name="rm_pc_charge" value=""/> | |
| 7796 <param name="pc_mz_range" value="832:836"/> | |
| 7797 <param name="pc_mz_list" value=""/> | |
| 7798 <param name="level" value="2"/> | |
| 7799 <param name="sort_peaks" value="false"/> | |
| 7800 <param name="no_chromatograms" value="false"/> | |
| 7801 <param name="remove_chromatograms" value="false"/> | |
| 7802 <param name="remove_empty" value="false"/> | |
| 7803 <param name="mz_precision" value="64"/> | |
| 7804 <param name="int_precision" value="32"/> | |
| 7805 <param name="indexed_file" value="true"/> | |
| 7806 <param name="zlib_compression" value="false"/> | |
| 7807 <section name="numpress"> | |
| 7808 <param name="masstime" value="none"/> | |
| 7809 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7810 <param name="intensity" value="none"/> | |
| 7811 <param name="float_da" value="none"/> | |
| 7812 </section> | |
| 7813 </section> | |
| 7814 <section name="spectra"> | |
| 7815 <param name="remove_zoom" value="false"/> | |
| 7816 <param name="remove_mode" value=""/> | |
| 7817 <param name="remove_activation" value=""/> | |
| 7818 <param name="remove_collision_energy" value=":"/> | |
| 7819 <param name="remove_isolation_window_width" value=":"/> | |
| 7820 <param name="select_zoom" value="false"/> | |
| 7821 <param name="select_mode" value=""/> | |
| 7822 <param name="select_activation" value=""/> | |
| 7823 <param name="select_collision_energy" value=":"/> | |
| 7824 <param name="select_isolation_window_width" value=":"/> | |
| 7825 <param name="select_polarity" value=""/> | |
| 7826 <section name="blackorwhitelist"> | |
| 7827 <param name="similarity_threshold" value="-1.0"/> | |
| 7828 <param name="rt" value="0.01"/> | |
| 7829 <param name="mz" value="0.01"/> | |
| 7830 <param name="use_ppm_tolerance" value="false"/> | |
| 7831 <param name="blacklist" value="true"/> | |
| 7832 </section> | |
| 7833 </section> | |
| 7834 <section name="feature"> | |
| 7835 <param name="q" value=":"/> | |
| 7836 </section> | |
| 7837 <section name="consensus"> | |
| 7838 <param name="map" value=""/> | |
| 7839 <param name="map_and" value="false"/> | |
| 7840 <section name="blackorwhitelist"> | |
| 7841 <param name="blacklist" value="true"/> | |
| 7842 <param name="maps" value=""/> | |
| 7843 <param name="rt" value="60.0"/> | |
| 7844 <param name="mz" value="0.01"/> | |
| 7845 <param name="use_ppm_tolerance" value="false"/> | |
| 7846 </section> | |
| 7847 </section> | |
| 7848 <section name="f_and_c"> | |
| 7849 <param name="charge" value=":"/> | |
| 7850 <param name="size" value=":"/> | |
| 7851 <param name="remove_meta" value=""/> | |
| 7852 </section> | |
| 7853 <section name="id"> | |
| 7854 <param name="remove_clashes" value="false"/> | |
| 7855 <param name="keep_best_score_id" value="false"/> | |
| 7856 <param name="sequences_whitelist" value=""/> | |
| 7857 <param name="sequence_comparison_method" value="substring"/> | |
| 7858 <param name="accessions_whitelist" value=""/> | |
| 7859 <param name="remove_annotated_features" value="false"/> | |
| 7860 <param name="remove_unannotated_features" value="false"/> | |
| 7861 <param name="remove_unassigned_ids" value="false"/> | |
| 7862 <param name="rt" value="0.1"/> | |
| 7863 <param name="mz" value="0.001"/> | |
| 7864 <param name="blacklist_imperfect" value="false"/> | |
| 7865 </section> | |
| 7866 <section name="algorithm"> | |
| 7867 <section name="SignalToNoise"> | |
| 7868 <param name="max_intensity" value="-1"/> | |
| 7869 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7870 <param name="auto_max_percentile" value="95"/> | |
| 7871 <param name="auto_mode" value="0"/> | |
| 7872 <param name="win_len" value="200.0"/> | |
| 7873 <param name="bin_count" value="30"/> | |
| 7874 <param name="min_required_elements" value="10"/> | |
| 7875 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7876 <param name="write_log_messages" value="true"/> | |
| 7877 </section> | |
| 7878 </section> | |
| 7879 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7880 <output name="ctd_out" ftype="xml"> | |
| 7881 <assert_contents> | |
| 7882 <is_valid_xml/> | |
| 7883 </assert_contents> | |
| 7884 </output> | |
| 7885 </test> | |
| 7886 <test expect_num_outputs="2"> | |
| 7887 <conditional name="adv_opts_cond"> | |
| 7888 <param name="adv_opts_selector" value="advanced"/> | |
| 7889 <param name="force" value="false"/> | |
| 7890 <param name="test" value="true"/> | |
| 7891 </conditional> | |
| 7892 <param name="in" value="FileFilter_28_input.mzML.gz"/> | |
| 7893 <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 7894 <param name="out_type" value="mzml"/> | |
| 7895 <param name="rt" value=":"/> | |
| 7896 <param name="mz" value=":"/> | |
| 7897 <param name="int" value=":"/> | |
| 7898 <param name="sort" value="false"/> | |
| 7899 <section name="peak_options"> | |
| 7900 <param name="sn" value="0.0"/> | |
| 7901 <param name="rm_pc_charge" value=""/> | |
| 7902 <param name="pc_mz_range" value="832:836"/> | |
| 7903 <param name="pc_mz_list" value=""/> | |
| 7904 <param name="level" value="1 2"/> | |
| 7905 <param name="sort_peaks" value="false"/> | |
| 7906 <param name="no_chromatograms" value="false"/> | |
| 7907 <param name="remove_chromatograms" value="false"/> | |
| 7908 <param name="remove_empty" value="false"/> | |
| 7909 <param name="mz_precision" value="64"/> | |
| 7910 <param name="int_precision" value="32"/> | |
| 7911 <param name="indexed_file" value="true"/> | |
| 7912 <param name="zlib_compression" value="false"/> | |
| 7913 <section name="numpress"> | |
| 7914 <param name="masstime" value="none"/> | |
| 7915 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 7916 <param name="intensity" value="none"/> | |
| 7917 <param name="float_da" value="none"/> | |
| 7918 </section> | |
| 7919 </section> | |
| 7920 <section name="spectra"> | |
| 7921 <param name="remove_zoom" value="false"/> | |
| 7922 <param name="remove_mode" value=""/> | |
| 7923 <param name="remove_activation" value=""/> | |
| 7924 <param name="remove_collision_energy" value=":"/> | |
| 7925 <param name="remove_isolation_window_width" value=":"/> | |
| 7926 <param name="select_zoom" value="false"/> | |
| 7927 <param name="select_mode" value=""/> | |
| 7928 <param name="select_activation" value=""/> | |
| 7929 <param name="select_collision_energy" value=":"/> | |
| 7930 <param name="select_isolation_window_width" value=":"/> | |
| 7931 <param name="select_polarity" value=""/> | |
| 7932 <section name="blackorwhitelist"> | |
| 7933 <param name="similarity_threshold" value="-1.0"/> | |
| 7934 <param name="rt" value="0.01"/> | |
| 7935 <param name="mz" value="0.01"/> | |
| 7936 <param name="use_ppm_tolerance" value="false"/> | |
| 7937 <param name="blacklist" value="true"/> | |
| 7938 </section> | |
| 7939 </section> | |
| 7940 <section name="feature"> | |
| 7941 <param name="q" value=":"/> | |
| 7942 </section> | |
| 7943 <section name="consensus"> | |
| 7944 <param name="map" value=""/> | |
| 7945 <param name="map_and" value="false"/> | |
| 7946 <section name="blackorwhitelist"> | |
| 7947 <param name="blacklist" value="true"/> | |
| 7948 <param name="maps" value=""/> | |
| 7949 <param name="rt" value="60.0"/> | |
| 7950 <param name="mz" value="0.01"/> | |
| 7951 <param name="use_ppm_tolerance" value="false"/> | |
| 7952 </section> | |
| 7953 </section> | |
| 7954 <section name="f_and_c"> | |
| 7955 <param name="charge" value=":"/> | |
| 7956 <param name="size" value=":"/> | |
| 7957 <param name="remove_meta" value=""/> | |
| 7958 </section> | |
| 7959 <section name="id"> | |
| 7960 <param name="remove_clashes" value="false"/> | |
| 7961 <param name="keep_best_score_id" value="false"/> | |
| 7962 <param name="sequences_whitelist" value=""/> | |
| 7963 <param name="sequence_comparison_method" value="substring"/> | |
| 7964 <param name="accessions_whitelist" value=""/> | |
| 7965 <param name="remove_annotated_features" value="false"/> | |
| 7966 <param name="remove_unannotated_features" value="false"/> | |
| 7967 <param name="remove_unassigned_ids" value="false"/> | |
| 7968 <param name="rt" value="0.1"/> | |
| 7969 <param name="mz" value="0.001"/> | |
| 7970 <param name="blacklist_imperfect" value="false"/> | |
| 7971 </section> | |
| 7972 <section name="algorithm"> | |
| 7973 <section name="SignalToNoise"> | |
| 7974 <param name="max_intensity" value="-1"/> | |
| 7975 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 7976 <param name="auto_max_percentile" value="95"/> | |
| 7977 <param name="auto_mode" value="0"/> | |
| 7978 <param name="win_len" value="200.0"/> | |
| 7979 <param name="bin_count" value="30"/> | |
| 7980 <param name="min_required_elements" value="10"/> | |
| 7981 <param name="noise_for_empty_window" value="1e+20"/> | |
| 7982 <param name="write_log_messages" value="true"/> | |
| 7983 </section> | |
| 7984 </section> | |
| 7985 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 7986 <output name="ctd_out" ftype="xml"> | |
| 7987 <assert_contents> | |
| 7988 <is_valid_xml/> | |
| 7989 </assert_contents> | |
| 7990 </output> | |
| 7991 </test> | |
| 7992 <test expect_num_outputs="2"> | |
| 7993 <conditional name="adv_opts_cond"> | |
| 7994 <param name="adv_opts_selector" value="advanced"/> | |
| 7995 <param name="force" value="false"/> | |
| 7996 <param name="test" value="true"/> | |
| 7997 </conditional> | |
| 7998 <param name="in" value="FileFilter_28_input.mzML.gz"/> | |
| 7999 <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8000 <param name="out_type" value="mzml"/> | |
| 8001 <param name="rt" value=":"/> | |
| 8002 <param name="mz" value=":"/> | |
| 8003 <param name="int" value=":"/> | |
| 8004 <param name="sort" value="false"/> | |
| 8005 <section name="peak_options"> | |
| 8006 <param name="sn" value="0.0"/> | |
| 8007 <param name="rm_pc_charge" value=""/> | |
| 8008 <param name="pc_mz_range" value="832:836"/> | |
| 8009 <param name="pc_mz_list" value=""/> | |
| 8010 <param name="level" value="1 2"/> | |
| 8011 <param name="sort_peaks" value="false"/> | |
| 8012 <param name="no_chromatograms" value="false"/> | |
| 8013 <param name="remove_chromatograms" value="false"/> | |
| 8014 <param name="remove_empty" value="false"/> | |
| 8015 <param name="mz_precision" value="64"/> | |
| 8016 <param name="int_precision" value="32"/> | |
| 8017 <param name="indexed_file" value="true"/> | |
| 8018 <param name="zlib_compression" value="false"/> | |
| 8019 <section name="numpress"> | |
| 8020 <param name="masstime" value="none"/> | |
| 8021 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8022 <param name="intensity" value="none"/> | |
| 8023 <param name="float_da" value="none"/> | |
| 8024 </section> | |
| 8025 </section> | |
| 8026 <section name="spectra"> | |
| 8027 <param name="remove_zoom" value="false"/> | |
| 8028 <param name="remove_mode" value=""/> | |
| 8029 <param name="remove_activation" value=""/> | |
| 8030 <param name="remove_collision_energy" value=":"/> | |
| 8031 <param name="remove_isolation_window_width" value=":"/> | |
| 8032 <param name="select_zoom" value="false"/> | |
| 8033 <param name="select_mode" value=""/> | |
| 8034 <param name="select_activation" value=""/> | |
| 8035 <param name="select_collision_energy" value=":"/> | |
| 8036 <param name="select_isolation_window_width" value=":"/> | |
| 8037 <param name="select_polarity" value=""/> | |
| 8038 <section name="blackorwhitelist"> | |
| 8039 <param name="similarity_threshold" value="-1.0"/> | |
| 8040 <param name="rt" value="0.01"/> | |
| 8041 <param name="mz" value="0.01"/> | |
| 8042 <param name="use_ppm_tolerance" value="false"/> | |
| 8043 <param name="blacklist" value="true"/> | |
| 8044 </section> | |
| 8045 </section> | |
| 8046 <section name="feature"> | |
| 8047 <param name="q" value=":"/> | |
| 8048 </section> | |
| 8049 <section name="consensus"> | |
| 8050 <param name="map" value=""/> | |
| 8051 <param name="map_and" value="false"/> | |
| 8052 <section name="blackorwhitelist"> | |
| 8053 <param name="blacklist" value="true"/> | |
| 8054 <param name="maps" value=""/> | |
| 8055 <param name="rt" value="60.0"/> | |
| 8056 <param name="mz" value="0.01"/> | |
| 8057 <param name="use_ppm_tolerance" value="false"/> | |
| 8058 </section> | |
| 8059 </section> | |
| 8060 <section name="f_and_c"> | |
| 8061 <param name="charge" value=":"/> | |
| 8062 <param name="size" value=":"/> | |
| 8063 <param name="remove_meta" value=""/> | |
| 8064 </section> | |
| 8065 <section name="id"> | |
| 8066 <param name="remove_clashes" value="false"/> | |
| 8067 <param name="keep_best_score_id" value="false"/> | |
| 8068 <param name="sequences_whitelist" value=""/> | |
| 8069 <param name="sequence_comparison_method" value="substring"/> | |
| 8070 <param name="accessions_whitelist" value=""/> | |
| 8071 <param name="remove_annotated_features" value="false"/> | |
| 8072 <param name="remove_unannotated_features" value="false"/> | |
| 8073 <param name="remove_unassigned_ids" value="false"/> | |
| 8074 <param name="rt" value="0.1"/> | |
| 8075 <param name="mz" value="0.001"/> | |
| 8076 <param name="blacklist_imperfect" value="false"/> | |
| 8077 </section> | |
| 8078 <section name="algorithm"> | |
| 8079 <section name="SignalToNoise"> | |
| 8080 <param name="max_intensity" value="-1"/> | |
| 8081 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8082 <param name="auto_max_percentile" value="95"/> | |
| 8083 <param name="auto_mode" value="0"/> | |
| 8084 <param name="win_len" value="200.0"/> | |
| 8085 <param name="bin_count" value="30"/> | |
| 8086 <param name="min_required_elements" value="10"/> | |
| 8087 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8088 <param name="write_log_messages" value="true"/> | |
| 8089 </section> | |
| 8090 </section> | |
| 8091 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8092 <output name="ctd_out" ftype="xml"> | |
| 8093 <assert_contents> | |
| 8094 <is_valid_xml/> | |
| 8095 </assert_contents> | |
| 8096 </output> | |
| 8097 </test> | |
| 8098 <test expect_num_outputs="2"> | |
| 8099 <conditional name="adv_opts_cond"> | |
| 8100 <param name="adv_opts_selector" value="advanced"/> | |
| 8101 <param name="force" value="false"/> | |
| 8102 <param name="test" value="true"/> | |
| 8103 </conditional> | |
| 8104 <param name="in" value="FileFilter_31_34_input.mzML"/> | |
| 8105 <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8106 <param name="out_type" value="mzml"/> | |
| 8107 <param name="rt" value=":"/> | |
| 8108 <param name="mz" value=":"/> | |
| 8109 <param name="int" value=":"/> | |
| 8110 <param name="sort" value="false"/> | |
| 8111 <section name="peak_options"> | |
| 8112 <param name="sn" value="0.0"/> | |
| 8113 <param name="rm_pc_charge" value=""/> | |
| 8114 <param name="pc_mz_range" value=":"/> | |
| 8115 <param name="pc_mz_list" value=""/> | |
| 8116 <param name="level" value="1 2 3"/> | |
| 8117 <param name="sort_peaks" value="false"/> | |
| 8118 <param name="no_chromatograms" value="false"/> | |
| 8119 <param name="remove_chromatograms" value="false"/> | |
| 8120 <param name="remove_empty" value="false"/> | |
| 8121 <param name="mz_precision" value="64"/> | |
| 8122 <param name="int_precision" value="32"/> | |
| 8123 <param name="indexed_file" value="true"/> | |
| 8124 <param name="zlib_compression" value="false"/> | |
| 8125 <section name="numpress"> | |
| 8126 <param name="masstime" value="none"/> | |
| 8127 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8128 <param name="intensity" value="none"/> | |
| 8129 <param name="float_da" value="none"/> | |
| 8130 </section> | |
| 8131 </section> | |
| 8132 <section name="spectra"> | |
| 8133 <param name="remove_zoom" value="false"/> | |
| 8134 <param name="remove_mode" value=""/> | |
| 8135 <param name="remove_activation" value=""/> | |
| 8136 <param name="remove_collision_energy" value=":"/> | |
| 8137 <param name="remove_isolation_window_width" value=":2"/> | |
| 8138 <param name="select_zoom" value="false"/> | |
| 8139 <param name="select_mode" value=""/> | |
| 8140 <param name="select_activation" value=""/> | |
| 8141 <param name="select_collision_energy" value=":"/> | |
| 8142 <param name="select_isolation_window_width" value=":"/> | |
| 8143 <param name="select_polarity" value=""/> | |
| 8144 <section name="blackorwhitelist"> | |
| 8145 <param name="similarity_threshold" value="-1.0"/> | |
| 8146 <param name="rt" value="0.01"/> | |
| 8147 <param name="mz" value="0.01"/> | |
| 8148 <param name="use_ppm_tolerance" value="false"/> | |
| 8149 <param name="blacklist" value="true"/> | |
| 8150 </section> | |
| 8151 </section> | |
| 8152 <section name="feature"> | |
| 8153 <param name="q" value=":"/> | |
| 8154 </section> | |
| 8155 <section name="consensus"> | |
| 8156 <param name="map" value=""/> | |
| 8157 <param name="map_and" value="false"/> | |
| 8158 <section name="blackorwhitelist"> | |
| 8159 <param name="blacklist" value="true"/> | |
| 8160 <param name="maps" value=""/> | |
| 8161 <param name="rt" value="60.0"/> | |
| 8162 <param name="mz" value="0.01"/> | |
| 8163 <param name="use_ppm_tolerance" value="false"/> | |
| 8164 </section> | |
| 8165 </section> | |
| 8166 <section name="f_and_c"> | |
| 8167 <param name="charge" value=":"/> | |
| 8168 <param name="size" value=":"/> | |
| 8169 <param name="remove_meta" value=""/> | |
| 8170 </section> | |
| 8171 <section name="id"> | |
| 8172 <param name="remove_clashes" value="false"/> | |
| 8173 <param name="keep_best_score_id" value="false"/> | |
| 8174 <param name="sequences_whitelist" value=""/> | |
| 8175 <param name="sequence_comparison_method" value="substring"/> | |
| 8176 <param name="accessions_whitelist" value=""/> | |
| 8177 <param name="remove_annotated_features" value="false"/> | |
| 8178 <param name="remove_unannotated_features" value="false"/> | |
| 8179 <param name="remove_unassigned_ids" value="false"/> | |
| 8180 <param name="rt" value="0.1"/> | |
| 8181 <param name="mz" value="0.001"/> | |
| 8182 <param name="blacklist_imperfect" value="false"/> | |
| 8183 </section> | |
| 8184 <section name="algorithm"> | |
| 8185 <section name="SignalToNoise"> | |
| 8186 <param name="max_intensity" value="-1"/> | |
| 8187 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8188 <param name="auto_max_percentile" value="95"/> | |
| 8189 <param name="auto_mode" value="0"/> | |
| 8190 <param name="win_len" value="200.0"/> | |
| 8191 <param name="bin_count" value="30"/> | |
| 8192 <param name="min_required_elements" value="10"/> | |
| 8193 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8194 <param name="write_log_messages" value="true"/> | |
| 8195 </section> | |
| 8196 </section> | |
| 8197 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8198 <output name="ctd_out" ftype="xml"> | |
| 8199 <assert_contents> | |
| 8200 <is_valid_xml/> | |
| 8201 </assert_contents> | |
| 8202 </output> | |
| 8203 </test> | |
| 8204 <test expect_num_outputs="2"> | |
| 8205 <conditional name="adv_opts_cond"> | |
| 8206 <param name="adv_opts_selector" value="advanced"/> | |
| 8207 <param name="force" value="false"/> | |
| 8208 <param name="test" value="true"/> | |
| 8209 </conditional> | |
| 8210 <param name="in" value="FileFilter_31_34_input.mzML"/> | |
| 8211 <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8212 <param name="out_type" value="mzml"/> | |
| 8213 <param name="rt" value=":"/> | |
| 8214 <param name="mz" value=":"/> | |
| 8215 <param name="int" value=":"/> | |
| 8216 <param name="sort" value="false"/> | |
| 8217 <section name="peak_options"> | |
| 8218 <param name="sn" value="0.0"/> | |
| 8219 <param name="rm_pc_charge" value=""/> | |
| 8220 <param name="pc_mz_range" value=":"/> | |
| 8221 <param name="pc_mz_list" value=""/> | |
| 8222 <param name="level" value="1 2 3"/> | |
| 8223 <param name="sort_peaks" value="false"/> | |
| 8224 <param name="no_chromatograms" value="false"/> | |
| 8225 <param name="remove_chromatograms" value="false"/> | |
| 8226 <param name="remove_empty" value="false"/> | |
| 8227 <param name="mz_precision" value="64"/> | |
| 8228 <param name="int_precision" value="32"/> | |
| 8229 <param name="indexed_file" value="true"/> | |
| 8230 <param name="zlib_compression" value="false"/> | |
| 8231 <section name="numpress"> | |
| 8232 <param name="masstime" value="none"/> | |
| 8233 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8234 <param name="intensity" value="none"/> | |
| 8235 <param name="float_da" value="none"/> | |
| 8236 </section> | |
| 8237 </section> | |
| 8238 <section name="spectra"> | |
| 8239 <param name="remove_zoom" value="false"/> | |
| 8240 <param name="remove_mode" value=""/> | |
| 8241 <param name="remove_activation" value=""/> | |
| 8242 <param name="remove_collision_energy" value=":"/> | |
| 8243 <param name="remove_isolation_window_width" value=":"/> | |
| 8244 <param name="select_zoom" value="false"/> | |
| 8245 <param name="select_mode" value=""/> | |
| 8246 <param name="select_activation" value=""/> | |
| 8247 <param name="select_collision_energy" value=":"/> | |
| 8248 <param name="select_isolation_window_width" value=":2"/> | |
| 8249 <param name="select_polarity" value=""/> | |
| 8250 <section name="blackorwhitelist"> | |
| 8251 <param name="similarity_threshold" value="-1.0"/> | |
| 8252 <param name="rt" value="0.01"/> | |
| 8253 <param name="mz" value="0.01"/> | |
| 8254 <param name="use_ppm_tolerance" value="false"/> | |
| 8255 <param name="blacklist" value="true"/> | |
| 8256 </section> | |
| 8257 </section> | |
| 8258 <section name="feature"> | |
| 8259 <param name="q" value=":"/> | |
| 8260 </section> | |
| 8261 <section name="consensus"> | |
| 8262 <param name="map" value=""/> | |
| 8263 <param name="map_and" value="false"/> | |
| 8264 <section name="blackorwhitelist"> | |
| 8265 <param name="blacklist" value="true"/> | |
| 8266 <param name="maps" value=""/> | |
| 8267 <param name="rt" value="60.0"/> | |
| 8268 <param name="mz" value="0.01"/> | |
| 8269 <param name="use_ppm_tolerance" value="false"/> | |
| 8270 </section> | |
| 8271 </section> | |
| 8272 <section name="f_and_c"> | |
| 8273 <param name="charge" value=":"/> | |
| 8274 <param name="size" value=":"/> | |
| 8275 <param name="remove_meta" value=""/> | |
| 8276 </section> | |
| 8277 <section name="id"> | |
| 8278 <param name="remove_clashes" value="false"/> | |
| 8279 <param name="keep_best_score_id" value="false"/> | |
| 8280 <param name="sequences_whitelist" value=""/> | |
| 8281 <param name="sequence_comparison_method" value="substring"/> | |
| 8282 <param name="accessions_whitelist" value=""/> | |
| 8283 <param name="remove_annotated_features" value="false"/> | |
| 8284 <param name="remove_unannotated_features" value="false"/> | |
| 8285 <param name="remove_unassigned_ids" value="false"/> | |
| 8286 <param name="rt" value="0.1"/> | |
| 8287 <param name="mz" value="0.001"/> | |
| 8288 <param name="blacklist_imperfect" value="false"/> | |
| 8289 </section> | |
| 8290 <section name="algorithm"> | |
| 8291 <section name="SignalToNoise"> | |
| 8292 <param name="max_intensity" value="-1"/> | |
| 8293 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8294 <param name="auto_max_percentile" value="95"/> | |
| 8295 <param name="auto_mode" value="0"/> | |
| 8296 <param name="win_len" value="200.0"/> | |
| 8297 <param name="bin_count" value="30"/> | |
| 8298 <param name="min_required_elements" value="10"/> | |
| 8299 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8300 <param name="write_log_messages" value="true"/> | |
| 8301 </section> | |
| 8302 </section> | |
| 8303 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8304 <output name="ctd_out" ftype="xml"> | |
| 8305 <assert_contents> | |
| 8306 <is_valid_xml/> | |
| 8307 </assert_contents> | |
| 8308 </output> | |
| 8309 </test> | |
| 8310 <test expect_num_outputs="2"> | |
| 8311 <conditional name="adv_opts_cond"> | |
| 8312 <param name="adv_opts_selector" value="advanced"/> | |
| 8313 <param name="force" value="false"/> | |
| 8314 <param name="test" value="true"/> | |
| 8315 </conditional> | |
| 8316 <param name="in" value="FileFilter_31_34_input.mzML"/> | |
| 8317 <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8318 <param name="out_type" value="mzml"/> | |
| 8319 <param name="rt" value=":"/> | |
| 8320 <param name="mz" value=":"/> | |
| 8321 <param name="int" value=":"/> | |
| 8322 <param name="sort" value="false"/> | |
| 8323 <section name="peak_options"> | |
| 8324 <param name="sn" value="0.0"/> | |
| 8325 <param name="rm_pc_charge" value=""/> | |
| 8326 <param name="pc_mz_range" value=":"/> | |
| 8327 <param name="pc_mz_list" value=""/> | |
| 8328 <param name="level" value="1 2 3"/> | |
| 8329 <param name="sort_peaks" value="false"/> | |
| 8330 <param name="no_chromatograms" value="false"/> | |
| 8331 <param name="remove_chromatograms" value="false"/> | |
| 8332 <param name="remove_empty" value="false"/> | |
| 8333 <param name="mz_precision" value="64"/> | |
| 8334 <param name="int_precision" value="32"/> | |
| 8335 <param name="indexed_file" value="true"/> | |
| 8336 <param name="zlib_compression" value="false"/> | |
| 8337 <section name="numpress"> | |
| 8338 <param name="masstime" value="none"/> | |
| 8339 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8340 <param name="intensity" value="none"/> | |
| 8341 <param name="float_da" value="none"/> | |
| 8342 </section> | |
| 8343 </section> | |
| 8344 <section name="spectra"> | |
| 8345 <param name="remove_zoom" value="false"/> | |
| 8346 <param name="remove_mode" value=""/> | |
| 8347 <param name="remove_activation" value=""/> | |
| 8348 <param name="remove_collision_energy" value=":35"/> | |
| 8349 <param name="remove_isolation_window_width" value=":"/> | |
| 8350 <param name="select_zoom" value="false"/> | |
| 8351 <param name="select_mode" value=""/> | |
| 8352 <param name="select_activation" value=""/> | |
| 8353 <param name="select_collision_energy" value=":"/> | |
| 8354 <param name="select_isolation_window_width" value=":"/> | |
| 8355 <param name="select_polarity" value=""/> | |
| 8356 <section name="blackorwhitelist"> | |
| 8357 <param name="similarity_threshold" value="-1.0"/> | |
| 8358 <param name="rt" value="0.01"/> | |
| 8359 <param name="mz" value="0.01"/> | |
| 8360 <param name="use_ppm_tolerance" value="false"/> | |
| 8361 <param name="blacklist" value="true"/> | |
| 8362 </section> | |
| 8363 </section> | |
| 8364 <section name="feature"> | |
| 8365 <param name="q" value=":"/> | |
| 8366 </section> | |
| 8367 <section name="consensus"> | |
| 8368 <param name="map" value=""/> | |
| 8369 <param name="map_and" value="false"/> | |
| 8370 <section name="blackorwhitelist"> | |
| 8371 <param name="blacklist" value="true"/> | |
| 8372 <param name="maps" value=""/> | |
| 8373 <param name="rt" value="60.0"/> | |
| 8374 <param name="mz" value="0.01"/> | |
| 8375 <param name="use_ppm_tolerance" value="false"/> | |
| 8376 </section> | |
| 8377 </section> | |
| 8378 <section name="f_and_c"> | |
| 8379 <param name="charge" value=":"/> | |
| 8380 <param name="size" value=":"/> | |
| 8381 <param name="remove_meta" value=""/> | |
| 8382 </section> | |
| 8383 <section name="id"> | |
| 8384 <param name="remove_clashes" value="false"/> | |
| 8385 <param name="keep_best_score_id" value="false"/> | |
| 8386 <param name="sequences_whitelist" value=""/> | |
| 8387 <param name="sequence_comparison_method" value="substring"/> | |
| 8388 <param name="accessions_whitelist" value=""/> | |
| 8389 <param name="remove_annotated_features" value="false"/> | |
| 8390 <param name="remove_unannotated_features" value="false"/> | |
| 8391 <param name="remove_unassigned_ids" value="false"/> | |
| 8392 <param name="rt" value="0.1"/> | |
| 8393 <param name="mz" value="0.001"/> | |
| 8394 <param name="blacklist_imperfect" value="false"/> | |
| 8395 </section> | |
| 8396 <section name="algorithm"> | |
| 8397 <section name="SignalToNoise"> | |
| 8398 <param name="max_intensity" value="-1"/> | |
| 8399 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8400 <param name="auto_max_percentile" value="95"/> | |
| 8401 <param name="auto_mode" value="0"/> | |
| 8402 <param name="win_len" value="200.0"/> | |
| 8403 <param name="bin_count" value="30"/> | |
| 8404 <param name="min_required_elements" value="10"/> | |
| 8405 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8406 <param name="write_log_messages" value="true"/> | |
| 8407 </section> | |
| 8408 </section> | |
| 8409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8410 <output name="ctd_out" ftype="xml"> | |
| 8411 <assert_contents> | |
| 8412 <is_valid_xml/> | |
| 8413 </assert_contents> | |
| 8414 </output> | |
| 8415 </test> | |
| 8416 <test expect_num_outputs="2"> | |
| 8417 <conditional name="adv_opts_cond"> | |
| 8418 <param name="adv_opts_selector" value="advanced"/> | |
| 8419 <param name="force" value="false"/> | |
| 8420 <param name="test" value="true"/> | |
| 8421 </conditional> | |
| 8422 <param name="in" value="FileFilter_31_34_input.mzML"/> | |
| 8423 <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8424 <param name="out_type" value="mzml"/> | |
| 8425 <param name="rt" value=":"/> | |
| 8426 <param name="mz" value=":"/> | |
| 8427 <param name="int" value=":"/> | |
| 8428 <param name="sort" value="false"/> | |
| 8429 <section name="peak_options"> | |
| 8430 <param name="sn" value="0.0"/> | |
| 8431 <param name="rm_pc_charge" value=""/> | |
| 8432 <param name="pc_mz_range" value=":"/> | |
| 8433 <param name="pc_mz_list" value=""/> | |
| 8434 <param name="level" value="1 2 3"/> | |
| 8435 <param name="sort_peaks" value="false"/> | |
| 8436 <param name="no_chromatograms" value="false"/> | |
| 8437 <param name="remove_chromatograms" value="false"/> | |
| 8438 <param name="remove_empty" value="false"/> | |
| 8439 <param name="mz_precision" value="64"/> | |
| 8440 <param name="int_precision" value="32"/> | |
| 8441 <param name="indexed_file" value="true"/> | |
| 8442 <param name="zlib_compression" value="false"/> | |
| 8443 <section name="numpress"> | |
| 8444 <param name="masstime" value="none"/> | |
| 8445 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8446 <param name="intensity" value="none"/> | |
| 8447 <param name="float_da" value="none"/> | |
| 8448 </section> | |
| 8449 </section> | |
| 8450 <section name="spectra"> | |
| 8451 <param name="remove_zoom" value="false"/> | |
| 8452 <param name="remove_mode" value=""/> | |
| 8453 <param name="remove_activation" value=""/> | |
| 8454 <param name="remove_collision_energy" value=":"/> | |
| 8455 <param name="remove_isolation_window_width" value=":"/> | |
| 8456 <param name="select_zoom" value="false"/> | |
| 8457 <param name="select_mode" value=""/> | |
| 8458 <param name="select_activation" value=""/> | |
| 8459 <param name="select_collision_energy" value=":35"/> | |
| 8460 <param name="select_isolation_window_width" value=":"/> | |
| 8461 <param name="select_polarity" value=""/> | |
| 8462 <section name="blackorwhitelist"> | |
| 8463 <param name="similarity_threshold" value="-1.0"/> | |
| 8464 <param name="rt" value="0.01"/> | |
| 8465 <param name="mz" value="0.01"/> | |
| 8466 <param name="use_ppm_tolerance" value="false"/> | |
| 8467 <param name="blacklist" value="true"/> | |
| 8468 </section> | |
| 8469 </section> | |
| 8470 <section name="feature"> | |
| 8471 <param name="q" value=":"/> | |
| 8472 </section> | |
| 8473 <section name="consensus"> | |
| 8474 <param name="map" value=""/> | |
| 8475 <param name="map_and" value="false"/> | |
| 8476 <section name="blackorwhitelist"> | |
| 8477 <param name="blacklist" value="true"/> | |
| 8478 <param name="maps" value=""/> | |
| 8479 <param name="rt" value="60.0"/> | |
| 8480 <param name="mz" value="0.01"/> | |
| 8481 <param name="use_ppm_tolerance" value="false"/> | |
| 8482 </section> | |
| 8483 </section> | |
| 8484 <section name="f_and_c"> | |
| 8485 <param name="charge" value=":"/> | |
| 8486 <param name="size" value=":"/> | |
| 8487 <param name="remove_meta" value=""/> | |
| 8488 </section> | |
| 8489 <section name="id"> | |
| 8490 <param name="remove_clashes" value="false"/> | |
| 8491 <param name="keep_best_score_id" value="false"/> | |
| 8492 <param name="sequences_whitelist" value=""/> | |
| 8493 <param name="sequence_comparison_method" value="substring"/> | |
| 8494 <param name="accessions_whitelist" value=""/> | |
| 8495 <param name="remove_annotated_features" value="false"/> | |
| 8496 <param name="remove_unannotated_features" value="false"/> | |
| 8497 <param name="remove_unassigned_ids" value="false"/> | |
| 8498 <param name="rt" value="0.1"/> | |
| 8499 <param name="mz" value="0.001"/> | |
| 8500 <param name="blacklist_imperfect" value="false"/> | |
| 8501 </section> | |
| 8502 <section name="algorithm"> | |
| 8503 <section name="SignalToNoise"> | |
| 8504 <param name="max_intensity" value="-1"/> | |
| 8505 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8506 <param name="auto_max_percentile" value="95"/> | |
| 8507 <param name="auto_mode" value="0"/> | |
| 8508 <param name="win_len" value="200.0"/> | |
| 8509 <param name="bin_count" value="30"/> | |
| 8510 <param name="min_required_elements" value="10"/> | |
| 8511 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8512 <param name="write_log_messages" value="true"/> | |
| 8513 </section> | |
| 8514 </section> | |
| 8515 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8516 <output name="ctd_out" ftype="xml"> | |
| 8517 <assert_contents> | |
| 8518 <is_valid_xml/> | |
| 8519 </assert_contents> | |
| 8520 </output> | |
| 8521 </test> | |
| 8522 <test expect_num_outputs="2"> | |
| 8523 <conditional name="adv_opts_cond"> | |
| 8524 <param name="adv_opts_selector" value="advanced"/> | |
| 8525 <param name="force" value="false"/> | |
| 8526 <param name="test" value="true"/> | |
| 8527 </conditional> | |
| 8528 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 8529 <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8530 <param name="out_type" value="mzML"/> | |
| 8531 <param name="rt" value=":"/> | |
| 8532 <param name="mz" value=":"/> | |
| 8533 <param name="int" value=":"/> | |
| 8534 <param name="sort" value="false"/> | |
| 8535 <section name="peak_options"> | |
| 8536 <param name="sn" value="0.0"/> | |
| 8537 <param name="rm_pc_charge" value=""/> | |
| 8538 <param name="pc_mz_range" value=":"/> | |
| 8539 <param name="pc_mz_list" value=""/> | |
| 8540 <param name="level" value="1 2 3"/> | |
| 8541 <param name="sort_peaks" value="false"/> | |
| 8542 <param name="no_chromatograms" value="false"/> | |
| 8543 <param name="remove_chromatograms" value="false"/> | |
| 8544 <param name="remove_empty" value="false"/> | |
| 8545 <param name="mz_precision" value="64"/> | |
| 8546 <param name="int_precision" value="32"/> | |
| 8547 <param name="indexed_file" value="true"/> | |
| 8548 <param name="zlib_compression" value="false"/> | |
| 8549 <section name="numpress"> | |
| 8550 <param name="masstime" value="none"/> | |
| 8551 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8552 <param name="intensity" value="none"/> | |
| 8553 <param name="float_da" value="none"/> | |
| 8554 </section> | |
| 8555 </section> | |
| 8556 <section name="spectra"> | |
| 8557 <param name="remove_zoom" value="false"/> | |
| 8558 <param name="remove_mode" value=""/> | |
| 8559 <param name="remove_activation" value=""/> | |
| 8560 <param name="remove_collision_energy" value=":"/> | |
| 8561 <param name="remove_isolation_window_width" value=":"/> | |
| 8562 <param name="select_zoom" value="false"/> | |
| 8563 <param name="select_mode" value=""/> | |
| 8564 <param name="select_activation" value=""/> | |
| 8565 <param name="select_collision_energy" value=":"/> | |
| 8566 <param name="select_isolation_window_width" value=":"/> | |
| 8567 <param name="select_polarity" value=""/> | |
| 8568 <section name="blackorwhitelist"> | |
| 8569 <param name="similarity_threshold" value="-1.0"/> | |
| 8570 <param name="rt" value="0.01"/> | |
| 8571 <param name="mz" value="0.01"/> | |
| 8572 <param name="use_ppm_tolerance" value="false"/> | |
| 8573 <param name="blacklist" value="true"/> | |
| 8574 </section> | |
| 8575 </section> | |
| 8576 <section name="feature"> | |
| 8577 <param name="q" value=":"/> | |
| 8578 </section> | |
| 8579 <section name="consensus"> | |
| 8580 <param name="map" value=""/> | |
| 8581 <param name="map_and" value="false"/> | |
| 8582 <section name="blackorwhitelist"> | |
| 8583 <param name="blacklist" value="true"/> | |
| 8584 <param name="maps" value=""/> | |
| 8585 <param name="rt" value="60.0"/> | |
| 8586 <param name="mz" value="0.01"/> | |
| 8587 <param name="use_ppm_tolerance" value="false"/> | |
| 8588 </section> | |
| 8589 </section> | |
| 8590 <section name="f_and_c"> | |
| 8591 <param name="charge" value=":"/> | |
| 8592 <param name="size" value=":"/> | |
| 8593 <param name="remove_meta" value=""/> | |
| 8594 </section> | |
| 8595 <section name="id"> | |
| 8596 <param name="remove_clashes" value="false"/> | |
| 8597 <param name="keep_best_score_id" value="false"/> | |
| 8598 <param name="sequences_whitelist" value=""/> | |
| 8599 <param name="sequence_comparison_method" value="substring"/> | |
| 8600 <param name="accessions_whitelist" value=""/> | |
| 8601 <param name="remove_annotated_features" value="false"/> | |
| 8602 <param name="remove_unannotated_features" value="false"/> | |
| 8603 <param name="remove_unassigned_ids" value="false"/> | |
| 8604 <param name="rt" value="0.1"/> | |
| 8605 <param name="mz" value="0.001"/> | |
| 8606 <param name="blacklist_imperfect" value="false"/> | |
| 8607 </section> | |
| 8608 <section name="algorithm"> | |
| 8609 <section name="SignalToNoise"> | |
| 8610 <param name="max_intensity" value="-1"/> | |
| 8611 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8612 <param name="auto_max_percentile" value="95"/> | |
| 8613 <param name="auto_mode" value="0"/> | |
| 8614 <param name="win_len" value="200.0"/> | |
| 8615 <param name="bin_count" value="30"/> | |
| 8616 <param name="min_required_elements" value="10"/> | |
| 8617 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8618 <param name="write_log_messages" value="true"/> | |
| 8619 </section> | |
| 8620 </section> | |
| 8621 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8622 <output name="ctd_out" ftype="xml"> | |
| 8623 <assert_contents> | |
| 8624 <is_valid_xml/> | |
| 8625 </assert_contents> | |
| 8626 </output> | |
| 8627 </test> | |
| 8628 <test expect_num_outputs="2"> | |
| 8629 <conditional name="adv_opts_cond"> | |
| 8630 <param name="adv_opts_selector" value="advanced"/> | |
| 8631 <param name="force" value="false"/> | |
| 8632 <param name="test" value="true"/> | |
| 8633 </conditional> | |
| 8634 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 8635 <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8636 <param name="out_type" value="mzML"/> | |
| 8637 <param name="rt" value=":"/> | |
| 8638 <param name="mz" value=":"/> | |
| 8639 <param name="int" value=":"/> | |
| 8640 <param name="sort" value="false"/> | |
| 8641 <section name="peak_options"> | |
| 8642 <param name="sn" value="0.0"/> | |
| 8643 <param name="rm_pc_charge" value=""/> | |
| 8644 <param name="pc_mz_range" value=":"/> | |
| 8645 <param name="pc_mz_list" value=""/> | |
| 8646 <param name="level" value="1 2 3"/> | |
| 8647 <param name="sort_peaks" value="false"/> | |
| 8648 <param name="no_chromatograms" value="false"/> | |
| 8649 <param name="remove_chromatograms" value="false"/> | |
| 8650 <param name="remove_empty" value="false"/> | |
| 8651 <param name="mz_precision" value="64"/> | |
| 8652 <param name="int_precision" value="32"/> | |
| 8653 <param name="indexed_file" value="false"/> | |
| 8654 <param name="zlib_compression" value="false"/> | |
| 8655 <section name="numpress"> | |
| 8656 <param name="masstime" value="none"/> | |
| 8657 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8658 <param name="intensity" value="none"/> | |
| 8659 <param name="float_da" value="none"/> | |
| 8660 </section> | |
| 8661 </section> | |
| 8662 <section name="spectra"> | |
| 8663 <param name="remove_zoom" value="false"/> | |
| 8664 <param name="remove_mode" value=""/> | |
| 8665 <param name="remove_activation" value=""/> | |
| 8666 <param name="remove_collision_energy" value=":"/> | |
| 8667 <param name="remove_isolation_window_width" value=":"/> | |
| 8668 <param name="select_zoom" value="false"/> | |
| 8669 <param name="select_mode" value=""/> | |
| 8670 <param name="select_activation" value=""/> | |
| 8671 <param name="select_collision_energy" value=":"/> | |
| 8672 <param name="select_isolation_window_width" value=":"/> | |
| 8673 <param name="select_polarity" value=""/> | |
| 8674 <section name="blackorwhitelist"> | |
| 8675 <param name="similarity_threshold" value="-1.0"/> | |
| 8676 <param name="rt" value="0.01"/> | |
| 8677 <param name="mz" value="0.01"/> | |
| 8678 <param name="use_ppm_tolerance" value="false"/> | |
| 8679 <param name="blacklist" value="true"/> | |
| 8680 </section> | |
| 8681 </section> | |
| 8682 <section name="feature"> | |
| 8683 <param name="q" value=":"/> | |
| 8684 </section> | |
| 8685 <section name="consensus"> | |
| 8686 <param name="map" value=""/> | |
| 8687 <param name="map_and" value="false"/> | |
| 8688 <section name="blackorwhitelist"> | |
| 8689 <param name="blacklist" value="true"/> | |
| 8690 <param name="maps" value=""/> | |
| 8691 <param name="rt" value="60.0"/> | |
| 8692 <param name="mz" value="0.01"/> | |
| 8693 <param name="use_ppm_tolerance" value="false"/> | |
| 8694 </section> | |
| 8695 </section> | |
| 8696 <section name="f_and_c"> | |
| 8697 <param name="charge" value=":"/> | |
| 8698 <param name="size" value=":"/> | |
| 8699 <param name="remove_meta" value=""/> | |
| 8700 </section> | |
| 8701 <section name="id"> | |
| 8702 <param name="remove_clashes" value="false"/> | |
| 8703 <param name="keep_best_score_id" value="false"/> | |
| 8704 <param name="sequences_whitelist" value=""/> | |
| 8705 <param name="sequence_comparison_method" value="substring"/> | |
| 8706 <param name="accessions_whitelist" value=""/> | |
| 8707 <param name="remove_annotated_features" value="false"/> | |
| 8708 <param name="remove_unannotated_features" value="false"/> | |
| 8709 <param name="remove_unassigned_ids" value="false"/> | |
| 8710 <param name="rt" value="0.1"/> | |
| 8711 <param name="mz" value="0.001"/> | |
| 8712 <param name="blacklist_imperfect" value="false"/> | |
| 8713 </section> | |
| 8714 <section name="algorithm"> | |
| 8715 <section name="SignalToNoise"> | |
| 8716 <param name="max_intensity" value="-1"/> | |
| 8717 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8718 <param name="auto_max_percentile" value="95"/> | |
| 8719 <param name="auto_mode" value="0"/> | |
| 8720 <param name="win_len" value="200.0"/> | |
| 8721 <param name="bin_count" value="30"/> | |
| 8722 <param name="min_required_elements" value="10"/> | |
| 8723 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8724 <param name="write_log_messages" value="true"/> | |
| 8725 </section> | |
| 8726 </section> | |
| 8727 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8728 <output name="ctd_out" ftype="xml"> | |
| 8729 <assert_contents> | |
| 8730 <is_valid_xml/> | |
| 8731 </assert_contents> | |
| 8732 </output> | |
| 8733 </test> | |
| 8734 <test expect_num_outputs="2"> | |
| 8735 <conditional name="adv_opts_cond"> | |
| 8736 <param name="adv_opts_selector" value="advanced"/> | |
| 8737 <param name="force" value="false"/> | |
| 8738 <param name="test" value="true"/> | |
| 8739 </conditional> | |
| 8740 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 8741 <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8742 <param name="out_type" value="mzML"/> | |
| 8743 <param name="rt" value=":"/> | |
| 8744 <param name="mz" value=":"/> | |
| 8745 <param name="int" value=":"/> | |
| 8746 <param name="sort" value="false"/> | |
| 8747 <section name="peak_options"> | |
| 8748 <param name="sn" value="0.0"/> | |
| 8749 <param name="rm_pc_charge" value=""/> | |
| 8750 <param name="pc_mz_range" value=":"/> | |
| 8751 <param name="pc_mz_list" value=""/> | |
| 8752 <param name="level" value="1 2 3"/> | |
| 8753 <param name="sort_peaks" value="false"/> | |
| 8754 <param name="no_chromatograms" value="false"/> | |
| 8755 <param name="remove_chromatograms" value="false"/> | |
| 8756 <param name="remove_empty" value="false"/> | |
| 8757 <param name="mz_precision" value="64"/> | |
| 8758 <param name="int_precision" value="32"/> | |
| 8759 <param name="indexed_file" value="true"/> | |
| 8760 <param name="zlib_compression" value="false"/> | |
| 8761 <section name="numpress"> | |
| 8762 <param name="masstime" value="linear"/> | |
| 8763 <param name="lossy_mass_accuracy" value="0.0001"/> | |
| 8764 <param name="intensity" value="slof"/> | |
| 8765 <param name="float_da" value="none"/> | |
| 8766 </section> | |
| 8767 </section> | |
| 8768 <section name="spectra"> | |
| 8769 <param name="remove_zoom" value="false"/> | |
| 8770 <param name="remove_mode" value=""/> | |
| 8771 <param name="remove_activation" value=""/> | |
| 8772 <param name="remove_collision_energy" value=":"/> | |
| 8773 <param name="remove_isolation_window_width" value=":"/> | |
| 8774 <param name="select_zoom" value="false"/> | |
| 8775 <param name="select_mode" value=""/> | |
| 8776 <param name="select_activation" value=""/> | |
| 8777 <param name="select_collision_energy" value=":"/> | |
| 8778 <param name="select_isolation_window_width" value=":"/> | |
| 8779 <param name="select_polarity" value=""/> | |
| 8780 <section name="blackorwhitelist"> | |
| 8781 <param name="similarity_threshold" value="-1.0"/> | |
| 8782 <param name="rt" value="0.01"/> | |
| 8783 <param name="mz" value="0.01"/> | |
| 8784 <param name="use_ppm_tolerance" value="false"/> | |
| 8785 <param name="blacklist" value="true"/> | |
| 8786 </section> | |
| 8787 </section> | |
| 8788 <section name="feature"> | |
| 8789 <param name="q" value=":"/> | |
| 8790 </section> | |
| 8791 <section name="consensus"> | |
| 8792 <param name="map" value=""/> | |
| 8793 <param name="map_and" value="false"/> | |
| 8794 <section name="blackorwhitelist"> | |
| 8795 <param name="blacklist" value="true"/> | |
| 8796 <param name="maps" value=""/> | |
| 8797 <param name="rt" value="60.0"/> | |
| 8798 <param name="mz" value="0.01"/> | |
| 8799 <param name="use_ppm_tolerance" value="false"/> | |
| 8800 </section> | |
| 8801 </section> | |
| 8802 <section name="f_and_c"> | |
| 8803 <param name="charge" value=":"/> | |
| 8804 <param name="size" value=":"/> | |
| 8805 <param name="remove_meta" value=""/> | |
| 8806 </section> | |
| 8807 <section name="id"> | |
| 8808 <param name="remove_clashes" value="false"/> | |
| 8809 <param name="keep_best_score_id" value="false"/> | |
| 8810 <param name="sequences_whitelist" value=""/> | |
| 8811 <param name="sequence_comparison_method" value="substring"/> | |
| 8812 <param name="accessions_whitelist" value=""/> | |
| 8813 <param name="remove_annotated_features" value="false"/> | |
| 8814 <param name="remove_unannotated_features" value="false"/> | |
| 8815 <param name="remove_unassigned_ids" value="false"/> | |
| 8816 <param name="rt" value="0.1"/> | |
| 8817 <param name="mz" value="0.001"/> | |
| 8818 <param name="blacklist_imperfect" value="false"/> | |
| 8819 </section> | |
| 8820 <section name="algorithm"> | |
| 8821 <section name="SignalToNoise"> | |
| 8822 <param name="max_intensity" value="-1"/> | |
| 8823 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8824 <param name="auto_max_percentile" value="95"/> | |
| 8825 <param name="auto_mode" value="0"/> | |
| 8826 <param name="win_len" value="200.0"/> | |
| 8827 <param name="bin_count" value="30"/> | |
| 8828 <param name="min_required_elements" value="10"/> | |
| 8829 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8830 <param name="write_log_messages" value="true"/> | |
| 8831 </section> | |
| 8832 </section> | |
| 8833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8834 <output name="ctd_out" ftype="xml"> | |
| 8835 <assert_contents> | |
| 8836 <is_valid_xml/> | |
| 8837 </assert_contents> | |
| 8838 </output> | |
| 8839 </test> | |
| 8840 <test expect_num_outputs="2"> | |
| 8841 <conditional name="adv_opts_cond"> | |
| 8842 <param name="adv_opts_selector" value="advanced"/> | |
| 8843 <param name="force" value="false"/> | |
| 8844 <param name="test" value="true"/> | |
| 8845 </conditional> | |
| 8846 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 8847 <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8848 <param name="out_type" value="mzML"/> | |
| 8849 <param name="rt" value=":"/> | |
| 8850 <param name="mz" value=":"/> | |
| 8851 <param name="int" value=":"/> | |
| 8852 <param name="sort" value="false"/> | |
| 8853 <section name="peak_options"> | |
| 8854 <param name="sn" value="0.0"/> | |
| 8855 <param name="rm_pc_charge" value=""/> | |
| 8856 <param name="pc_mz_range" value=":"/> | |
| 8857 <param name="pc_mz_list" value=""/> | |
| 8858 <param name="level" value="1 2 3"/> | |
| 8859 <param name="sort_peaks" value="false"/> | |
| 8860 <param name="no_chromatograms" value="false"/> | |
| 8861 <param name="remove_chromatograms" value="false"/> | |
| 8862 <param name="remove_empty" value="false"/> | |
| 8863 <param name="mz_precision" value="64"/> | |
| 8864 <param name="int_precision" value="32"/> | |
| 8865 <param name="indexed_file" value="true"/> | |
| 8866 <param name="zlib_compression" value="false"/> | |
| 8867 <section name="numpress"> | |
| 8868 <param name="masstime" value="linear"/> | |
| 8869 <param name="lossy_mass_accuracy" value="0.0001"/> | |
| 8870 <param name="intensity" value="pic"/> | |
| 8871 <param name="float_da" value="none"/> | |
| 8872 </section> | |
| 8873 </section> | |
| 8874 <section name="spectra"> | |
| 8875 <param name="remove_zoom" value="false"/> | |
| 8876 <param name="remove_mode" value=""/> | |
| 8877 <param name="remove_activation" value=""/> | |
| 8878 <param name="remove_collision_energy" value=":"/> | |
| 8879 <param name="remove_isolation_window_width" value=":"/> | |
| 8880 <param name="select_zoom" value="false"/> | |
| 8881 <param name="select_mode" value=""/> | |
| 8882 <param name="select_activation" value=""/> | |
| 8883 <param name="select_collision_energy" value=":"/> | |
| 8884 <param name="select_isolation_window_width" value=":"/> | |
| 8885 <param name="select_polarity" value=""/> | |
| 8886 <section name="blackorwhitelist"> | |
| 8887 <param name="similarity_threshold" value="-1.0"/> | |
| 8888 <param name="rt" value="0.01"/> | |
| 8889 <param name="mz" value="0.01"/> | |
| 8890 <param name="use_ppm_tolerance" value="false"/> | |
| 8891 <param name="blacklist" value="true"/> | |
| 8892 </section> | |
| 8893 </section> | |
| 8894 <section name="feature"> | |
| 8895 <param name="q" value=":"/> | |
| 8896 </section> | |
| 8897 <section name="consensus"> | |
| 8898 <param name="map" value=""/> | |
| 8899 <param name="map_and" value="false"/> | |
| 8900 <section name="blackorwhitelist"> | |
| 8901 <param name="blacklist" value="true"/> | |
| 8902 <param name="maps" value=""/> | |
| 8903 <param name="rt" value="60.0"/> | |
| 8904 <param name="mz" value="0.01"/> | |
| 8905 <param name="use_ppm_tolerance" value="false"/> | |
| 8906 </section> | |
| 8907 </section> | |
| 8908 <section name="f_and_c"> | |
| 8909 <param name="charge" value=":"/> | |
| 8910 <param name="size" value=":"/> | |
| 8911 <param name="remove_meta" value=""/> | |
| 8912 </section> | |
| 8913 <section name="id"> | |
| 8914 <param name="remove_clashes" value="false"/> | |
| 8915 <param name="keep_best_score_id" value="false"/> | |
| 8916 <param name="sequences_whitelist" value=""/> | |
| 8917 <param name="sequence_comparison_method" value="substring"/> | |
| 8918 <param name="accessions_whitelist" value=""/> | |
| 8919 <param name="remove_annotated_features" value="false"/> | |
| 8920 <param name="remove_unannotated_features" value="false"/> | |
| 8921 <param name="remove_unassigned_ids" value="false"/> | |
| 8922 <param name="rt" value="0.1"/> | |
| 8923 <param name="mz" value="0.001"/> | |
| 8924 <param name="blacklist_imperfect" value="false"/> | |
| 8925 </section> | |
| 8926 <section name="algorithm"> | |
| 8927 <section name="SignalToNoise"> | |
| 8928 <param name="max_intensity" value="-1"/> | |
| 8929 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 8930 <param name="auto_max_percentile" value="95"/> | |
| 8931 <param name="auto_mode" value="0"/> | |
| 8932 <param name="win_len" value="200.0"/> | |
| 8933 <param name="bin_count" value="30"/> | |
| 8934 <param name="min_required_elements" value="10"/> | |
| 8935 <param name="noise_for_empty_window" value="1e+20"/> | |
| 8936 <param name="write_log_messages" value="true"/> | |
| 8937 </section> | |
| 8938 </section> | |
| 8939 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 8940 <output name="ctd_out" ftype="xml"> | |
| 8941 <assert_contents> | |
| 8942 <is_valid_xml/> | |
| 8943 </assert_contents> | |
| 8944 </output> | |
| 8945 </test> | |
| 8946 <test expect_num_outputs="2"> | |
| 8947 <conditional name="adv_opts_cond"> | |
| 8948 <param name="adv_opts_selector" value="advanced"/> | |
| 8949 <param name="force" value="false"/> | |
| 8950 <param name="test" value="true"/> | |
| 8951 </conditional> | |
| 8952 <param name="in" value="FileFilter_40_input.mzML"/> | |
| 8953 <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 8954 <param name="out_type" value="mzML"/> | |
| 8955 <param name="rt" value=":"/> | |
| 8956 <param name="mz" value=":"/> | |
| 8957 <param name="int" value=":"/> | |
| 8958 <param name="sort" value="false"/> | |
| 8959 <section name="peak_options"> | |
| 8960 <param name="sn" value="0.0"/> | |
| 8961 <param name="rm_pc_charge" value=""/> | |
| 8962 <param name="pc_mz_range" value=":"/> | |
| 8963 <param name="pc_mz_list" value=""/> | |
| 8964 <param name="level" value="1 2 3"/> | |
| 8965 <param name="sort_peaks" value="false"/> | |
| 8966 <param name="no_chromatograms" value="false"/> | |
| 8967 <param name="remove_chromatograms" value="false"/> | |
| 8968 <param name="remove_empty" value="false"/> | |
| 8969 <param name="mz_precision" value="64"/> | |
| 8970 <param name="int_precision" value="32"/> | |
| 8971 <param name="indexed_file" value="true"/> | |
| 8972 <param name="zlib_compression" value="false"/> | |
| 8973 <section name="numpress"> | |
| 8974 <param name="masstime" value="none"/> | |
| 8975 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 8976 <param name="intensity" value="none"/> | |
| 8977 <param name="float_da" value="none"/> | |
| 8978 </section> | |
| 8979 </section> | |
| 8980 <section name="spectra"> | |
| 8981 <param name="remove_zoom" value="false"/> | |
| 8982 <param name="remove_mode" value=""/> | |
| 8983 <param name="remove_activation" value=""/> | |
| 8984 <param name="remove_collision_energy" value=":"/> | |
| 8985 <param name="remove_isolation_window_width" value=":"/> | |
| 8986 <param name="select_zoom" value="false"/> | |
| 8987 <param name="select_mode" value=""/> | |
| 8988 <param name="select_activation" value=""/> | |
| 8989 <param name="select_collision_energy" value=":"/> | |
| 8990 <param name="select_isolation_window_width" value=":"/> | |
| 8991 <param name="select_polarity" value="positive"/> | |
| 8992 <section name="blackorwhitelist"> | |
| 8993 <param name="similarity_threshold" value="-1.0"/> | |
| 8994 <param name="rt" value="0.01"/> | |
| 8995 <param name="mz" value="0.01"/> | |
| 8996 <param name="use_ppm_tolerance" value="false"/> | |
| 8997 <param name="blacklist" value="true"/> | |
| 8998 </section> | |
| 8999 </section> | |
| 9000 <section name="feature"> | |
| 9001 <param name="q" value=":"/> | |
| 9002 </section> | |
| 9003 <section name="consensus"> | |
| 9004 <param name="map" value=""/> | |
| 9005 <param name="map_and" value="false"/> | |
| 9006 <section name="blackorwhitelist"> | |
| 9007 <param name="blacklist" value="true"/> | |
| 9008 <param name="maps" value=""/> | |
| 9009 <param name="rt" value="60.0"/> | |
| 9010 <param name="mz" value="0.01"/> | |
| 9011 <param name="use_ppm_tolerance" value="false"/> | |
| 9012 </section> | |
| 9013 </section> | |
| 9014 <section name="f_and_c"> | |
| 9015 <param name="charge" value=":"/> | |
| 9016 <param name="size" value=":"/> | |
| 9017 <param name="remove_meta" value=""/> | |
| 9018 </section> | |
| 9019 <section name="id"> | |
| 9020 <param name="remove_clashes" value="false"/> | |
| 9021 <param name="keep_best_score_id" value="false"/> | |
| 9022 <param name="sequences_whitelist" value=""/> | |
| 9023 <param name="sequence_comparison_method" value="substring"/> | |
| 9024 <param name="accessions_whitelist" value=""/> | |
| 9025 <param name="remove_annotated_features" value="false"/> | |
| 9026 <param name="remove_unannotated_features" value="false"/> | |
| 9027 <param name="remove_unassigned_ids" value="false"/> | |
| 9028 <param name="rt" value="0.1"/> | |
| 9029 <param name="mz" value="0.001"/> | |
| 9030 <param name="blacklist_imperfect" value="false"/> | |
| 9031 </section> | |
| 9032 <section name="algorithm"> | |
| 9033 <section name="SignalToNoise"> | |
| 9034 <param name="max_intensity" value="-1"/> | |
| 9035 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9036 <param name="auto_max_percentile" value="95"/> | |
| 9037 <param name="auto_mode" value="0"/> | |
| 9038 <param name="win_len" value="200.0"/> | |
| 9039 <param name="bin_count" value="30"/> | |
| 9040 <param name="min_required_elements" value="10"/> | |
| 9041 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9042 <param name="write_log_messages" value="true"/> | |
| 9043 </section> | |
| 9044 </section> | |
| 9045 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9046 <output name="ctd_out" ftype="xml"> | |
| 9047 <assert_contents> | |
| 9048 <is_valid_xml/> | |
| 9049 </assert_contents> | |
| 9050 </output> | |
| 9051 </test> | |
| 9052 <test expect_num_outputs="2"> | |
| 9053 <conditional name="adv_opts_cond"> | |
| 9054 <param name="adv_opts_selector" value="advanced"/> | |
| 9055 <param name="force" value="false"/> | |
| 9056 <param name="test" value="true"/> | |
| 9057 </conditional> | |
| 9058 <param name="in" value="FileFilter_40_input.mzML"/> | |
| 9059 <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 9060 <param name="out_type" value="mzML"/> | |
| 9061 <param name="rt" value=":"/> | |
| 9062 <param name="mz" value=":"/> | |
| 9063 <param name="int" value=":"/> | |
| 9064 <param name="sort" value="false"/> | |
| 9065 <section name="peak_options"> | |
| 9066 <param name="sn" value="0.0"/> | |
| 9067 <param name="rm_pc_charge" value=""/> | |
| 9068 <param name="pc_mz_range" value=":"/> | |
| 9069 <param name="pc_mz_list" value=""/> | |
| 9070 <param name="level" value="1 2 3"/> | |
| 9071 <param name="sort_peaks" value="false"/> | |
| 9072 <param name="no_chromatograms" value="false"/> | |
| 9073 <param name="remove_chromatograms" value="false"/> | |
| 9074 <param name="remove_empty" value="false"/> | |
| 9075 <param name="mz_precision" value="64"/> | |
| 9076 <param name="int_precision" value="32"/> | |
| 9077 <param name="indexed_file" value="true"/> | |
| 9078 <param name="zlib_compression" value="false"/> | |
| 9079 <section name="numpress"> | |
| 9080 <param name="masstime" value="none"/> | |
| 9081 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9082 <param name="intensity" value="none"/> | |
| 9083 <param name="float_da" value="none"/> | |
| 9084 </section> | |
| 9085 </section> | |
| 9086 <section name="spectra"> | |
| 9087 <param name="remove_zoom" value="false"/> | |
| 9088 <param name="remove_mode" value=""/> | |
| 9089 <param name="remove_activation" value=""/> | |
| 9090 <param name="remove_collision_energy" value=":"/> | |
| 9091 <param name="remove_isolation_window_width" value=":"/> | |
| 9092 <param name="select_zoom" value="false"/> | |
| 9093 <param name="select_mode" value=""/> | |
| 9094 <param name="select_activation" value=""/> | |
| 9095 <param name="select_collision_energy" value=":"/> | |
| 9096 <param name="select_isolation_window_width" value=":"/> | |
| 9097 <param name="select_polarity" value="negative"/> | |
| 9098 <section name="blackorwhitelist"> | |
| 9099 <param name="similarity_threshold" value="-1.0"/> | |
| 9100 <param name="rt" value="0.01"/> | |
| 9101 <param name="mz" value="0.01"/> | |
| 9102 <param name="use_ppm_tolerance" value="false"/> | |
| 9103 <param name="blacklist" value="true"/> | |
| 9104 </section> | |
| 9105 </section> | |
| 9106 <section name="feature"> | |
| 9107 <param name="q" value=":"/> | |
| 9108 </section> | |
| 9109 <section name="consensus"> | |
| 9110 <param name="map" value=""/> | |
| 9111 <param name="map_and" value="false"/> | |
| 9112 <section name="blackorwhitelist"> | |
| 9113 <param name="blacklist" value="true"/> | |
| 9114 <param name="maps" value=""/> | |
| 9115 <param name="rt" value="60.0"/> | |
| 9116 <param name="mz" value="0.01"/> | |
| 9117 <param name="use_ppm_tolerance" value="false"/> | |
| 9118 </section> | |
| 9119 </section> | |
| 9120 <section name="f_and_c"> | |
| 9121 <param name="charge" value=":"/> | |
| 9122 <param name="size" value=":"/> | |
| 9123 <param name="remove_meta" value=""/> | |
| 9124 </section> | |
| 9125 <section name="id"> | |
| 9126 <param name="remove_clashes" value="false"/> | |
| 9127 <param name="keep_best_score_id" value="false"/> | |
| 9128 <param name="sequences_whitelist" value=""/> | |
| 9129 <param name="sequence_comparison_method" value="substring"/> | |
| 9130 <param name="accessions_whitelist" value=""/> | |
| 9131 <param name="remove_annotated_features" value="false"/> | |
| 9132 <param name="remove_unannotated_features" value="false"/> | |
| 9133 <param name="remove_unassigned_ids" value="false"/> | |
| 9134 <param name="rt" value="0.1"/> | |
| 9135 <param name="mz" value="0.001"/> | |
| 9136 <param name="blacklist_imperfect" value="false"/> | |
| 9137 </section> | |
| 9138 <section name="algorithm"> | |
| 9139 <section name="SignalToNoise"> | |
| 9140 <param name="max_intensity" value="-1"/> | |
| 9141 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9142 <param name="auto_max_percentile" value="95"/> | |
| 9143 <param name="auto_mode" value="0"/> | |
| 9144 <param name="win_len" value="200.0"/> | |
| 9145 <param name="bin_count" value="30"/> | |
| 9146 <param name="min_required_elements" value="10"/> | |
| 9147 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9148 <param name="write_log_messages" value="true"/> | |
| 9149 </section> | |
| 9150 </section> | |
| 9151 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9152 <output name="ctd_out" ftype="xml"> | |
| 9153 <assert_contents> | |
| 9154 <is_valid_xml/> | |
| 9155 </assert_contents> | |
| 9156 </output> | |
| 9157 </test> | |
| 9158 <test expect_num_outputs="2"> | |
| 9159 <conditional name="adv_opts_cond"> | |
| 9160 <param name="adv_opts_selector" value="advanced"/> | |
| 9161 <param name="force" value="false"/> | |
| 9162 <param name="test" value="true"/> | |
| 9163 </conditional> | |
| 9164 <param name="in" value="FileFilter_40_input.mzML"/> | |
| 9165 <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 9166 <param name="out_type" value="mzML"/> | |
| 9167 <param name="rt" value=":"/> | |
| 9168 <param name="mz" value=":"/> | |
| 9169 <param name="int" value=":"/> | |
| 9170 <param name="sort" value="false"/> | |
| 9171 <section name="peak_options"> | |
| 9172 <param name="sn" value="0.0"/> | |
| 9173 <param name="rm_pc_charge" value=""/> | |
| 9174 <param name="pc_mz_range" value=":"/> | |
| 9175 <param name="pc_mz_list" value=""/> | |
| 9176 <param name="level" value="1 2 3"/> | |
| 9177 <param name="sort_peaks" value="false"/> | |
| 9178 <param name="no_chromatograms" value="false"/> | |
| 9179 <param name="remove_chromatograms" value="false"/> | |
| 9180 <param name="remove_empty" value="false"/> | |
| 9181 <param name="mz_precision" value="64"/> | |
| 9182 <param name="int_precision" value="32"/> | |
| 9183 <param name="indexed_file" value="true"/> | |
| 9184 <param name="zlib_compression" value="false"/> | |
| 9185 <section name="numpress"> | |
| 9186 <param name="masstime" value="none"/> | |
| 9187 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9188 <param name="intensity" value="none"/> | |
| 9189 <param name="float_da" value="none"/> | |
| 9190 </section> | |
| 9191 </section> | |
| 9192 <section name="spectra"> | |
| 9193 <param name="remove_zoom" value="false"/> | |
| 9194 <param name="remove_mode" value=""/> | |
| 9195 <param name="remove_activation" value=""/> | |
| 9196 <param name="remove_collision_energy" value=":"/> | |
| 9197 <param name="remove_isolation_window_width" value=":"/> | |
| 9198 <param name="select_zoom" value="false"/> | |
| 9199 <param name="select_mode" value=""/> | |
| 9200 <param name="select_activation" value=""/> | |
| 9201 <param name="select_collision_energy" value=":"/> | |
| 9202 <param name="select_isolation_window_width" value=":"/> | |
| 9203 <param name="select_polarity" value=""/> | |
| 9204 <section name="blackorwhitelist"> | |
| 9205 <param name="similarity_threshold" value="-1.0"/> | |
| 9206 <param name="rt" value="0.01"/> | |
| 9207 <param name="mz" value="0.01"/> | |
| 9208 <param name="use_ppm_tolerance" value="false"/> | |
| 9209 <param name="blacklist" value="true"/> | |
| 9210 </section> | |
| 9211 </section> | |
| 9212 <section name="feature"> | |
| 9213 <param name="q" value=":"/> | |
| 9214 </section> | |
| 9215 <section name="consensus"> | |
| 9216 <param name="map" value=""/> | |
| 9217 <param name="map_and" value="false"/> | |
| 9218 <section name="blackorwhitelist"> | |
| 9219 <param name="blacklist" value="true"/> | |
| 9220 <param name="maps" value=""/> | |
| 9221 <param name="rt" value="60.0"/> | |
| 9222 <param name="mz" value="0.01"/> | |
| 9223 <param name="use_ppm_tolerance" value="false"/> | |
| 9224 </section> | |
| 9225 </section> | |
| 9226 <section name="f_and_c"> | |
| 9227 <param name="charge" value=":"/> | |
| 9228 <param name="size" value=":"/> | |
| 9229 <param name="remove_meta" value=""/> | |
| 9230 </section> | |
| 9231 <section name="id"> | |
| 9232 <param name="remove_clashes" value="false"/> | |
| 9233 <param name="keep_best_score_id" value="false"/> | |
| 9234 <param name="sequences_whitelist" value=""/> | |
| 9235 <param name="sequence_comparison_method" value="substring"/> | |
| 9236 <param name="accessions_whitelist" value=""/> | |
| 9237 <param name="remove_annotated_features" value="false"/> | |
| 9238 <param name="remove_unannotated_features" value="false"/> | |
| 9239 <param name="remove_unassigned_ids" value="false"/> | |
| 9240 <param name="rt" value="0.1"/> | |
| 9241 <param name="mz" value="0.001"/> | |
| 9242 <param name="blacklist_imperfect" value="false"/> | |
| 9243 </section> | |
| 9244 <section name="algorithm"> | |
| 9245 <section name="SignalToNoise"> | |
| 9246 <param name="max_intensity" value="-1"/> | |
| 9247 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9248 <param name="auto_max_percentile" value="95"/> | |
| 9249 <param name="auto_mode" value="0"/> | |
| 9250 <param name="win_len" value="200.0"/> | |
| 9251 <param name="bin_count" value="30"/> | |
| 9252 <param name="min_required_elements" value="10"/> | |
| 9253 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9254 <param name="write_log_messages" value="true"/> | |
| 9255 </section> | |
| 9256 </section> | |
| 9257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9258 <output name="ctd_out" ftype="xml"> | |
| 9259 <assert_contents> | |
| 9260 <is_valid_xml/> | |
| 9261 </assert_contents> | |
| 9262 </output> | |
| 9263 </test> | |
| 9264 <test expect_num_outputs="2"> | |
| 9265 <conditional name="adv_opts_cond"> | |
| 9266 <param name="adv_opts_selector" value="advanced"/> | |
| 9267 <param name="force" value="false"/> | |
| 9268 <param name="test" value="true"/> | |
| 9269 </conditional> | |
| 9270 <param name="in" value="FileFilter_43_input.mzML"/> | |
| 9271 <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 9272 <param name="out_type" value="mzML"/> | |
| 9273 <param name="rt" value=":"/> | |
| 9274 <param name="mz" value=":"/> | |
| 9275 <param name="int" value=":"/> | |
| 9276 <param name="sort" value="false"/> | |
| 9277 <section name="peak_options"> | |
| 9278 <param name="sn" value="0.0"/> | |
| 9279 <param name="rm_pc_charge" value=""/> | |
| 9280 <param name="pc_mz_range" value=":"/> | |
| 9281 <param name="pc_mz_list" value=""/> | |
| 9282 <param name="level" value="1 2 3"/> | |
| 9283 <param name="sort_peaks" value="false"/> | |
| 9284 <param name="no_chromatograms" value="false"/> | |
| 9285 <param name="remove_chromatograms" value="false"/> | |
| 9286 <param name="remove_empty" value="false"/> | |
| 9287 <param name="mz_precision" value="64"/> | |
| 9288 <param name="int_precision" value="32"/> | |
| 9289 <param name="indexed_file" value="true"/> | |
| 9290 <param name="zlib_compression" value="false"/> | |
| 9291 <section name="numpress"> | |
| 9292 <param name="masstime" value="none"/> | |
| 9293 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9294 <param name="intensity" value="none"/> | |
| 9295 <param name="float_da" value="none"/> | |
| 9296 </section> | |
| 9297 </section> | |
| 9298 <section name="spectra"> | |
| 9299 <param name="remove_zoom" value="false"/> | |
| 9300 <param name="remove_mode" value=""/> | |
| 9301 <param name="remove_activation" value=""/> | |
| 9302 <param name="remove_collision_energy" value=":"/> | |
| 9303 <param name="remove_isolation_window_width" value=":"/> | |
| 9304 <param name="select_zoom" value="false"/> | |
| 9305 <param name="select_mode" value=""/> | |
| 9306 <param name="select_activation" value=""/> | |
| 9307 <param name="select_collision_energy" value=":"/> | |
| 9308 <param name="select_isolation_window_width" value=":"/> | |
| 9309 <param name="select_polarity" value=""/> | |
| 9310 <section name="blackorwhitelist"> | |
| 9311 <param name="similarity_threshold" value="-1.0"/> | |
| 9312 <param name="rt" value="0.01"/> | |
| 9313 <param name="mz" value="0.01"/> | |
| 9314 <param name="use_ppm_tolerance" value="false"/> | |
| 9315 <param name="blacklist" value="true"/> | |
| 9316 </section> | |
| 9317 </section> | |
| 9318 <section name="feature"> | |
| 9319 <param name="q" value=":"/> | |
| 9320 </section> | |
| 9321 <section name="consensus"> | |
| 9322 <param name="map" value=""/> | |
| 9323 <param name="map_and" value="false"/> | |
| 9324 <section name="blackorwhitelist"> | |
| 9325 <param name="blacklist" value="true"/> | |
| 9326 <param name="maps" value=""/> | |
| 9327 <param name="rt" value="60.0"/> | |
| 9328 <param name="mz" value="0.01"/> | |
| 9329 <param name="use_ppm_tolerance" value="false"/> | |
| 9330 </section> | |
| 9331 </section> | |
| 9332 <section name="f_and_c"> | |
| 9333 <param name="charge" value=":"/> | |
| 9334 <param name="size" value=":"/> | |
| 9335 <param name="remove_meta" value=""/> | |
| 9336 </section> | |
| 9337 <section name="id"> | |
| 9338 <param name="remove_clashes" value="false"/> | |
| 9339 <param name="keep_best_score_id" value="false"/> | |
| 9340 <param name="sequences_whitelist" value=""/> | |
| 9341 <param name="sequence_comparison_method" value="substring"/> | |
| 9342 <param name="accessions_whitelist" value=""/> | |
| 9343 <param name="remove_annotated_features" value="false"/> | |
| 9344 <param name="remove_unannotated_features" value="false"/> | |
| 9345 <param name="remove_unassigned_ids" value="false"/> | |
| 9346 <param name="rt" value="0.1"/> | |
| 9347 <param name="mz" value="0.001"/> | |
| 9348 <param name="blacklist_imperfect" value="false"/> | |
| 9349 </section> | |
| 9350 <section name="algorithm"> | |
| 9351 <section name="SignalToNoise"> | |
| 9352 <param name="max_intensity" value="-1"/> | |
| 9353 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9354 <param name="auto_max_percentile" value="95"/> | |
| 9355 <param name="auto_mode" value="0"/> | |
| 9356 <param name="win_len" value="200.0"/> | |
| 9357 <param name="bin_count" value="30"/> | |
| 9358 <param name="min_required_elements" value="10"/> | |
| 9359 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9360 <param name="write_log_messages" value="true"/> | |
| 9361 </section> | |
| 9362 </section> | |
| 9363 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9364 <output name="ctd_out" ftype="xml"> | |
| 9365 <assert_contents> | |
| 9366 <is_valid_xml/> | |
| 9367 </assert_contents> | |
| 9368 </output> | |
| 9369 </test> | |
| 9370 <test expect_num_outputs="2"> | |
| 9371 <conditional name="adv_opts_cond"> | |
| 9372 <param name="adv_opts_selector" value="advanced"/> | |
| 9373 <param name="force" value="false"/> | |
| 9374 <param name="test" value="true"/> | |
| 9375 </conditional> | |
| 9376 <param name="in" value="FileFilter_43.tmp.mzML"/> | |
| 9377 <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/> | |
| 9378 <param name="out_type" value="mzML"/> | |
| 9379 <param name="rt" value=":"/> | |
| 9380 <param name="mz" value=":"/> | |
| 9381 <param name="int" value=":"/> | |
| 9382 <param name="sort" value="false"/> | |
| 9383 <section name="peak_options"> | |
| 9384 <param name="sn" value="0.0"/> | |
| 9385 <param name="rm_pc_charge" value=""/> | |
| 9386 <param name="pc_mz_range" value=":"/> | |
| 9387 <param name="pc_mz_list" value=""/> | |
| 9388 <param name="level" value="1 2 3"/> | |
| 9389 <param name="sort_peaks" value="false"/> | |
| 9390 <param name="no_chromatograms" value="false"/> | |
| 9391 <param name="remove_chromatograms" value="false"/> | |
| 9392 <param name="remove_empty" value="false"/> | |
| 9393 <param name="mz_precision" value="64"/> | |
| 9394 <param name="int_precision" value="32"/> | |
| 9395 <param name="indexed_file" value="true"/> | |
| 9396 <param name="zlib_compression" value="false"/> | |
| 9397 <section name="numpress"> | |
| 9398 <param name="masstime" value="none"/> | |
| 9399 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9400 <param name="intensity" value="none"/> | |
| 9401 <param name="float_da" value="none"/> | |
| 9402 </section> | |
| 9403 </section> | |
| 9404 <section name="spectra"> | |
| 9405 <param name="remove_zoom" value="false"/> | |
| 9406 <param name="remove_mode" value=""/> | |
| 9407 <param name="remove_activation" value=""/> | |
| 9408 <param name="remove_collision_energy" value=":"/> | |
| 9409 <param name="remove_isolation_window_width" value=":"/> | |
| 9410 <param name="select_zoom" value="false"/> | |
| 9411 <param name="select_mode" value=""/> | |
| 9412 <param name="select_activation" value=""/> | |
| 9413 <param name="select_collision_energy" value=":"/> | |
| 9414 <param name="select_isolation_window_width" value=":"/> | |
| 9415 <param name="select_polarity" value=""/> | |
| 9416 <section name="blackorwhitelist"> | |
| 9417 <param name="similarity_threshold" value="-1.0"/> | |
| 9418 <param name="rt" value="0.01"/> | |
| 9419 <param name="mz" value="0.01"/> | |
| 9420 <param name="use_ppm_tolerance" value="false"/> | |
| 9421 <param name="blacklist" value="true"/> | |
| 9422 </section> | |
| 9423 </section> | |
| 9424 <section name="feature"> | |
| 9425 <param name="q" value=":"/> | |
| 9426 </section> | |
| 9427 <section name="consensus"> | |
| 9428 <param name="map" value=""/> | |
| 9429 <param name="map_and" value="false"/> | |
| 9430 <section name="blackorwhitelist"> | |
| 9431 <param name="blacklist" value="true"/> | |
| 9432 <param name="maps" value=""/> | |
| 9433 <param name="rt" value="60.0"/> | |
| 9434 <param name="mz" value="0.01"/> | |
| 9435 <param name="use_ppm_tolerance" value="false"/> | |
| 9436 </section> | |
| 9437 </section> | |
| 9438 <section name="f_and_c"> | |
| 9439 <param name="charge" value=":"/> | |
| 9440 <param name="size" value=":"/> | |
| 9441 <param name="remove_meta" value=""/> | |
| 9442 </section> | |
| 9443 <section name="id"> | |
| 9444 <param name="remove_clashes" value="false"/> | |
| 9445 <param name="keep_best_score_id" value="false"/> | |
| 9446 <param name="sequences_whitelist" value=""/> | |
| 9447 <param name="sequence_comparison_method" value="substring"/> | |
| 9448 <param name="accessions_whitelist" value=""/> | |
| 9449 <param name="remove_annotated_features" value="false"/> | |
| 9450 <param name="remove_unannotated_features" value="false"/> | |
| 9451 <param name="remove_unassigned_ids" value="false"/> | |
| 9452 <param name="rt" value="0.1"/> | |
| 9453 <param name="mz" value="0.001"/> | |
| 9454 <param name="blacklist_imperfect" value="false"/> | |
| 9455 </section> | |
| 9456 <section name="algorithm"> | |
| 9457 <section name="SignalToNoise"> | |
| 9458 <param name="max_intensity" value="-1"/> | |
| 9459 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9460 <param name="auto_max_percentile" value="95"/> | |
| 9461 <param name="auto_mode" value="0"/> | |
| 9462 <param name="win_len" value="200.0"/> | |
| 9463 <param name="bin_count" value="30"/> | |
| 9464 <param name="min_required_elements" value="10"/> | |
| 9465 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9466 <param name="write_log_messages" value="true"/> | |
| 9467 </section> | |
| 9468 </section> | |
| 9469 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9470 <output name="ctd_out" ftype="xml"> | |
| 9471 <assert_contents> | |
| 9472 <is_valid_xml/> | |
| 9473 </assert_contents> | |
| 9474 </output> | |
| 9475 </test> | |
| 9476 <test expect_num_outputs="2"> | |
| 9477 <conditional name="adv_opts_cond"> | |
| 9478 <param name="adv_opts_selector" value="advanced"/> | |
| 9479 <param name="force" value="false"/> | |
| 9480 <param name="test" value="true"/> | |
| 9481 </conditional> | |
| 9482 <param name="in" value="FileFilter_44_input.mzML"/> | |
| 9483 <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 9484 <param name="out_type" value="mzML"/> | |
| 9485 <param name="rt" value=":"/> | |
| 9486 <param name="mz" value=":"/> | |
| 9487 <param name="int" value=":"/> | |
| 9488 <param name="sort" value="false"/> | |
| 9489 <section name="peak_options"> | |
| 9490 <param name="sn" value="0.0"/> | |
| 9491 <param name="rm_pc_charge" value=""/> | |
| 9492 <param name="pc_mz_range" value=":"/> | |
| 9493 <param name="pc_mz_list" value=""/> | |
| 9494 <param name="level" value="1 2 3"/> | |
| 9495 <param name="sort_peaks" value="false"/> | |
| 9496 <param name="no_chromatograms" value="false"/> | |
| 9497 <param name="remove_chromatograms" value="false"/> | |
| 9498 <param name="remove_empty" value="false"/> | |
| 9499 <param name="mz_precision" value="64"/> | |
| 9500 <param name="int_precision" value="32"/> | |
| 9501 <param name="indexed_file" value="true"/> | |
| 9502 <param name="zlib_compression" value="false"/> | |
| 9503 <section name="numpress"> | |
| 9504 <param name="masstime" value="none"/> | |
| 9505 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9506 <param name="intensity" value="none"/> | |
| 9507 <param name="float_da" value="none"/> | |
| 9508 </section> | |
| 9509 </section> | |
| 9510 <section name="spectra"> | |
| 9511 <param name="remove_zoom" value="false"/> | |
| 9512 <param name="remove_mode" value=""/> | |
| 9513 <param name="remove_activation" value=""/> | |
| 9514 <param name="remove_collision_energy" value=":"/> | |
| 9515 <param name="remove_isolation_window_width" value=":"/> | |
| 9516 <param name="select_zoom" value="false"/> | |
| 9517 <param name="select_mode" value=""/> | |
| 9518 <param name="select_activation" value=""/> | |
| 9519 <param name="select_collision_energy" value=":"/> | |
| 9520 <param name="select_isolation_window_width" value=":"/> | |
| 9521 <param name="select_polarity" value=""/> | |
| 9522 <section name="blackorwhitelist"> | |
| 9523 <param name="similarity_threshold" value="-1.0"/> | |
| 9524 <param name="rt" value="0.01"/> | |
| 9525 <param name="mz" value="0.01"/> | |
| 9526 <param name="use_ppm_tolerance" value="false"/> | |
| 9527 <param name="blacklist" value="true"/> | |
| 9528 </section> | |
| 9529 </section> | |
| 9530 <section name="feature"> | |
| 9531 <param name="q" value=":"/> | |
| 9532 </section> | |
| 9533 <section name="consensus"> | |
| 9534 <param name="map" value=""/> | |
| 9535 <param name="map_and" value="false"/> | |
| 9536 <section name="blackorwhitelist"> | |
| 9537 <param name="blacklist" value="true"/> | |
| 9538 <param name="maps" value=""/> | |
| 9539 <param name="rt" value="60.0"/> | |
| 9540 <param name="mz" value="0.01"/> | |
| 9541 <param name="use_ppm_tolerance" value="false"/> | |
| 9542 </section> | |
| 9543 </section> | |
| 9544 <section name="f_and_c"> | |
| 9545 <param name="charge" value=":"/> | |
| 9546 <param name="size" value=":"/> | |
| 9547 <param name="remove_meta" value=""/> | |
| 9548 </section> | |
| 9549 <section name="id"> | |
| 9550 <param name="remove_clashes" value="false"/> | |
| 9551 <param name="keep_best_score_id" value="false"/> | |
| 9552 <param name="sequences_whitelist" value=""/> | |
| 9553 <param name="sequence_comparison_method" value="substring"/> | |
| 9554 <param name="accessions_whitelist" value=""/> | |
| 9555 <param name="remove_annotated_features" value="false"/> | |
| 9556 <param name="remove_unannotated_features" value="false"/> | |
| 9557 <param name="remove_unassigned_ids" value="false"/> | |
| 9558 <param name="rt" value="0.1"/> | |
| 9559 <param name="mz" value="0.001"/> | |
| 9560 <param name="blacklist_imperfect" value="false"/> | |
| 9561 </section> | |
| 9562 <section name="algorithm"> | |
| 9563 <section name="SignalToNoise"> | |
| 9564 <param name="max_intensity" value="-1"/> | |
| 9565 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9566 <param name="auto_max_percentile" value="95"/> | |
| 9567 <param name="auto_mode" value="0"/> | |
| 9568 <param name="win_len" value="200.0"/> | |
| 9569 <param name="bin_count" value="30"/> | |
| 9570 <param name="min_required_elements" value="10"/> | |
| 9571 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9572 <param name="write_log_messages" value="true"/> | |
| 9573 </section> | |
| 9574 </section> | |
| 9575 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9576 <output name="ctd_out" ftype="xml"> | |
| 9577 <assert_contents> | |
| 9578 <is_valid_xml/> | |
| 9579 </assert_contents> | |
| 9580 </output> | |
| 9581 </test> | |
| 9582 <test expect_num_outputs="2"> | |
| 9583 <conditional name="adv_opts_cond"> | |
| 9584 <param name="adv_opts_selector" value="advanced"/> | |
| 9585 <param name="force" value="false"/> | |
| 9586 <param name="test" value="true"/> | |
| 9587 </conditional> | |
| 9588 <param name="in" value="FileFilter_45_input.featureXML"/> | |
| 9589 <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 9590 <param name="out_type" value="featurexml"/> | |
| 9591 <param name="rt" value=":"/> | |
| 9592 <param name="mz" value=":"/> | |
| 9593 <param name="int" value=":"/> | |
| 9594 <param name="sort" value="false"/> | |
| 9595 <section name="peak_options"> | |
| 9596 <param name="sn" value="0.0"/> | |
| 9597 <param name="rm_pc_charge" value=""/> | |
| 9598 <param name="pc_mz_range" value=":"/> | |
| 9599 <param name="pc_mz_list" value=""/> | |
| 9600 <param name="level" value="1 2 3"/> | |
| 9601 <param name="sort_peaks" value="false"/> | |
| 9602 <param name="no_chromatograms" value="false"/> | |
| 9603 <param name="remove_chromatograms" value="false"/> | |
| 9604 <param name="remove_empty" value="false"/> | |
| 9605 <param name="mz_precision" value="64"/> | |
| 9606 <param name="int_precision" value="32"/> | |
| 9607 <param name="indexed_file" value="true"/> | |
| 9608 <param name="zlib_compression" value="false"/> | |
| 9609 <section name="numpress"> | |
| 9610 <param name="masstime" value="none"/> | |
| 9611 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9612 <param name="intensity" value="none"/> | |
| 9613 <param name="float_da" value="none"/> | |
| 9614 </section> | |
| 9615 </section> | |
| 9616 <section name="spectra"> | |
| 9617 <param name="remove_zoom" value="false"/> | |
| 9618 <param name="remove_mode" value=""/> | |
| 9619 <param name="remove_activation" value=""/> | |
| 9620 <param name="remove_collision_energy" value=":"/> | |
| 9621 <param name="remove_isolation_window_width" value=":"/> | |
| 9622 <param name="select_zoom" value="false"/> | |
| 9623 <param name="select_mode" value=""/> | |
| 9624 <param name="select_activation" value=""/> | |
| 9625 <param name="select_collision_energy" value=":"/> | |
| 9626 <param name="select_isolation_window_width" value=":"/> | |
| 9627 <param name="select_polarity" value=""/> | |
| 9628 <section name="blackorwhitelist"> | |
| 9629 <param name="similarity_threshold" value="-1.0"/> | |
| 9630 <param name="rt" value="0.01"/> | |
| 9631 <param name="mz" value="0.01"/> | |
| 9632 <param name="use_ppm_tolerance" value="false"/> | |
| 9633 <param name="blacklist" value="true"/> | |
| 9634 </section> | |
| 9635 </section> | |
| 9636 <section name="feature"> | |
| 9637 <param name="q" value=":"/> | |
| 9638 </section> | |
| 9639 <section name="consensus"> | |
| 9640 <param name="map" value=""/> | |
| 9641 <param name="map_and" value="false"/> | |
| 9642 <section name="blackorwhitelist"> | |
| 9643 <param name="blacklist" value="true"/> | |
| 9644 <param name="maps" value=""/> | |
| 9645 <param name="rt" value="60.0"/> | |
| 9646 <param name="mz" value="0.01"/> | |
| 9647 <param name="use_ppm_tolerance" value="false"/> | |
| 9648 </section> | |
| 9649 </section> | |
| 9650 <section name="f_and_c"> | |
| 9651 <param name="charge" value=":"/> | |
| 9652 <param name="size" value=":"/> | |
| 9653 <param name="remove_meta" value=""/> | |
| 9654 </section> | |
| 9655 <section name="id"> | |
| 9656 <param name="remove_clashes" value="false"/> | |
| 9657 <param name="keep_best_score_id" value="false"/> | |
| 9658 <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> | |
| 9659 <param name="sequence_comparison_method" value="substring"/> | |
| 9660 <param name="accessions_whitelist" value=""/> | |
| 9661 <param name="remove_annotated_features" value="false"/> | |
| 9662 <param name="remove_unannotated_features" value="false"/> | |
| 9663 <param name="remove_unassigned_ids" value="false"/> | |
| 9664 <param name="rt" value="0.1"/> | |
| 9665 <param name="mz" value="0.001"/> | |
| 9666 <param name="blacklist_imperfect" value="false"/> | |
| 9667 </section> | |
| 9668 <section name="algorithm"> | |
| 9669 <section name="SignalToNoise"> | |
| 9670 <param name="max_intensity" value="-1"/> | |
| 9671 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9672 <param name="auto_max_percentile" value="95"/> | |
| 9673 <param name="auto_mode" value="0"/> | |
| 9674 <param name="win_len" value="200.0"/> | |
| 9675 <param name="bin_count" value="30"/> | |
| 9676 <param name="min_required_elements" value="10"/> | |
| 9677 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9678 <param name="write_log_messages" value="true"/> | |
| 9679 </section> | |
| 9680 </section> | |
| 9681 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9682 <output name="ctd_out" ftype="xml"> | |
| 9683 <assert_contents> | |
| 9684 <is_valid_xml/> | |
| 9685 </assert_contents> | |
| 9686 </output> | |
| 9687 </test> | |
| 9688 <test expect_num_outputs="2"> | |
| 9689 <conditional name="adv_opts_cond"> | |
| 9690 <param name="adv_opts_selector" value="advanced"/> | |
| 9691 <param name="force" value="false"/> | |
| 9692 <param name="test" value="true"/> | |
| 9693 </conditional> | |
| 9694 <param name="in" value="FileFilter_46_input.featureXML"/> | |
| 9695 <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 9696 <param name="out_type" value="featurexml"/> | |
| 9697 <param name="rt" value=":"/> | |
| 9698 <param name="mz" value=":"/> | |
| 9699 <param name="int" value=":"/> | |
| 9700 <param name="sort" value="false"/> | |
| 9701 <section name="peak_options"> | |
| 9702 <param name="sn" value="0.0"/> | |
| 9703 <param name="rm_pc_charge" value=""/> | |
| 9704 <param name="pc_mz_range" value=":"/> | |
| 9705 <param name="pc_mz_list" value=""/> | |
| 9706 <param name="level" value="1 2 3"/> | |
| 9707 <param name="sort_peaks" value="false"/> | |
| 9708 <param name="no_chromatograms" value="false"/> | |
| 9709 <param name="remove_chromatograms" value="false"/> | |
| 9710 <param name="remove_empty" value="false"/> | |
| 9711 <param name="mz_precision" value="64"/> | |
| 9712 <param name="int_precision" value="32"/> | |
| 9713 <param name="indexed_file" value="true"/> | |
| 9714 <param name="zlib_compression" value="false"/> | |
| 9715 <section name="numpress"> | |
| 9716 <param name="masstime" value="none"/> | |
| 9717 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9718 <param name="intensity" value="none"/> | |
| 9719 <param name="float_da" value="none"/> | |
| 9720 </section> | |
| 9721 </section> | |
| 9722 <section name="spectra"> | |
| 9723 <param name="remove_zoom" value="false"/> | |
| 9724 <param name="remove_mode" value=""/> | |
| 9725 <param name="remove_activation" value=""/> | |
| 9726 <param name="remove_collision_energy" value=":"/> | |
| 9727 <param name="remove_isolation_window_width" value=":"/> | |
| 9728 <param name="select_zoom" value="false"/> | |
| 9729 <param name="select_mode" value=""/> | |
| 9730 <param name="select_activation" value=""/> | |
| 9731 <param name="select_collision_energy" value=":"/> | |
| 9732 <param name="select_isolation_window_width" value=":"/> | |
| 9733 <param name="select_polarity" value=""/> | |
| 9734 <section name="blackorwhitelist"> | |
| 9735 <param name="similarity_threshold" value="-1.0"/> | |
| 9736 <param name="rt" value="0.01"/> | |
| 9737 <param name="mz" value="0.01"/> | |
| 9738 <param name="use_ppm_tolerance" value="false"/> | |
| 9739 <param name="blacklist" value="true"/> | |
| 9740 </section> | |
| 9741 </section> | |
| 9742 <section name="feature"> | |
| 9743 <param name="q" value=":"/> | |
| 9744 </section> | |
| 9745 <section name="consensus"> | |
| 9746 <param name="map" value=""/> | |
| 9747 <param name="map_and" value="false"/> | |
| 9748 <section name="blackorwhitelist"> | |
| 9749 <param name="blacklist" value="true"/> | |
| 9750 <param name="maps" value=""/> | |
| 9751 <param name="rt" value="60.0"/> | |
| 9752 <param name="mz" value="0.01"/> | |
| 9753 <param name="use_ppm_tolerance" value="false"/> | |
| 9754 </section> | |
| 9755 </section> | |
| 9756 <section name="f_and_c"> | |
| 9757 <param name="charge" value=":"/> | |
| 9758 <param name="size" value=":"/> | |
| 9759 <param name="remove_meta" value=""/> | |
| 9760 </section> | |
| 9761 <section name="id"> | |
| 9762 <param name="remove_clashes" value="false"/> | |
| 9763 <param name="keep_best_score_id" value="false"/> | |
| 9764 <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> | |
| 9765 <param name="sequence_comparison_method" value="exact"/> | |
| 9766 <param name="accessions_whitelist" value=""/> | |
| 9767 <param name="remove_annotated_features" value="false"/> | |
| 9768 <param name="remove_unannotated_features" value="false"/> | |
| 9769 <param name="remove_unassigned_ids" value="false"/> | |
| 9770 <param name="rt" value="0.1"/> | |
| 9771 <param name="mz" value="0.001"/> | |
| 9772 <param name="blacklist_imperfect" value="false"/> | |
| 9773 </section> | |
| 9774 <section name="algorithm"> | |
| 9775 <section name="SignalToNoise"> | |
| 9776 <param name="max_intensity" value="-1"/> | |
| 9777 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9778 <param name="auto_max_percentile" value="95"/> | |
| 9779 <param name="auto_mode" value="0"/> | |
| 9780 <param name="win_len" value="200.0"/> | |
| 9781 <param name="bin_count" value="30"/> | |
| 9782 <param name="min_required_elements" value="10"/> | |
| 9783 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9784 <param name="write_log_messages" value="true"/> | |
| 9785 </section> | |
| 9786 </section> | |
| 9787 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9788 <output name="ctd_out" ftype="xml"> | |
| 9789 <assert_contents> | |
| 9790 <is_valid_xml/> | |
| 9791 </assert_contents> | |
| 9792 </output> | |
| 9793 </test> | |
| 9794 <test expect_num_outputs="2"> | |
| 9795 <conditional name="adv_opts_cond"> | |
| 9796 <param name="adv_opts_selector" value="advanced"/> | |
| 9797 <param name="force" value="false"/> | |
| 9798 <param name="test" value="true"/> | |
| 9799 </conditional> | |
| 9800 <param name="in" value="FileFilter_47_input.mzML"/> | |
| 9801 <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 9802 <param name="out_type" value="mzml"/> | |
| 9803 <param name="rt" value=":"/> | |
| 9804 <param name="mz" value=":"/> | |
| 9805 <param name="int" value=":"/> | |
| 9806 <param name="sort" value="false"/> | |
| 9807 <section name="peak_options"> | |
| 9808 <param name="sn" value="0.0"/> | |
| 9809 <param name="rm_pc_charge" value=""/> | |
| 9810 <param name="pc_mz_range" value=":"/> | |
| 9811 <param name="pc_mz_list" value=""/> | |
| 9812 <param name="level" value="1 2 3"/> | |
| 9813 <param name="sort_peaks" value="false"/> | |
| 9814 <param name="no_chromatograms" value="false"/> | |
| 9815 <param name="remove_chromatograms" value="false"/> | |
| 9816 <param name="remove_empty" value="false"/> | |
| 9817 <param name="mz_precision" value="64"/> | |
| 9818 <param name="int_precision" value="32"/> | |
| 9819 <param name="indexed_file" value="true"/> | |
| 9820 <param name="zlib_compression" value="false"/> | |
| 9821 <section name="numpress"> | |
| 9822 <param name="masstime" value="none"/> | |
| 9823 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9824 <param name="intensity" value="none"/> | |
| 9825 <param name="float_da" value="none"/> | |
| 9826 </section> | |
| 9827 </section> | |
| 9828 <section name="spectra"> | |
| 9829 <param name="remove_zoom" value="false"/> | |
| 9830 <param name="remove_mode" value=""/> | |
| 9831 <param name="remove_activation" value=""/> | |
| 9832 <param name="remove_collision_energy" value=":"/> | |
| 9833 <param name="remove_isolation_window_width" value=":"/> | |
| 9834 <param name="select_zoom" value="false"/> | |
| 9835 <param name="select_mode" value=""/> | |
| 9836 <param name="select_activation" value=""/> | |
| 9837 <param name="select_collision_energy" value=":"/> | |
| 9838 <param name="select_isolation_window_width" value=":"/> | |
| 9839 <param name="select_polarity" value=""/> | |
| 9840 <section name="blackorwhitelist"> | |
| 9841 <param name="file" value="FileFilter_47_input_select.mzML"/> | |
| 9842 <param name="similarity_threshold" value="0.9"/> | |
| 9843 <param name="rt" value="0.01"/> | |
| 9844 <param name="mz" value="0.01"/> | |
| 9845 <param name="use_ppm_tolerance" value="false"/> | |
| 9846 <param name="blacklist" value="true"/> | |
| 9847 </section> | |
| 9848 </section> | |
| 9849 <section name="feature"> | |
| 9850 <param name="q" value=":"/> | |
| 9851 </section> | |
| 9852 <section name="consensus"> | |
| 9853 <param name="map" value=""/> | |
| 9854 <param name="map_and" value="false"/> | |
| 9855 <section name="blackorwhitelist"> | |
| 9856 <param name="blacklist" value="true"/> | |
| 9857 <param name="maps" value=""/> | |
| 9858 <param name="rt" value="60.0"/> | |
| 9859 <param name="mz" value="0.01"/> | |
| 9860 <param name="use_ppm_tolerance" value="false"/> | |
| 9861 </section> | |
| 9862 </section> | |
| 9863 <section name="f_and_c"> | |
| 9864 <param name="charge" value=":"/> | |
| 9865 <param name="size" value=":"/> | |
| 9866 <param name="remove_meta" value=""/> | |
| 9867 </section> | |
| 9868 <section name="id"> | |
| 9869 <param name="remove_clashes" value="false"/> | |
| 9870 <param name="keep_best_score_id" value="false"/> | |
| 9871 <param name="sequences_whitelist" value=""/> | |
| 9872 <param name="sequence_comparison_method" value="substring"/> | |
| 9873 <param name="accessions_whitelist" value=""/> | |
| 9874 <param name="remove_annotated_features" value="false"/> | |
| 9875 <param name="remove_unannotated_features" value="false"/> | |
| 9876 <param name="remove_unassigned_ids" value="false"/> | |
| 9877 <param name="rt" value="0.1"/> | |
| 9878 <param name="mz" value="0.001"/> | |
| 9879 <param name="blacklist_imperfect" value="false"/> | |
| 9880 </section> | |
| 9881 <section name="algorithm"> | |
| 9882 <section name="SignalToNoise"> | |
| 9883 <param name="max_intensity" value="-1"/> | |
| 9884 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9885 <param name="auto_max_percentile" value="95"/> | |
| 9886 <param name="auto_mode" value="0"/> | |
| 9887 <param name="win_len" value="200.0"/> | |
| 9888 <param name="bin_count" value="30"/> | |
| 9889 <param name="min_required_elements" value="10"/> | |
| 9890 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9891 <param name="write_log_messages" value="true"/> | |
| 9892 </section> | |
| 9893 </section> | |
| 9894 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 9895 <output name="ctd_out" ftype="xml"> | |
| 9896 <assert_contents> | |
| 9897 <is_valid_xml/> | |
| 9898 </assert_contents> | |
| 9899 </output> | |
| 9900 </test> | |
| 9901 <test expect_num_outputs="2"> | |
| 9902 <conditional name="adv_opts_cond"> | |
| 9903 <param name="adv_opts_selector" value="advanced"/> | |
| 9904 <param name="force" value="false"/> | |
| 9905 <param name="test" value="true"/> | |
| 9906 </conditional> | |
| 9907 <param name="in" value="FileFilter_47_input.mzML"/> | |
| 9908 <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 9909 <param name="out_type" value="mzml"/> | |
| 9910 <param name="rt" value=":"/> | |
| 9911 <param name="mz" value=":"/> | |
| 9912 <param name="int" value=":"/> | |
| 9913 <param name="sort" value="false"/> | |
| 9914 <section name="peak_options"> | |
| 9915 <param name="sn" value="0.0"/> | |
| 9916 <param name="rm_pc_charge" value=""/> | |
| 9917 <param name="pc_mz_range" value=":"/> | |
| 9918 <param name="pc_mz_list" value=""/> | |
| 9919 <param name="level" value="1 2 3"/> | |
| 9920 <param name="sort_peaks" value="false"/> | |
| 9921 <param name="no_chromatograms" value="false"/> | |
| 9922 <param name="remove_chromatograms" value="false"/> | |
| 9923 <param name="remove_empty" value="false"/> | |
| 9924 <param name="mz_precision" value="64"/> | |
| 9925 <param name="int_precision" value="32"/> | |
| 9926 <param name="indexed_file" value="true"/> | |
| 9927 <param name="zlib_compression" value="false"/> | |
| 9928 <section name="numpress"> | |
| 9929 <param name="masstime" value="none"/> | |
| 9930 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 9931 <param name="intensity" value="none"/> | |
| 9932 <param name="float_da" value="none"/> | |
| 9933 </section> | |
| 9934 </section> | |
| 9935 <section name="spectra"> | |
| 9936 <param name="remove_zoom" value="false"/> | |
| 9937 <param name="remove_mode" value=""/> | |
| 9938 <param name="remove_activation" value=""/> | |
| 9939 <param name="remove_collision_energy" value=":"/> | |
| 9940 <param name="remove_isolation_window_width" value=":"/> | |
| 9941 <param name="select_zoom" value="false"/> | |
| 9942 <param name="select_mode" value=""/> | |
| 9943 <param name="select_activation" value=""/> | |
| 9944 <param name="select_collision_energy" value=":"/> | |
| 9945 <param name="select_isolation_window_width" value=":"/> | |
| 9946 <param name="select_polarity" value=""/> | |
| 9947 <section name="blackorwhitelist"> | |
| 9948 <param name="file" value="FileFilter_47_input_select.mzML"/> | |
| 9949 <param name="similarity_threshold" value="0.9"/> | |
| 9950 <param name="rt" value="0.01"/> | |
| 9951 <param name="mz" value="0.01"/> | |
| 9952 <param name="use_ppm_tolerance" value="false"/> | |
| 9953 <param name="blacklist" value="false"/> | |
| 9954 </section> | |
| 9955 </section> | |
| 9956 <section name="feature"> | |
| 9957 <param name="q" value=":"/> | |
| 9958 </section> | |
| 9959 <section name="consensus"> | |
| 9960 <param name="map" value=""/> | |
| 9961 <param name="map_and" value="false"/> | |
| 9962 <section name="blackorwhitelist"> | |
| 9963 <param name="blacklist" value="true"/> | |
| 9964 <param name="maps" value=""/> | |
| 9965 <param name="rt" value="60.0"/> | |
| 9966 <param name="mz" value="0.01"/> | |
| 9967 <param name="use_ppm_tolerance" value="false"/> | |
| 9968 </section> | |
| 9969 </section> | |
| 9970 <section name="f_and_c"> | |
| 9971 <param name="charge" value=":"/> | |
| 9972 <param name="size" value=":"/> | |
| 9973 <param name="remove_meta" value=""/> | |
| 9974 </section> | |
| 9975 <section name="id"> | |
| 9976 <param name="remove_clashes" value="false"/> | |
| 9977 <param name="keep_best_score_id" value="false"/> | |
| 9978 <param name="sequences_whitelist" value=""/> | |
| 9979 <param name="sequence_comparison_method" value="substring"/> | |
| 9980 <param name="accessions_whitelist" value=""/> | |
| 9981 <param name="remove_annotated_features" value="false"/> | |
| 9982 <param name="remove_unannotated_features" value="false"/> | |
| 9983 <param name="remove_unassigned_ids" value="false"/> | |
| 9984 <param name="rt" value="0.1"/> | |
| 9985 <param name="mz" value="0.001"/> | |
| 9986 <param name="blacklist_imperfect" value="false"/> | |
| 9987 </section> | |
| 9988 <section name="algorithm"> | |
| 9989 <section name="SignalToNoise"> | |
| 9990 <param name="max_intensity" value="-1"/> | |
| 9991 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 9992 <param name="auto_max_percentile" value="95"/> | |
| 9993 <param name="auto_mode" value="0"/> | |
| 9994 <param name="win_len" value="200.0"/> | |
| 9995 <param name="bin_count" value="30"/> | |
| 9996 <param name="min_required_elements" value="10"/> | |
| 9997 <param name="noise_for_empty_window" value="1e+20"/> | |
| 9998 <param name="write_log_messages" value="true"/> | |
| 9999 </section> | |
| 10000 </section> | |
| 10001 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10002 <output name="ctd_out" ftype="xml"> | |
| 10003 <assert_contents> | |
| 10004 <is_valid_xml/> | |
| 10005 </assert_contents> | |
| 10006 </output> | |
| 10007 </test> | |
| 10008 <test expect_num_outputs="2"> | |
| 10009 <conditional name="adv_opts_cond"> | |
| 10010 <param name="adv_opts_selector" value="advanced"/> | |
| 10011 <param name="force" value="false"/> | |
| 10012 <param name="test" value="true"/> | |
| 10013 </conditional> | |
| 10014 <param name="in" value="FileFilter_49_input.mzML"/> | |
| 10015 <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10016 <param name="out_type" value="mzml"/> | |
| 10017 <param name="rt" value=":"/> | |
| 10018 <param name="mz" value=":"/> | |
| 10019 <param name="int" value=":"/> | |
| 10020 <param name="sort" value="false"/> | |
| 10021 <section name="peak_options"> | |
| 10022 <param name="sn" value="0.0"/> | |
| 10023 <param name="rm_pc_charge" value=""/> | |
| 10024 <param name="pc_mz_range" value=":"/> | |
| 10025 <param name="pc_mz_list" value=""/> | |
| 10026 <param name="level" value="1 2 3"/> | |
| 10027 <param name="sort_peaks" value="false"/> | |
| 10028 <param name="no_chromatograms" value="false"/> | |
| 10029 <param name="remove_chromatograms" value="false"/> | |
| 10030 <param name="remove_empty" value="false"/> | |
| 10031 <param name="mz_precision" value="64"/> | |
| 10032 <param name="int_precision" value="32"/> | |
| 10033 <param name="indexed_file" value="true"/> | |
| 10034 <param name="zlib_compression" value="true"/> | |
| 10035 <section name="numpress"> | |
| 10036 <param name="masstime" value="linear"/> | |
| 10037 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 10038 <param name="intensity" value="pic"/> | |
| 10039 <param name="float_da" value="slof"/> | |
| 10040 </section> | |
| 10041 </section> | |
| 10042 <section name="spectra"> | |
| 10043 <param name="remove_zoom" value="false"/> | |
| 10044 <param name="remove_mode" value=""/> | |
| 10045 <param name="remove_activation" value=""/> | |
| 10046 <param name="remove_collision_energy" value=":"/> | |
| 10047 <param name="remove_isolation_window_width" value=":"/> | |
| 10048 <param name="select_zoom" value="false"/> | |
| 10049 <param name="select_mode" value=""/> | |
| 10050 <param name="select_activation" value=""/> | |
| 10051 <param name="select_collision_energy" value=":"/> | |
| 10052 <param name="select_isolation_window_width" value=":"/> | |
| 10053 <param name="select_polarity" value=""/> | |
| 10054 <section name="blackorwhitelist"> | |
| 10055 <param name="similarity_threshold" value="-1.0"/> | |
| 10056 <param name="rt" value="0.01"/> | |
| 10057 <param name="mz" value="0.01"/> | |
| 10058 <param name="use_ppm_tolerance" value="false"/> | |
| 10059 <param name="blacklist" value="true"/> | |
| 10060 </section> | |
| 10061 </section> | |
| 10062 <section name="feature"> | |
| 10063 <param name="q" value=":"/> | |
| 10064 </section> | |
| 10065 <section name="consensus"> | |
| 10066 <param name="map" value=""/> | |
| 10067 <param name="map_and" value="false"/> | |
| 10068 <section name="blackorwhitelist"> | |
| 10069 <param name="blacklist" value="true"/> | |
| 10070 <param name="maps" value=""/> | |
| 10071 <param name="rt" value="60.0"/> | |
| 10072 <param name="mz" value="0.01"/> | |
| 10073 <param name="use_ppm_tolerance" value="false"/> | |
| 10074 </section> | |
| 10075 </section> | |
| 10076 <section name="f_and_c"> | |
| 10077 <param name="charge" value=":"/> | |
| 10078 <param name="size" value=":"/> | |
| 10079 <param name="remove_meta" value=""/> | |
| 10080 </section> | |
| 10081 <section name="id"> | |
| 10082 <param name="remove_clashes" value="false"/> | |
| 10083 <param name="keep_best_score_id" value="false"/> | |
| 10084 <param name="sequences_whitelist" value=""/> | |
| 10085 <param name="sequence_comparison_method" value="substring"/> | |
| 10086 <param name="accessions_whitelist" value=""/> | |
| 10087 <param name="remove_annotated_features" value="false"/> | |
| 10088 <param name="remove_unannotated_features" value="false"/> | |
| 10089 <param name="remove_unassigned_ids" value="false"/> | |
| 10090 <param name="rt" value="0.1"/> | |
| 10091 <param name="mz" value="0.001"/> | |
| 10092 <param name="blacklist_imperfect" value="false"/> | |
| 10093 </section> | |
| 10094 <section name="algorithm"> | |
| 10095 <section name="SignalToNoise"> | |
| 10096 <param name="max_intensity" value="-1"/> | |
| 10097 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 10098 <param name="auto_max_percentile" value="95"/> | |
| 10099 <param name="auto_mode" value="0"/> | |
| 10100 <param name="win_len" value="200.0"/> | |
| 10101 <param name="bin_count" value="30"/> | |
| 10102 <param name="min_required_elements" value="10"/> | |
| 10103 <param name="noise_for_empty_window" value="1e+20"/> | |
| 10104 <param name="write_log_messages" value="true"/> | |
| 10105 </section> | |
| 10106 </section> | |
| 10107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10108 <output name="ctd_out" ftype="xml"> | |
| 10109 <assert_contents> | |
| 10110 <is_valid_xml/> | |
| 10111 </assert_contents> | |
| 10112 </output> | |
| 10113 </test> | |
| 10114 </xml> | |
| 10115 <xml name="autotest_FileInfo"> | |
| 10116 <test expect_num_outputs="2"> | |
| 10117 <conditional name="adv_opts_cond"> | |
| 10118 <param name="adv_opts_selector" value="advanced"/> | |
| 10119 <param name="force" value="false"/> | |
| 10120 <param name="test" value="true"/> | |
| 10121 </conditional> | |
| 10122 <param name="in" value="FileInfo_1_input.dta" ftype="dta"/> | |
| 10123 <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10124 <param name="m" value="false"/> | |
| 10125 <param name="p" value="false"/> | |
| 10126 <param name="s" value="false"/> | |
| 10127 <param name="d" value="false"/> | |
| 10128 <param name="c" value="false"/> | |
| 10129 <param name="v" value="false"/> | |
| 10130 <param name="i" value="false"/> | |
| 10131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10132 <output name="ctd_out" ftype="xml"> | |
| 10133 <assert_contents> | |
| 10134 <is_valid_xml/> | |
| 10135 </assert_contents> | |
| 10136 </output> | |
| 10137 </test> | |
| 10138 <test expect_num_outputs="2"> | |
| 10139 <conditional name="adv_opts_cond"> | |
| 10140 <param name="adv_opts_selector" value="advanced"/> | |
| 10141 <param name="force" value="false"/> | |
| 10142 <param name="test" value="true"/> | |
| 10143 </conditional> | |
| 10144 <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> | |
| 10145 <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10146 <param name="m" value="false"/> | |
| 10147 <param name="p" value="false"/> | |
| 10148 <param name="s" value="false"/> | |
| 10149 <param name="d" value="false"/> | |
| 10150 <param name="c" value="false"/> | |
| 10151 <param name="v" value="false"/> | |
| 10152 <param name="i" value="false"/> | |
| 10153 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10154 <output name="ctd_out" ftype="xml"> | |
| 10155 <assert_contents> | |
| 10156 <is_valid_xml/> | |
| 10157 </assert_contents> | |
| 10158 </output> | |
| 10159 </test> | |
| 10160 <test expect_num_outputs="2"> | |
| 10161 <conditional name="adv_opts_cond"> | |
| 10162 <param name="adv_opts_selector" value="advanced"/> | |
| 10163 <param name="force" value="false"/> | |
| 10164 <param name="test" value="true"/> | |
| 10165 </conditional> | |
| 10166 <param name="in" value="FileInfo_3_input.featureXML"/> | |
| 10167 <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10168 <param name="m" value="true"/> | |
| 10169 <param name="p" value="true"/> | |
| 10170 <param name="s" value="true"/> | |
| 10171 <param name="d" value="false"/> | |
| 10172 <param name="c" value="false"/> | |
| 10173 <param name="v" value="false"/> | |
| 10174 <param name="i" value="false"/> | |
| 10175 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10176 <output name="ctd_out" ftype="xml"> | |
| 10177 <assert_contents> | |
| 10178 <is_valid_xml/> | |
| 10179 </assert_contents> | |
| 10180 </output> | |
| 10181 </test> | |
| 10182 <test expect_num_outputs="2"> | |
| 10183 <conditional name="adv_opts_cond"> | |
| 10184 <param name="adv_opts_selector" value="advanced"/> | |
| 10185 <param name="force" value="false"/> | |
| 10186 <param name="test" value="true"/> | |
| 10187 </conditional> | |
| 10188 <param name="in" value="FileInfo_4_input.mzXML"/> | |
| 10189 <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10190 <param name="m" value="true"/> | |
| 10191 <param name="p" value="false"/> | |
| 10192 <param name="s" value="false"/> | |
| 10193 <param name="d" value="false"/> | |
| 10194 <param name="c" value="false"/> | |
| 10195 <param name="v" value="false"/> | |
| 10196 <param name="i" value="false"/> | |
| 10197 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10198 <output name="ctd_out" ftype="xml"> | |
| 10199 <assert_contents> | |
| 10200 <is_valid_xml/> | |
| 10201 </assert_contents> | |
| 10202 </output> | |
| 10203 </test> | |
| 10204 <test expect_num_outputs="2"> | |
| 10205 <conditional name="adv_opts_cond"> | |
| 10206 <param name="adv_opts_selector" value="advanced"/> | |
| 10207 <param name="force" value="false"/> | |
| 10208 <param name="test" value="true"/> | |
| 10209 </conditional> | |
| 10210 <param name="in" value="FileInfo_5_input.mzDat"/> | |
| 10211 <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10212 <param name="m" value="true"/> | |
| 10213 <param name="p" value="false"/> | |
| 10214 <param name="s" value="true"/> | |
| 10215 <param name="d" value="false"/> | |
| 10216 <param name="c" value="false"/> | |
| 10217 <param name="v" value="false"/> | |
| 10218 <param name="i" value="false"/> | |
| 10219 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10220 <output name="ctd_out" ftype="xml"> | |
| 10221 <assert_contents> | |
| 10222 <is_valid_xml/> | |
| 10223 </assert_contents> | |
| 10224 </output> | |
| 10225 </test> | |
| 10226 <test expect_num_outputs="2"> | |
| 10227 <conditional name="adv_opts_cond"> | |
| 10228 <param name="adv_opts_selector" value="advanced"/> | |
| 10229 <param name="force" value="false"/> | |
| 10230 <param name="test" value="true"/> | |
| 10231 </conditional> | |
| 10232 <param name="in" value="FileInfo_6_input.mzData"/> | |
| 10233 <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10234 <param name="m" value="false"/> | |
| 10235 <param name="p" value="false"/> | |
| 10236 <param name="s" value="true"/> | |
| 10237 <param name="d" value="true"/> | |
| 10238 <param name="c" value="false"/> | |
| 10239 <param name="v" value="false"/> | |
| 10240 <param name="i" value="false"/> | |
| 10241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10242 <output name="ctd_out" ftype="xml"> | |
| 10243 <assert_contents> | |
| 10244 <is_valid_xml/> | |
| 10245 </assert_contents> | |
| 10246 </output> | |
| 10247 </test> | |
| 10248 <test expect_num_outputs="2"> | |
| 10249 <conditional name="adv_opts_cond"> | |
| 10250 <param name="adv_opts_selector" value="advanced"/> | |
| 10251 <param name="force" value="false"/> | |
| 10252 <param name="test" value="true"/> | |
| 10253 </conditional> | |
| 10254 <param name="in" value="FileInfo_7_input.consensusXML"/> | |
| 10255 <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10256 <param name="m" value="true"/> | |
| 10257 <param name="p" value="true"/> | |
| 10258 <param name="s" value="true"/> | |
| 10259 <param name="d" value="false"/> | |
| 10260 <param name="c" value="false"/> | |
| 10261 <param name="v" value="false"/> | |
| 10262 <param name="i" value="false"/> | |
| 10263 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10264 <output name="ctd_out" ftype="xml"> | |
| 10265 <assert_contents> | |
| 10266 <is_valid_xml/> | |
| 10267 </assert_contents> | |
| 10268 </output> | |
| 10269 </test> | |
| 10270 <test expect_num_outputs="2"> | |
| 10271 <conditional name="adv_opts_cond"> | |
| 10272 <param name="adv_opts_selector" value="advanced"/> | |
| 10273 <param name="force" value="false"/> | |
| 10274 <param name="test" value="true"/> | |
| 10275 </conditional> | |
| 10276 <param name="in" value="FileInfo_9_input.mzML"/> | |
| 10277 <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10278 <param name="m" value="true"/> | |
| 10279 <param name="p" value="true"/> | |
| 10280 <param name="s" value="true"/> | |
| 10281 <param name="d" value="false"/> | |
| 10282 <param name="c" value="false"/> | |
| 10283 <param name="v" value="false"/> | |
| 10284 <param name="i" value="false"/> | |
| 10285 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10286 <output name="ctd_out" ftype="xml"> | |
| 10287 <assert_contents> | |
| 10288 <is_valid_xml/> | |
| 10289 </assert_contents> | |
| 10290 </output> | |
| 10291 </test> | |
| 10292 <test expect_num_outputs="2"> | |
| 10293 <conditional name="adv_opts_cond"> | |
| 10294 <param name="adv_opts_selector" value="advanced"/> | |
| 10295 <param name="force" value="false"/> | |
| 10296 <param name="test" value="true"/> | |
| 10297 </conditional> | |
| 10298 <param name="in" value="FileInfo_10_input.idXML"/> | |
| 10299 <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10300 <param name="m" value="false"/> | |
| 10301 <param name="p" value="false"/> | |
| 10302 <param name="s" value="false"/> | |
| 10303 <param name="d" value="false"/> | |
| 10304 <param name="c" value="false"/> | |
| 10305 <param name="v" value="false"/> | |
| 10306 <param name="i" value="false"/> | |
| 10307 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10308 <output name="ctd_out" ftype="xml"> | |
| 10309 <assert_contents> | |
| 10310 <is_valid_xml/> | |
| 10311 </assert_contents> | |
| 10312 </output> | |
| 10313 </test> | |
| 10314 <test expect_num_outputs="2"> | |
| 10315 <conditional name="adv_opts_cond"> | |
| 10316 <param name="adv_opts_selector" value="advanced"/> | |
| 10317 <param name="force" value="false"/> | |
| 10318 <param name="test" value="true"/> | |
| 10319 </conditional> | |
| 10320 <param name="in" value="FileInfo_12_input.mzML"/> | |
| 10321 <param name="m" value="false"/> | |
| 10322 <param name="p" value="false"/> | |
| 10323 <param name="s" value="false"/> | |
| 10324 <param name="d" value="false"/> | |
| 10325 <param name="c" value="false"/> | |
| 10326 <param name="v" value="false"/> | |
| 10327 <param name="i" value="true"/> | |
| 10328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10329 <output name="ctd_out" ftype="xml"> | |
| 10330 <assert_contents> | |
| 10331 <is_valid_xml/> | |
| 10332 </assert_contents> | |
| 10333 </output> | |
| 10334 </test> | |
| 10335 <test expect_num_outputs="2"> | |
| 10336 <conditional name="adv_opts_cond"> | |
| 10337 <param name="adv_opts_selector" value="advanced"/> | |
| 10338 <param name="force" value="false"/> | |
| 10339 <param name="test" value="true"/> | |
| 10340 </conditional> | |
| 10341 <param name="in" value="FileInfo_13_input.consensusXML"/> | |
| 10342 <param name="m" value="false"/> | |
| 10343 <param name="p" value="false"/> | |
| 10344 <param name="s" value="false"/> | |
| 10345 <param name="d" value="false"/> | |
| 10346 <param name="c" value="false"/> | |
| 10347 <param name="v" value="false"/> | |
| 10348 <param name="i" value="false"/> | |
| 10349 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10350 <output name="ctd_out" ftype="xml"> | |
| 10351 <assert_contents> | |
| 10352 <is_valid_xml/> | |
| 10353 </assert_contents> | |
| 10354 </output> | |
| 10355 </test> | |
| 10356 <test expect_num_outputs="2"> | |
| 10357 <conditional name="adv_opts_cond"> | |
| 10358 <param name="adv_opts_selector" value="advanced"/> | |
| 10359 <param name="force" value="false"/> | |
| 10360 <param name="test" value="true"/> | |
| 10361 </conditional> | |
| 10362 <param name="in" value="FileInfo_14_input.mzid"/> | |
| 10363 <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10364 <param name="m" value="false"/> | |
| 10365 <param name="p" value="false"/> | |
| 10366 <param name="s" value="false"/> | |
| 10367 <param name="d" value="false"/> | |
| 10368 <param name="c" value="false"/> | |
| 10369 <param name="v" value="true"/> | |
| 10370 <param name="i" value="false"/> | |
| 10371 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10372 <output name="ctd_out" ftype="xml"> | |
| 10373 <assert_contents> | |
| 10374 <is_valid_xml/> | |
| 10375 </assert_contents> | |
| 10376 </output> | |
| 10377 </test> | |
| 10378 <test expect_num_outputs="2"> | |
| 10379 <conditional name="adv_opts_cond"> | |
| 10380 <param name="adv_opts_selector" value="advanced"/> | |
| 10381 <param name="force" value="false"/> | |
| 10382 <param name="test" value="true"/> | |
| 10383 </conditional> | |
| 10384 <param name="in" value="FileInfo_15_input.mzid"/> | |
| 10385 <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10386 <param name="m" value="false"/> | |
| 10387 <param name="p" value="false"/> | |
| 10388 <param name="s" value="false"/> | |
| 10389 <param name="d" value="false"/> | |
| 10390 <param name="c" value="false"/> | |
| 10391 <param name="v" value="true"/> | |
| 10392 <param name="i" value="false"/> | |
| 10393 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10394 <output name="ctd_out" ftype="xml"> | |
| 10395 <assert_contents> | |
| 10396 <is_valid_xml/> | |
| 10397 </assert_contents> | |
| 10398 </output> | |
| 10399 </test> | |
| 10400 <test expect_num_outputs="2"> | |
| 10401 <conditional name="adv_opts_cond"> | |
| 10402 <param name="adv_opts_selector" value="advanced"/> | |
| 10403 <param name="force" value="false"/> | |
| 10404 <param name="test" value="true"/> | |
| 10405 </conditional> | |
| 10406 <param name="in" value="FileInfo_16_input.trafoXML"/> | |
| 10407 <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10408 <param name="m" value="false"/> | |
| 10409 <param name="p" value="false"/> | |
| 10410 <param name="s" value="false"/> | |
| 10411 <param name="d" value="false"/> | |
| 10412 <param name="c" value="false"/> | |
| 10413 <param name="v" value="false"/> | |
| 10414 <param name="i" value="false"/> | |
| 10415 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10416 <output name="ctd_out" ftype="xml"> | |
| 10417 <assert_contents> | |
| 10418 <is_valid_xml/> | |
| 10419 </assert_contents> | |
| 10420 </output> | |
| 10421 </test> | |
| 10422 <test expect_num_outputs="2"> | |
| 10423 <conditional name="adv_opts_cond"> | |
| 10424 <param name="adv_opts_selector" value="advanced"/> | |
| 10425 <param name="force" value="false"/> | |
| 10426 <param name="test" value="true"/> | |
| 10427 </conditional> | |
| 10428 <param name="in" value="FileInfo_17_input.fasta"/> | |
| 10429 <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10430 <param name="m" value="false"/> | |
| 10431 <param name="p" value="false"/> | |
| 10432 <param name="s" value="false"/> | |
| 10433 <param name="d" value="false"/> | |
| 10434 <param name="c" value="false"/> | |
| 10435 <param name="v" value="false"/> | |
| 10436 <param name="i" value="false"/> | |
| 10437 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10438 <output name="ctd_out" ftype="xml"> | |
| 10439 <assert_contents> | |
| 10440 <is_valid_xml/> | |
| 10441 </assert_contents> | |
| 10442 </output> | |
| 10443 </test> | |
| 10444 <test expect_num_outputs="2"> | |
| 10445 <conditional name="adv_opts_cond"> | |
| 10446 <param name="adv_opts_selector" value="advanced"/> | |
| 10447 <param name="force" value="false"/> | |
| 10448 <param name="test" value="true"/> | |
| 10449 </conditional> | |
| 10450 <param name="in" value="FileInfo_18_input.fasta"/> | |
| 10451 <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 10452 <param name="m" value="false"/> | |
| 10453 <param name="p" value="false"/> | |
| 10454 <param name="s" value="false"/> | |
| 10455 <param name="d" value="false"/> | |
| 10456 <param name="c" value="false"/> | |
| 10457 <param name="v" value="false"/> | |
| 10458 <param name="i" value="false"/> | |
| 10459 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10460 <output name="ctd_out" ftype="xml"> | |
| 10461 <assert_contents> | |
| 10462 <is_valid_xml/> | |
| 10463 </assert_contents> | |
| 10464 </output> | |
| 10465 </test> | |
| 10466 </xml> | |
| 10467 <xml name="autotest_FileMerger"> | |
| 10468 <test expect_num_outputs="2"> | |
| 10469 <conditional name="adv_opts_cond"> | |
| 10470 <param name="adv_opts_selector" value="advanced"/> | |
| 10471 <param name="force" value="false"/> | |
| 10472 <param name="test" value="true"/> | |
| 10473 </conditional> | |
| 10474 <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/> | |
| 10475 <param name="out_type" value="mzML"/> | |
| 10476 <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10477 <param name="annotate_file_origin" value="false"/> | |
| 10478 <param name="append_method" value="append_rows"/> | |
| 10479 <section name="rt_concat"> | |
| 10480 <param name="gap" value="0.0"/> | |
| 10481 </section> | |
| 10482 <section name="raw"> | |
| 10483 <param name="rt_auto" value="false"/> | |
| 10484 <param name="rt_custom" value="5.0 10.0"/> | |
| 10485 <param name="rt_filename" value="false"/> | |
| 10486 <param name="ms_level" value="0"/> | |
| 10487 </section> | |
| 10488 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10489 <output name="ctd_out" ftype="xml"> | |
| 10490 <assert_contents> | |
| 10491 <is_valid_xml/> | |
| 10492 </assert_contents> | |
| 10493 </output> | |
| 10494 </test> | |
| 10495 <test expect_num_outputs="2"> | |
| 10496 <conditional name="adv_opts_cond"> | |
| 10497 <param name="adv_opts_selector" value="advanced"/> | |
| 10498 <param name="force" value="false"/> | |
| 10499 <param name="test" value="true"/> | |
| 10500 </conditional> | |
| 10501 <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/> | |
| 10502 <param name="out_type" value="mzML"/> | |
| 10503 <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10504 <param name="annotate_file_origin" value="false"/> | |
| 10505 <param name="append_method" value="append_rows"/> | |
| 10506 <section name="rt_concat"> | |
| 10507 <param name="gap" value="0.0"/> | |
| 10508 </section> | |
| 10509 <section name="raw"> | |
| 10510 <param name="rt_auto" value="true"/> | |
| 10511 <param name="rt_custom" value=""/> | |
| 10512 <param name="rt_filename" value="false"/> | |
| 10513 <param name="ms_level" value="0"/> | |
| 10514 </section> | |
| 10515 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10516 <output name="ctd_out" ftype="xml"> | |
| 10517 <assert_contents> | |
| 10518 <is_valid_xml/> | |
| 10519 </assert_contents> | |
| 10520 </output> | |
| 10521 </test> | |
| 10522 <test expect_num_outputs="2"> | |
| 10523 <conditional name="adv_opts_cond"> | |
| 10524 <param name="adv_opts_selector" value="advanced"/> | |
| 10525 <param name="force" value="false"/> | |
| 10526 <param name="test" value="true"/> | |
| 10527 </conditional> | |
| 10528 <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/> | |
| 10529 <param name="out_type" value="mzML"/> | |
| 10530 <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10531 <param name="annotate_file_origin" value="false"/> | |
| 10532 <param name="append_method" value="append_rows"/> | |
| 10533 <section name="rt_concat"> | |
| 10534 <param name="gap" value="0.0"/> | |
| 10535 </section> | |
| 10536 <section name="raw"> | |
| 10537 <param name="rt_auto" value="false"/> | |
| 10538 <param name="rt_custom" value=""/> | |
| 10539 <param name="rt_filename" value="false"/> | |
| 10540 <param name="ms_level" value="0"/> | |
| 10541 </section> | |
| 10542 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10543 <output name="ctd_out" ftype="xml"> | |
| 10544 <assert_contents> | |
| 10545 <is_valid_xml/> | |
| 10546 </assert_contents> | |
| 10547 </output> | |
| 10548 </test> | |
| 10549 <test expect_num_outputs="2"> | |
| 10550 <conditional name="adv_opts_cond"> | |
| 10551 <param name="adv_opts_selector" value="advanced"/> | |
| 10552 <param name="force" value="false"/> | |
| 10553 <param name="test" value="true"/> | |
| 10554 </conditional> | |
| 10555 <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/> | |
| 10556 <param name="out_type" value="mzML"/> | |
| 10557 <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10558 <param name="annotate_file_origin" value="false"/> | |
| 10559 <param name="append_method" value="append_rows"/> | |
| 10560 <section name="rt_concat"> | |
| 10561 <param name="gap" value="0.0"/> | |
| 10562 </section> | |
| 10563 <section name="raw"> | |
| 10564 <param name="rt_auto" value="false"/> | |
| 10565 <param name="rt_custom" value=""/> | |
| 10566 <param name="rt_filename" value="true"/> | |
| 10567 <param name="ms_level" value="2"/> | |
| 10568 </section> | |
| 10569 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10570 <output name="ctd_out" ftype="xml"> | |
| 10571 <assert_contents> | |
| 10572 <is_valid_xml/> | |
| 10573 </assert_contents> | |
| 10574 </output> | |
| 10575 </test> | |
| 10576 <test expect_num_outputs="2"> | |
| 10577 <conditional name="adv_opts_cond"> | |
| 10578 <param name="adv_opts_selector" value="advanced"/> | |
| 10579 <param name="force" value="false"/> | |
| 10580 <param name="test" value="true"/> | |
| 10581 </conditional> | |
| 10582 <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/> | |
| 10583 <param name="out_type" value="mzML"/> | |
| 10584 <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10585 <param name="annotate_file_origin" value="false"/> | |
| 10586 <param name="append_method" value="append_rows"/> | |
| 10587 <section name="rt_concat"> | |
| 10588 <param name="gap" value="0.0"/> | |
| 10589 </section> | |
| 10590 <section name="raw"> | |
| 10591 <param name="rt_auto" value="false"/> | |
| 10592 <param name="rt_custom" value=""/> | |
| 10593 <param name="rt_filename" value="false"/> | |
| 10594 <param name="ms_level" value="0"/> | |
| 10595 </section> | |
| 10596 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10597 <output name="ctd_out" ftype="xml"> | |
| 10598 <assert_contents> | |
| 10599 <is_valid_xml/> | |
| 10600 </assert_contents> | |
| 10601 </output> | |
| 10602 </test> | |
| 10603 <test expect_num_outputs="2"> | |
| 10604 <conditional name="adv_opts_cond"> | |
| 10605 <param name="adv_opts_selector" value="advanced"/> | |
| 10606 <param name="force" value="false"/> | |
| 10607 <param name="test" value="true"/> | |
| 10608 </conditional> | |
| 10609 <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/> | |
| 10610 <param name="out_type" value="featureXML"/> | |
| 10611 <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 10612 <param name="annotate_file_origin" value="false"/> | |
| 10613 <param name="append_method" value="append_rows"/> | |
| 10614 <section name="rt_concat"> | |
| 10615 <param name="gap" value="0.0"/> | |
| 10616 </section> | |
| 10617 <section name="raw"> | |
| 10618 <param name="rt_auto" value="false"/> | |
| 10619 <param name="rt_custom" value=""/> | |
| 10620 <param name="rt_filename" value="false"/> | |
| 10621 <param name="ms_level" value="0"/> | |
| 10622 </section> | |
| 10623 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10624 <output name="ctd_out" ftype="xml"> | |
| 10625 <assert_contents> | |
| 10626 <is_valid_xml/> | |
| 10627 </assert_contents> | |
| 10628 </output> | |
| 10629 </test> | |
| 10630 <test expect_num_outputs="2"> | |
| 10631 <conditional name="adv_opts_cond"> | |
| 10632 <param name="adv_opts_selector" value="advanced"/> | |
| 10633 <param name="force" value="false"/> | |
| 10634 <param name="test" value="true"/> | |
| 10635 </conditional> | |
| 10636 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> | |
| 10637 <param name="out_type" value="consensusXML"/> | |
| 10638 <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 10639 <param name="annotate_file_origin" value="false"/> | |
| 10640 <param name="append_method" value="append_rows"/> | |
| 10641 <section name="rt_concat"> | |
| 10642 <param name="gap" value="0.0"/> | |
| 10643 </section> | |
| 10644 <section name="raw"> | |
| 10645 <param name="rt_auto" value="false"/> | |
| 10646 <param name="rt_custom" value=""/> | |
| 10647 <param name="rt_filename" value="false"/> | |
| 10648 <param name="ms_level" value="0"/> | |
| 10649 </section> | |
| 10650 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10651 <output name="ctd_out" ftype="xml"> | |
| 10652 <assert_contents> | |
| 10653 <is_valid_xml/> | |
| 10654 </assert_contents> | |
| 10655 </output> | |
| 10656 </test> | |
| 10657 <test expect_num_outputs="2"> | |
| 10658 <conditional name="adv_opts_cond"> | |
| 10659 <param name="adv_opts_selector" value="advanced"/> | |
| 10660 <param name="force" value="false"/> | |
| 10661 <param name="test" value="true"/> | |
| 10662 </conditional> | |
| 10663 <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/> | |
| 10664 <param name="out_type" value="traML"/> | |
| 10665 <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 10666 <param name="annotate_file_origin" value="false"/> | |
| 10667 <param name="append_method" value="append_rows"/> | |
| 10668 <section name="rt_concat"> | |
| 10669 <param name="gap" value="0.0"/> | |
| 10670 </section> | |
| 10671 <section name="raw"> | |
| 10672 <param name="rt_auto" value="false"/> | |
| 10673 <param name="rt_custom" value=""/> | |
| 10674 <param name="rt_filename" value="false"/> | |
| 10675 <param name="ms_level" value="0"/> | |
| 10676 </section> | |
| 10677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10678 <output name="ctd_out" ftype="xml"> | |
| 10679 <assert_contents> | |
| 10680 <is_valid_xml/> | |
| 10681 </assert_contents> | |
| 10682 </output> | |
| 10683 </test> | |
| 10684 <test expect_num_outputs="3"> | |
| 10685 <conditional name="adv_opts_cond"> | |
| 10686 <param name="adv_opts_selector" value="advanced"/> | |
| 10687 <param name="force" value="false"/> | |
| 10688 <param name="test" value="true"/> | |
| 10689 </conditional> | |
| 10690 <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/> | |
| 10691 <param name="out_type" value="mzML"/> | |
| 10692 <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10693 <param name="annotate_file_origin" value="false"/> | |
| 10694 <param name="append_method" value="append_rows"/> | |
| 10695 <section name="rt_concat"> | |
| 10696 <param name="gap" value="10.0"/> | |
| 10697 </section> | |
| 10698 <output_collection name="rt_concat_trafo_out" count="2"/> | |
| 10699 <section name="raw"> | |
| 10700 <param name="rt_auto" value="false"/> | |
| 10701 <param name="rt_custom" value=""/> | |
| 10702 <param name="rt_filename" value="false"/> | |
| 10703 <param name="ms_level" value="0"/> | |
| 10704 </section> | |
| 10705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> | |
| 10706 <output name="ctd_out" ftype="xml"> | |
| 10707 <assert_contents> | |
| 10708 <is_valid_xml/> | |
| 10709 </assert_contents> | |
| 10710 </output> | |
| 10711 </test> | |
| 10712 <test expect_num_outputs="2"> | |
| 10713 <conditional name="adv_opts_cond"> | |
| 10714 <param name="adv_opts_selector" value="advanced"/> | |
| 10715 <param name="force" value="false"/> | |
| 10716 <param name="test" value="true"/> | |
| 10717 </conditional> | |
| 10718 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> | |
| 10719 <param name="out_type" value="consensusXML"/> | |
| 10720 <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 10721 <param name="annotate_file_origin" value="false"/> | |
| 10722 <param name="append_method" value="append_cols"/> | |
| 10723 <section name="rt_concat"> | |
| 10724 <param name="gap" value="0.0"/> | |
| 10725 </section> | |
| 10726 <section name="raw"> | |
| 10727 <param name="rt_auto" value="false"/> | |
| 10728 <param name="rt_custom" value=""/> | |
| 10729 <param name="rt_filename" value="false"/> | |
| 10730 <param name="ms_level" value="0"/> | |
| 10731 </section> | |
| 10732 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10733 <output name="ctd_out" ftype="xml"> | |
| 10734 <assert_contents> | |
| 10735 <is_valid_xml/> | |
| 10736 </assert_contents> | |
| 10737 </output> | |
| 10738 </test> | |
| 10739 </xml> | |
| 10740 <xml name="autotest_FuzzyDiff"> | |
| 10741 <test expect_num_outputs="1"> | |
| 10742 <conditional name="adv_opts_cond"> | |
| 10743 <param name="adv_opts_selector" value="advanced"/> | |
| 10744 <param name="whitelist" value=""<?xml-stylesheet""/> | |
| 10745 <param name="matched_whitelist" value=""/> | |
| 10746 <param name="force" value="false"/> | |
| 10747 <param name="test" value="true"/> | |
| 10748 </conditional> | |
| 10749 <param name="in1" value="FuzzyDiff_3_in1.featureXML"/> | |
| 10750 <param name="in2" value="FuzzyDiff_3_in2.featureXML"/> | |
| 10751 <param name="ratio" value="1.01"/> | |
| 10752 <param name="absdiff" value="0.01"/> | |
| 10753 <param name="verbose" value="1"/> | |
| 10754 <param name="tab_width" value="8"/> | |
| 10755 <param name="first_column" value="1"/> | |
| 10756 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10757 <output name="ctd_out" ftype="xml"> | |
| 10758 <assert_contents> | |
| 10759 <is_valid_xml/> | |
| 10760 </assert_contents> | |
| 10761 </output> | |
| 10762 </test> | |
| 10763 </xml> | |
| 10764 <xml name="autotest_GNPSExport"> | |
| 10765 <test expect_num_outputs="2"> | |
| 10766 <conditional name="adv_opts_cond"> | |
| 10767 <param name="adv_opts_selector" value="advanced"/> | |
| 10768 <param name="force" value="false"/> | |
| 10769 <param name="test" value="true"/> | |
| 10770 </conditional> | |
| 10771 <param name="in_cm" value="GNPSExport_single.consensusXML"/> | |
| 10772 <param name="in_mzml" value="GNPSExport_mz1.mzML"/> | |
| 10773 <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> | |
| 10774 <param name="output_type" value="full_spectra"/> | |
| 10775 <param name="precursor_mz_tolerance" value="0.0001"/> | |
| 10776 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 10777 <section name="merged_spectra"> | |
| 10778 <param name="cos_similarity" value="0.95"/> | |
| 10779 </section> | |
| 10780 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10781 <output name="ctd_out" ftype="xml"> | |
| 10782 <assert_contents> | |
| 10783 <is_valid_xml/> | |
| 10784 </assert_contents> | |
| 10785 </output> | |
| 10786 </test> | |
| 10787 <test expect_num_outputs="2"> | |
| 10788 <conditional name="adv_opts_cond"> | |
| 10789 <param name="adv_opts_selector" value="advanced"/> | |
| 10790 <param name="force" value="false"/> | |
| 10791 <param name="test" value="true"/> | |
| 10792 </conditional> | |
| 10793 <param name="in_cm" value="GNPSExport_single.consensusXML"/> | |
| 10794 <param name="in_mzml" value="GNPSExport_mz1.mzML"/> | |
| 10795 <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> | |
| 10796 <param name="output_type" value="merged_spectra"/> | |
| 10797 <param name="precursor_mz_tolerance" value="0.0001"/> | |
| 10798 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 10799 <section name="merged_spectra"> | |
| 10800 <param name="cos_similarity" value="0.95"/> | |
| 10801 </section> | |
| 10802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10803 <output name="ctd_out" ftype="xml"> | |
| 10804 <assert_contents> | |
| 10805 <is_valid_xml/> | |
| 10806 </assert_contents> | |
| 10807 </output> | |
| 10808 </test> | |
| 10809 <test expect_num_outputs="2"> | |
| 10810 <conditional name="adv_opts_cond"> | |
| 10811 <param name="adv_opts_selector" value="advanced"/> | |
| 10812 <param name="force" value="false"/> | |
| 10813 <param name="test" value="true"/> | |
| 10814 </conditional> | |
| 10815 <param name="in_cm" value="GNPSExport_merged.consensusXML"/> | |
| 10816 <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> | |
| 10817 <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> | |
| 10818 <param name="output_type" value="full_spectra"/> | |
| 10819 <param name="precursor_mz_tolerance" value="0.0001"/> | |
| 10820 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 10821 <section name="merged_spectra"> | |
| 10822 <param name="cos_similarity" value="0.95"/> | |
| 10823 </section> | |
| 10824 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10825 <output name="ctd_out" ftype="xml"> | |
| 10826 <assert_contents> | |
| 10827 <is_valid_xml/> | |
| 10828 </assert_contents> | |
| 10829 </output> | |
| 10830 </test> | |
| 10831 <test expect_num_outputs="2"> | |
| 10832 <conditional name="adv_opts_cond"> | |
| 10833 <param name="adv_opts_selector" value="advanced"/> | |
| 10834 <param name="force" value="false"/> | |
| 10835 <param name="test" value="true"/> | |
| 10836 </conditional> | |
| 10837 <param name="in_cm" value="GNPSExport_merged.consensusXML"/> | |
| 10838 <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> | |
| 10839 <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> | |
| 10840 <param name="output_type" value="full_spectra"/> | |
| 10841 <param name="precursor_mz_tolerance" value="0.0001"/> | |
| 10842 <param name="precursor_rt_tolerance" value="5.0"/> | |
| 10843 <section name="merged_spectra"> | |
| 10844 <param name="cos_similarity" value="0.95"/> | |
| 10845 </section> | |
| 10846 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10847 <output name="ctd_out" ftype="xml"> | |
| 10848 <assert_contents> | |
| 10849 <is_valid_xml/> | |
| 10850 </assert_contents> | |
| 10851 </output> | |
| 10852 </test> | |
| 10853 </xml> | |
| 10854 <xml name="autotest_HighResPrecursorMassCorrector"> | |
| 10855 <test expect_num_outputs="2"> | |
| 10856 <conditional name="adv_opts_cond"> | |
| 10857 <param name="adv_opts_selector" value="advanced"/> | |
| 10858 <param name="force" value="false"/> | |
| 10859 <param name="test" value="true"/> | |
| 10860 </conditional> | |
| 10861 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/> | |
| 10862 <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10863 <section name="feature"> | |
| 10864 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/> | |
| 10865 <param name="mz_tolerance" value="5.0"/> | |
| 10866 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10867 <param name="rt_tolerance" value="0.0"/> | |
| 10868 <param name="max_trace" value="2"/> | |
| 10869 <param name="believe_charge" value="false"/> | |
| 10870 <param name="keep_original" value="false"/> | |
| 10871 <param name="assign_all_matching" value="false"/> | |
| 10872 </section> | |
| 10873 <section name="nearest_peak"> | |
| 10874 <param name="mz_tolerance" value="0.0"/> | |
| 10875 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10876 </section> | |
| 10877 <section name="highest_intensity_peak"> | |
| 10878 <param name="mz_tolerance" value="0.0"/> | |
| 10879 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10880 </section> | |
| 10881 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10882 <output name="ctd_out" ftype="xml"> | |
| 10883 <assert_contents> | |
| 10884 <is_valid_xml/> | |
| 10885 </assert_contents> | |
| 10886 </output> | |
| 10887 </test> | |
| 10888 <test expect_num_outputs="2"> | |
| 10889 <conditional name="adv_opts_cond"> | |
| 10890 <param name="adv_opts_selector" value="advanced"/> | |
| 10891 <param name="force" value="false"/> | |
| 10892 <param name="test" value="true"/> | |
| 10893 </conditional> | |
| 10894 <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/> | |
| 10895 <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10896 <section name="feature"> | |
| 10897 <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/> | |
| 10898 <param name="mz_tolerance" value="10.0"/> | |
| 10899 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10900 <param name="rt_tolerance" value="0.0"/> | |
| 10901 <param name="max_trace" value="4"/> | |
| 10902 <param name="believe_charge" value="false"/> | |
| 10903 <param name="keep_original" value="false"/> | |
| 10904 <param name="assign_all_matching" value="false"/> | |
| 10905 </section> | |
| 10906 <section name="nearest_peak"> | |
| 10907 <param name="mz_tolerance" value="0.0"/> | |
| 10908 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10909 </section> | |
| 10910 <section name="highest_intensity_peak"> | |
| 10911 <param name="mz_tolerance" value="0.0"/> | |
| 10912 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10913 </section> | |
| 10914 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10915 <output name="ctd_out" ftype="xml"> | |
| 10916 <assert_contents> | |
| 10917 <is_valid_xml/> | |
| 10918 </assert_contents> | |
| 10919 </output> | |
| 10920 </test> | |
| 10921 <test expect_num_outputs="2"> | |
| 10922 <conditional name="adv_opts_cond"> | |
| 10923 <param name="adv_opts_selector" value="advanced"/> | |
| 10924 <param name="force" value="false"/> | |
| 10925 <param name="test" value="true"/> | |
| 10926 </conditional> | |
| 10927 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/> | |
| 10928 <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10929 <section name="feature"> | |
| 10930 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/> | |
| 10931 <param name="mz_tolerance" value="5.0"/> | |
| 10932 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10933 <param name="rt_tolerance" value="0.0"/> | |
| 10934 <param name="max_trace" value="2"/> | |
| 10935 <param name="believe_charge" value="false"/> | |
| 10936 <param name="keep_original" value="false"/> | |
| 10937 <param name="assign_all_matching" value="false"/> | |
| 10938 </section> | |
| 10939 <section name="nearest_peak"> | |
| 10940 <param name="mz_tolerance" value="0.0"/> | |
| 10941 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10942 </section> | |
| 10943 <section name="highest_intensity_peak"> | |
| 10944 <param name="mz_tolerance" value="0.0"/> | |
| 10945 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10946 </section> | |
| 10947 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10948 <output name="ctd_out" ftype="xml"> | |
| 10949 <assert_contents> | |
| 10950 <is_valid_xml/> | |
| 10951 </assert_contents> | |
| 10952 </output> | |
| 10953 </test> | |
| 10954 <test expect_num_outputs="2"> | |
| 10955 <conditional name="adv_opts_cond"> | |
| 10956 <param name="adv_opts_selector" value="advanced"/> | |
| 10957 <param name="force" value="false"/> | |
| 10958 <param name="test" value="true"/> | |
| 10959 </conditional> | |
| 10960 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/> | |
| 10961 <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10962 <section name="feature"> | |
| 10963 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/> | |
| 10964 <param name="mz_tolerance" value="5.0"/> | |
| 10965 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10966 <param name="rt_tolerance" value="0.0"/> | |
| 10967 <param name="max_trace" value="2"/> | |
| 10968 <param name="believe_charge" value="false"/> | |
| 10969 <param name="keep_original" value="false"/> | |
| 10970 <param name="assign_all_matching" value="false"/> | |
| 10971 </section> | |
| 10972 <section name="nearest_peak"> | |
| 10973 <param name="mz_tolerance" value="0.0"/> | |
| 10974 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10975 </section> | |
| 10976 <section name="highest_intensity_peak"> | |
| 10977 <param name="mz_tolerance" value="0.0"/> | |
| 10978 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10979 </section> | |
| 10980 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 10981 <output name="ctd_out" ftype="xml"> | |
| 10982 <assert_contents> | |
| 10983 <is_valid_xml/> | |
| 10984 </assert_contents> | |
| 10985 </output> | |
| 10986 </test> | |
| 10987 <test expect_num_outputs="2"> | |
| 10988 <conditional name="adv_opts_cond"> | |
| 10989 <param name="adv_opts_selector" value="advanced"/> | |
| 10990 <param name="force" value="false"/> | |
| 10991 <param name="test" value="true"/> | |
| 10992 </conditional> | |
| 10993 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/> | |
| 10994 <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 10995 <section name="feature"> | |
| 10996 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/> | |
| 10997 <param name="mz_tolerance" value="5.0"/> | |
| 10998 <param name="mz_tolerance_unit" value="ppm"/> | |
| 10999 <param name="rt_tolerance" value="0.0"/> | |
| 11000 <param name="max_trace" value="2"/> | |
| 11001 <param name="believe_charge" value="false"/> | |
| 11002 <param name="keep_original" value="false"/> | |
| 11003 <param name="assign_all_matching" value="false"/> | |
| 11004 </section> | |
| 11005 <section name="nearest_peak"> | |
| 11006 <param name="mz_tolerance" value="0.0"/> | |
| 11007 <param name="mz_tolerance_unit" value="ppm"/> | |
| 11008 </section> | |
| 11009 <section name="highest_intensity_peak"> | |
| 11010 <param name="mz_tolerance" value="0.0"/> | |
| 11011 <param name="mz_tolerance_unit" value="ppm"/> | |
| 11012 </section> | |
| 11013 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11014 <output name="ctd_out" ftype="xml"> | |
| 11015 <assert_contents> | |
| 11016 <is_valid_xml/> | |
| 11017 </assert_contents> | |
| 11018 </output> | |
| 11019 </test> | |
| 11020 <test expect_num_outputs="2"> | |
| 11021 <conditional name="adv_opts_cond"> | |
| 11022 <param name="adv_opts_selector" value="advanced"/> | |
| 11023 <param name="force" value="false"/> | |
| 11024 <param name="test" value="true"/> | |
| 11025 </conditional> | |
| 11026 <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/> | |
| 11027 <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 11028 <section name="feature"> | |
| 11029 <param name="mz_tolerance" value="5.0"/> | |
| 11030 <param name="mz_tolerance_unit" value="ppm"/> | |
| 11031 <param name="rt_tolerance" value="0.0"/> | |
| 11032 <param name="max_trace" value="2"/> | |
| 11033 <param name="believe_charge" value="false"/> | |
| 11034 <param name="keep_original" value="false"/> | |
| 11035 <param name="assign_all_matching" value="false"/> | |
| 11036 </section> | |
| 11037 <section name="nearest_peak"> | |
| 11038 <param name="mz_tolerance" value="0.0"/> | |
| 11039 <param name="mz_tolerance_unit" value="ppm"/> | |
| 11040 </section> | |
| 11041 <section name="highest_intensity_peak"> | |
| 11042 <param name="mz_tolerance" value="0.2"/> | |
| 11043 <param name="mz_tolerance_unit" value="ppm"/> | |
| 11044 </section> | |
| 11045 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11046 <output name="ctd_out" ftype="xml"> | |
| 11047 <assert_contents> | |
| 11048 <is_valid_xml/> | |
| 11049 </assert_contents> | |
| 11050 </output> | |
| 11051 </test> | |
| 11052 </xml> | |
| 11053 <xml name="autotest_IDConflictResolver"> | |
| 11054 <test expect_num_outputs="2"> | |
| 11055 <conditional name="adv_opts_cond"> | |
| 11056 <param name="adv_opts_selector" value="advanced"/> | |
| 11057 <param name="force" value="false"/> | |
| 11058 <param name="test" value="true"/> | |
| 11059 </conditional> | |
| 11060 <param name="in" value="IDConflictResolver_1_input.featureXML"/> | |
| 11061 <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 11062 <param name="resolve_between_features" value="off"/> | |
| 11063 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11064 <output name="ctd_out" ftype="xml"> | |
| 11065 <assert_contents> | |
| 11066 <is_valid_xml/> | |
| 11067 </assert_contents> | |
| 11068 </output> | |
| 11069 </test> | |
| 11070 <test expect_num_outputs="2"> | |
| 11071 <conditional name="adv_opts_cond"> | |
| 11072 <param name="adv_opts_selector" value="advanced"/> | |
| 11073 <param name="force" value="false"/> | |
| 11074 <param name="test" value="true"/> | |
| 11075 </conditional> | |
| 11076 <param name="in" value="IDConflictResolver_2_input.consensusXML"/> | |
| 11077 <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 11078 <param name="resolve_between_features" value="off"/> | |
| 11079 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11080 <output name="ctd_out" ftype="xml"> | |
| 11081 <assert_contents> | |
| 11082 <is_valid_xml/> | |
| 11083 </assert_contents> | |
| 11084 </output> | |
| 11085 </test> | |
| 11086 <test expect_num_outputs="2"> | |
| 11087 <conditional name="adv_opts_cond"> | |
| 11088 <param name="adv_opts_selector" value="advanced"/> | |
| 11089 <param name="force" value="false"/> | |
| 11090 <param name="test" value="true"/> | |
| 11091 </conditional> | |
| 11092 <param name="in" value="IDConflictResolver_3_input.consensusXML"/> | |
| 11093 <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 11094 <param name="resolve_between_features" value="off"/> | |
| 11095 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11096 <output name="ctd_out" ftype="xml"> | |
| 11097 <assert_contents> | |
| 11098 <is_valid_xml/> | |
| 11099 </assert_contents> | |
| 11100 </output> | |
| 11101 </test> | |
| 11102 <test expect_num_outputs="2"> | |
| 11103 <conditional name="adv_opts_cond"> | |
| 11104 <param name="adv_opts_selector" value="advanced"/> | |
| 11105 <param name="force" value="false"/> | |
| 11106 <param name="test" value="true"/> | |
| 11107 </conditional> | |
| 11108 <param name="in" value="IDConflictResolver_4_input.featureXML"/> | |
| 11109 <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 11110 <param name="resolve_between_features" value="highest_intensity"/> | |
| 11111 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11112 <output name="ctd_out" ftype="xml"> | |
| 11113 <assert_contents> | |
| 11114 <is_valid_xml/> | |
| 11115 </assert_contents> | |
| 11116 </output> | |
| 11117 </test> | |
| 11118 </xml> | |
| 11119 <xml name="autotest_IDExtractor"> | |
| 11120 </xml> | |
| 11121 <xml name="autotest_IDFileConverter"> | |
| 11122 <test expect_num_outputs="2"> | |
| 11123 <conditional name="adv_opts_cond"> | |
| 11124 <param name="adv_opts_selector" value="advanced"/> | |
| 11125 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11126 <param name="scan_regex" value=""/> | |
| 11127 <param name="no_spectra_data_override" value="false"/> | |
| 11128 <param name="no_spectra_references_override" value="false"/> | |
| 11129 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11130 <param name="force" value="false"/> | |
| 11131 <param name="test" value="true"/> | |
| 11132 </conditional> | |
| 11133 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> | |
| 11134 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11135 <param name="out_type" value="idXML"/> | |
| 11136 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> | |
| 11137 <param name="mz_name" value=""/> | |
| 11138 <param name="peptideprophet_analyzed" value="false"/> | |
| 11139 <param name="score_type" value="qvalue"/> | |
| 11140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11141 <output name="ctd_out" ftype="xml"> | |
| 11142 <assert_contents> | |
| 11143 <is_valid_xml/> | |
| 11144 </assert_contents> | |
| 11145 </output> | |
| 11146 </test> | |
| 11147 <test expect_num_outputs="2"> | |
| 11148 <conditional name="adv_opts_cond"> | |
| 11149 <param name="adv_opts_selector" value="advanced"/> | |
| 11150 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11151 <param name="scan_regex" value=""/> | |
| 11152 <param name="no_spectra_data_override" value="false"/> | |
| 11153 <param name="no_spectra_references_override" value="false"/> | |
| 11154 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11155 <param name="force" value="false"/> | |
| 11156 <param name="test" value="true"/> | |
| 11157 </conditional> | |
| 11158 <param name="in" value="PepXMLFile_test.pepxml"/> | |
| 11159 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11160 <param name="out_type" value="idXML"/> | |
| 11161 <param name="mz_file" value="PepXMLFile_test.mzML"/> | |
| 11162 <param name="mz_name" value="PepXMLFile_test"/> | |
| 11163 <param name="peptideprophet_analyzed" value="false"/> | |
| 11164 <param name="score_type" value="qvalue"/> | |
| 11165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11166 <output name="ctd_out" ftype="xml"> | |
| 11167 <assert_contents> | |
| 11168 <is_valid_xml/> | |
| 11169 </assert_contents> | |
| 11170 </output> | |
| 11171 </test> | |
| 11172 <test expect_num_outputs="2"> | |
| 11173 <conditional name="adv_opts_cond"> | |
| 11174 <param name="adv_opts_selector" value="advanced"/> | |
| 11175 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11176 <param name="scan_regex" value=""/> | |
| 11177 <param name="no_spectra_data_override" value="false"/> | |
| 11178 <param name="no_spectra_references_override" value="false"/> | |
| 11179 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11180 <param name="force" value="false"/> | |
| 11181 <param name="test" value="true"/> | |
| 11182 </conditional> | |
| 11183 <param name="in" value="IDFileConverter_3_input.protXML"/> | |
| 11184 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11185 <param name="out_type" value="idXML"/> | |
| 11186 <param name="mz_name" value=""/> | |
| 11187 <param name="peptideprophet_analyzed" value="false"/> | |
| 11188 <param name="score_type" value="qvalue"/> | |
| 11189 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11190 <output name="ctd_out" ftype="xml"> | |
| 11191 <assert_contents> | |
| 11192 <is_valid_xml/> | |
| 11193 </assert_contents> | |
| 11194 </output> | |
| 11195 </test> | |
| 11196 <test expect_num_outputs="2"> | |
| 11197 <conditional name="adv_opts_cond"> | |
| 11198 <param name="adv_opts_selector" value="advanced"/> | |
| 11199 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11200 <param name="scan_regex" value="scan=(?<SCAN>\d+)"/> | |
| 11201 <param name="no_spectra_data_override" value="false"/> | |
| 11202 <param name="no_spectra_references_override" value="false"/> | |
| 11203 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11204 <param name="force" value="false"/> | |
| 11205 <param name="test" value="true"/> | |
| 11206 </conditional> | |
| 11207 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> | |
| 11208 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11209 <param name="out_type" value="idXML"/> | |
| 11210 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> | |
| 11211 <param name="mz_name" value=""/> | |
| 11212 <param name="peptideprophet_analyzed" value="false"/> | |
| 11213 <param name="score_type" value="qvalue"/> | |
| 11214 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11215 <output name="ctd_out" ftype="xml"> | |
| 11216 <assert_contents> | |
| 11217 <is_valid_xml/> | |
| 11218 </assert_contents> | |
| 11219 </output> | |
| 11220 </test> | |
| 11221 <test expect_num_outputs="2"> | |
| 11222 <conditional name="adv_opts_cond"> | |
| 11223 <param name="adv_opts_selector" value="advanced"/> | |
| 11224 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11225 <param name="scan_regex" value=""/> | |
| 11226 <param name="no_spectra_data_override" value="false"/> | |
| 11227 <param name="no_spectra_references_override" value="false"/> | |
| 11228 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11229 <param name="force" value="false"/> | |
| 11230 <param name="test" value="true"/> | |
| 11231 </conditional> | |
| 11232 <param name="in" value="IDFileConverter_6_input1.pepXML"/> | |
| 11233 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11234 <param name="out_type" value="idXML"/> | |
| 11235 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> | |
| 11236 <param name="mz_name" value="F025589.dat.mzML"/> | |
| 11237 <param name="peptideprophet_analyzed" value="false"/> | |
| 11238 <param name="score_type" value="qvalue"/> | |
| 11239 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11240 <output name="ctd_out" ftype="xml"> | |
| 11241 <assert_contents> | |
| 11242 <is_valid_xml/> | |
| 11243 </assert_contents> | |
| 11244 </output> | |
| 11245 </test> | |
| 11246 <test expect_num_outputs="2"> | |
| 11247 <conditional name="adv_opts_cond"> | |
| 11248 <param name="adv_opts_selector" value="advanced"/> | |
| 11249 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11250 <param name="scan_regex" value=""/> | |
| 11251 <param name="no_spectra_data_override" value="false"/> | |
| 11252 <param name="no_spectra_references_override" value="false"/> | |
| 11253 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11254 <param name="force" value="false"/> | |
| 11255 <param name="test" value="true"/> | |
| 11256 </conditional> | |
| 11257 <param name="in" value="IDFileConverter_7_input1.xml"/> | |
| 11258 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11259 <param name="out_type" value="idXML"/> | |
| 11260 <param name="mz_name" value=""/> | |
| 11261 <param name="peptideprophet_analyzed" value="false"/> | |
| 11262 <param name="score_type" value="qvalue"/> | |
| 11263 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11264 <output name="ctd_out" ftype="xml"> | |
| 11265 <assert_contents> | |
| 11266 <is_valid_xml/> | |
| 11267 </assert_contents> | |
| 11268 </output> | |
| 11269 </test> | |
| 11270 <test expect_num_outputs="2"> | |
| 11271 <conditional name="adv_opts_cond"> | |
| 11272 <param name="adv_opts_selector" value="advanced"/> | |
| 11273 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11274 <param name="scan_regex" value=""/> | |
| 11275 <param name="no_spectra_data_override" value="false"/> | |
| 11276 <param name="no_spectra_references_override" value="false"/> | |
| 11277 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11278 <param name="force" value="false"/> | |
| 11279 <param name="test" value="true"/> | |
| 11280 </conditional> | |
| 11281 <param name="in" value="IDFileConverter_8_input.mzid"/> | |
| 11282 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11283 <param name="out_type" value="idXML"/> | |
| 11284 <param name="mz_name" value=""/> | |
| 11285 <param name="peptideprophet_analyzed" value="false"/> | |
| 11286 <param name="score_type" value="qvalue"/> | |
| 11287 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11288 <output name="ctd_out" ftype="xml"> | |
| 11289 <assert_contents> | |
| 11290 <is_valid_xml/> | |
| 11291 </assert_contents> | |
| 11292 </output> | |
| 11293 </test> | |
| 11294 <test expect_num_outputs="2"> | |
| 11295 <conditional name="adv_opts_cond"> | |
| 11296 <param name="adv_opts_selector" value="advanced"/> | |
| 11297 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11298 <param name="scan_regex" value=""/> | |
| 11299 <param name="no_spectra_data_override" value="false"/> | |
| 11300 <param name="no_spectra_references_override" value="false"/> | |
| 11301 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11302 <param name="force" value="false"/> | |
| 11303 <param name="test" value="true"/> | |
| 11304 </conditional> | |
| 11305 <param name="in" value="IDFileConverter_9_input.idXML"/> | |
| 11306 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 11307 <param name="out_type" value="mzid"/> | |
| 11308 <param name="mz_name" value=""/> | |
| 11309 <param name="peptideprophet_analyzed" value="false"/> | |
| 11310 <param name="score_type" value="qvalue"/> | |
| 11311 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11312 <output name="ctd_out" ftype="xml"> | |
| 11313 <assert_contents> | |
| 11314 <is_valid_xml/> | |
| 11315 </assert_contents> | |
| 11316 </output> | |
| 11317 </test> | |
| 11318 <test expect_num_outputs="2"> | |
| 11319 <conditional name="adv_opts_cond"> | |
| 11320 <param name="adv_opts_selector" value="advanced"/> | |
| 11321 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11322 <param name="scan_regex" value=""/> | |
| 11323 <param name="no_spectra_data_override" value="false"/> | |
| 11324 <param name="no_spectra_references_override" value="false"/> | |
| 11325 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11326 <param name="force" value="false"/> | |
| 11327 <param name="test" value="true"/> | |
| 11328 </conditional> | |
| 11329 <param name="in" value="IDFileConverter_10_input.pepXML"/> | |
| 11330 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11331 <param name="out_type" value="idXML"/> | |
| 11332 <param name="mz_name" value=""/> | |
| 11333 <param name="peptideprophet_analyzed" value="false"/> | |
| 11334 <param name="score_type" value="qvalue"/> | |
| 11335 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11336 <output name="ctd_out" ftype="xml"> | |
| 11337 <assert_contents> | |
| 11338 <is_valid_xml/> | |
| 11339 </assert_contents> | |
| 11340 </output> | |
| 11341 </test> | |
| 11342 <test expect_num_outputs="2"> | |
| 11343 <conditional name="adv_opts_cond"> | |
| 11344 <param name="adv_opts_selector" value="advanced"/> | |
| 11345 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11346 <param name="scan_regex" value=""/> | |
| 11347 <param name="no_spectra_data_override" value="false"/> | |
| 11348 <param name="no_spectra_references_override" value="false"/> | |
| 11349 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11350 <param name="force" value="false"/> | |
| 11351 <param name="test" value="true"/> | |
| 11352 </conditional> | |
| 11353 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> | |
| 11354 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11355 <param name="out_type" value="idXML"/> | |
| 11356 <param name="mz_name" value=""/> | |
| 11357 <param name="peptideprophet_analyzed" value="false"/> | |
| 11358 <param name="score_type" value="qvalue"/> | |
| 11359 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11360 <output name="ctd_out" ftype="xml"> | |
| 11361 <assert_contents> | |
| 11362 <is_valid_xml/> | |
| 11363 </assert_contents> | |
| 11364 </output> | |
| 11365 </test> | |
| 11366 <test expect_num_outputs="2"> | |
| 11367 <conditional name="adv_opts_cond"> | |
| 11368 <param name="adv_opts_selector" value="advanced"/> | |
| 11369 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11370 <param name="scan_regex" value=""/> | |
| 11371 <param name="no_spectra_data_override" value="false"/> | |
| 11372 <param name="no_spectra_references_override" value="false"/> | |
| 11373 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11374 <param name="force" value="false"/> | |
| 11375 <param name="test" value="true"/> | |
| 11376 </conditional> | |
| 11377 <param name="in" value="IDFileConverter_12_input.psms"/> | |
| 11378 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11379 <param name="out_type" value="idXML"/> | |
| 11380 <param name="mz_name" value=""/> | |
| 11381 <param name="peptideprophet_analyzed" value="false"/> | |
| 11382 <param name="score_type" value="qvalue"/> | |
| 11383 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11384 <output name="ctd_out" ftype="xml"> | |
| 11385 <assert_contents> | |
| 11386 <is_valid_xml/> | |
| 11387 </assert_contents> | |
| 11388 </output> | |
| 11389 </test> | |
| 11390 <test expect_num_outputs="2"> | |
| 11391 <conditional name="adv_opts_cond"> | |
| 11392 <param name="adv_opts_selector" value="advanced"/> | |
| 11393 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11394 <param name="scan_regex" value=""/> | |
| 11395 <param name="no_spectra_data_override" value="false"/> | |
| 11396 <param name="no_spectra_references_override" value="false"/> | |
| 11397 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11398 <param name="force" value="false"/> | |
| 11399 <param name="test" value="true"/> | |
| 11400 </conditional> | |
| 11401 <param name="in" value="IDFileConverter_12_input.psms"/> | |
| 11402 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11403 <param name="out_type" value="idXML"/> | |
| 11404 <param name="mz_name" value=""/> | |
| 11405 <param name="peptideprophet_analyzed" value="false"/> | |
| 11406 <param name="score_type" value="PEP"/> | |
| 11407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11408 <output name="ctd_out" ftype="xml"> | |
| 11409 <assert_contents> | |
| 11410 <is_valid_xml/> | |
| 11411 </assert_contents> | |
| 11412 </output> | |
| 11413 </test> | |
| 11414 <test expect_num_outputs="2"> | |
| 11415 <conditional name="adv_opts_cond"> | |
| 11416 <param name="adv_opts_selector" value="advanced"/> | |
| 11417 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11418 <param name="scan_regex" value=""/> | |
| 11419 <param name="no_spectra_data_override" value="false"/> | |
| 11420 <param name="no_spectra_references_override" value="false"/> | |
| 11421 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11422 <param name="force" value="false"/> | |
| 11423 <param name="test" value="true"/> | |
| 11424 </conditional> | |
| 11425 <param name="in" value="IDFileConverter_12_input.psms"/> | |
| 11426 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11427 <param name="out_type" value="idXML"/> | |
| 11428 <param name="mz_name" value=""/> | |
| 11429 <param name="peptideprophet_analyzed" value="false"/> | |
| 11430 <param name="score_type" value="score"/> | |
| 11431 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11432 <output name="ctd_out" ftype="xml"> | |
| 11433 <assert_contents> | |
| 11434 <is_valid_xml/> | |
| 11435 </assert_contents> | |
| 11436 </output> | |
| 11437 </test> | |
| 11438 <test expect_num_outputs="2"> | |
| 11439 <conditional name="adv_opts_cond"> | |
| 11440 <param name="adv_opts_selector" value="advanced"/> | |
| 11441 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11442 <param name="scan_regex" value=""/> | |
| 11443 <param name="no_spectra_data_override" value="false"/> | |
| 11444 <param name="no_spectra_references_override" value="false"/> | |
| 11445 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11446 <param name="force" value="false"/> | |
| 11447 <param name="test" value="true"/> | |
| 11448 </conditional> | |
| 11449 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> | |
| 11450 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11451 <param name="out_type" value="idXML"/> | |
| 11452 <param name="mz_file" value="spectra.mzML"/> | |
| 11453 <param name="mz_name" value=""/> | |
| 11454 <param name="peptideprophet_analyzed" value="false"/> | |
| 11455 <param name="score_type" value="qvalue"/> | |
| 11456 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11457 <output name="ctd_out" ftype="xml"> | |
| 11458 <assert_contents> | |
| 11459 <is_valid_xml/> | |
| 11460 </assert_contents> | |
| 11461 </output> | |
| 11462 </test> | |
| 11463 <test expect_num_outputs="2"> | |
| 11464 <conditional name="adv_opts_cond"> | |
| 11465 <param name="adv_opts_selector" value="advanced"/> | |
| 11466 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11467 <param name="scan_regex" value=""/> | |
| 11468 <param name="no_spectra_data_override" value="false"/> | |
| 11469 <param name="no_spectra_references_override" value="false"/> | |
| 11470 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11471 <param name="force" value="false"/> | |
| 11472 <param name="test" value="true"/> | |
| 11473 </conditional> | |
| 11474 <param name="in" value="IDFileConverter_16_input.pepXML"/> | |
| 11475 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11476 <param name="out_type" value="idXML"/> | |
| 11477 <param name="mz_name" value=""/> | |
| 11478 <param name="peptideprophet_analyzed" value="false"/> | |
| 11479 <param name="score_type" value="qvalue"/> | |
| 11480 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11481 <output name="ctd_out" ftype="xml"> | |
| 11482 <assert_contents> | |
| 11483 <is_valid_xml/> | |
| 11484 </assert_contents> | |
| 11485 </output> | |
| 11486 </test> | |
| 11487 <test expect_num_outputs="2"> | |
| 11488 <conditional name="adv_opts_cond"> | |
| 11489 <param name="adv_opts_selector" value="advanced"/> | |
| 11490 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11491 <param name="scan_regex" value=""/> | |
| 11492 <param name="no_spectra_data_override" value="false"/> | |
| 11493 <param name="no_spectra_references_override" value="false"/> | |
| 11494 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11495 <param name="force" value="false"/> | |
| 11496 <param name="test" value="true"/> | |
| 11497 </conditional> | |
| 11498 <param name="in" value="IDFileConverter_17_input.idXML"/> | |
| 11499 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> | |
| 11500 <param name="out_type" value="pepXML"/> | |
| 11501 <param name="mz_name" value=""/> | |
| 11502 <param name="peptideprophet_analyzed" value="false"/> | |
| 11503 <param name="score_type" value="qvalue"/> | |
| 11504 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11505 <output name="ctd_out" ftype="xml"> | |
| 11506 <assert_contents> | |
| 11507 <is_valid_xml/> | |
| 11508 </assert_contents> | |
| 11509 </output> | |
| 11510 </test> | |
| 11511 <test expect_num_outputs="2"> | |
| 11512 <conditional name="adv_opts_cond"> | |
| 11513 <param name="adv_opts_selector" value="advanced"/> | |
| 11514 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11515 <param name="scan_regex" value=""/> | |
| 11516 <param name="no_spectra_data_override" value="false"/> | |
| 11517 <param name="no_spectra_references_override" value="false"/> | |
| 11518 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11519 <param name="force" value="false"/> | |
| 11520 <param name="test" value="true"/> | |
| 11521 </conditional> | |
| 11522 <param name="in" value="IDFileConverter_18_input.idXML"/> | |
| 11523 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> | |
| 11524 <param name="out_type" value="pepXML"/> | |
| 11525 <param name="mz_name" value=""/> | |
| 11526 <param name="peptideprophet_analyzed" value="false"/> | |
| 11527 <param name="score_type" value="qvalue"/> | |
| 11528 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11529 <output name="ctd_out" ftype="xml"> | |
| 11530 <assert_contents> | |
| 11531 <is_valid_xml/> | |
| 11532 </assert_contents> | |
| 11533 </output> | |
| 11534 </test> | |
| 11535 <test expect_num_outputs="2"> | |
| 11536 <conditional name="adv_opts_cond"> | |
| 11537 <param name="adv_opts_selector" value="advanced"/> | |
| 11538 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11539 <param name="scan_regex" value=""/> | |
| 11540 <param name="no_spectra_data_override" value="false"/> | |
| 11541 <param name="no_spectra_references_override" value="false"/> | |
| 11542 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11543 <param name="force" value="false"/> | |
| 11544 <param name="test" value="true"/> | |
| 11545 </conditional> | |
| 11546 <param name="in" value="IDFileConverter_19_input.idXML"/> | |
| 11547 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> | |
| 11548 <param name="out_type" value="pepXML"/> | |
| 11549 <param name="mz_name" value=""/> | |
| 11550 <param name="peptideprophet_analyzed" value="false"/> | |
| 11551 <param name="score_type" value="qvalue"/> | |
| 11552 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11553 <output name="ctd_out" ftype="xml"> | |
| 11554 <assert_contents> | |
| 11555 <is_valid_xml/> | |
| 11556 </assert_contents> | |
| 11557 </output> | |
| 11558 </test> | |
| 11559 <test expect_num_outputs="2"> | |
| 11560 <conditional name="adv_opts_cond"> | |
| 11561 <param name="adv_opts_selector" value="advanced"/> | |
| 11562 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11563 <param name="scan_regex" value=""/> | |
| 11564 <param name="no_spectra_data_override" value="false"/> | |
| 11565 <param name="no_spectra_references_override" value="false"/> | |
| 11566 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11567 <param name="force" value="false"/> | |
| 11568 <param name="test" value="true"/> | |
| 11569 </conditional> | |
| 11570 <param name="in" value="IDFileConverter_20_input.idXML"/> | |
| 11571 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> | |
| 11572 <param name="out_type" value="pepXML"/> | |
| 11573 <param name="mz_name" value=""/> | |
| 11574 <param name="peptideprophet_analyzed" value="false"/> | |
| 11575 <param name="score_type" value="qvalue"/> | |
| 11576 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11577 <output name="ctd_out" ftype="xml"> | |
| 11578 <assert_contents> | |
| 11579 <is_valid_xml/> | |
| 11580 </assert_contents> | |
| 11581 </output> | |
| 11582 </test> | |
| 11583 <test expect_num_outputs="2"> | |
| 11584 <conditional name="adv_opts_cond"> | |
| 11585 <param name="adv_opts_selector" value="advanced"/> | |
| 11586 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11587 <param name="scan_regex" value=""/> | |
| 11588 <param name="no_spectra_data_override" value="false"/> | |
| 11589 <param name="no_spectra_references_override" value="false"/> | |
| 11590 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11591 <param name="force" value="false"/> | |
| 11592 <param name="test" value="true"/> | |
| 11593 </conditional> | |
| 11594 <param name="in" value="IDFileConverter_21_input.idXML"/> | |
| 11595 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11596 <param name="out_type" value="idXML"/> | |
| 11597 <param name="mz_file" value="IDMapper_4_input.mzML"/> | |
| 11598 <param name="mz_name" value=""/> | |
| 11599 <param name="peptideprophet_analyzed" value="false"/> | |
| 11600 <param name="score_type" value="qvalue"/> | |
| 11601 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11602 <output name="ctd_out" ftype="xml"> | |
| 11603 <assert_contents> | |
| 11604 <is_valid_xml/> | |
| 11605 </assert_contents> | |
| 11606 </output> | |
| 11607 </test> | |
| 11608 <test expect_num_outputs="2"> | |
| 11609 <conditional name="adv_opts_cond"> | |
| 11610 <param name="adv_opts_selector" value="advanced"/> | |
| 11611 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11612 <param name="scan_regex" value=""/> | |
| 11613 <param name="no_spectra_data_override" value="false"/> | |
| 11614 <param name="no_spectra_references_override" value="false"/> | |
| 11615 <param name="add_ionmatch_annotation" value="0.01"/> | |
| 11616 <param name="force" value="false"/> | |
| 11617 <param name="test" value="true"/> | |
| 11618 </conditional> | |
| 11619 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> | |
| 11620 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11621 <param name="out_type" value="idXML"/> | |
| 11622 <param name="mz_file" value="spectra.mzML"/> | |
| 11623 <param name="mz_name" value=""/> | |
| 11624 <param name="peptideprophet_analyzed" value="false"/> | |
| 11625 <param name="score_type" value="qvalue"/> | |
| 11626 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11627 <output name="ctd_out" ftype="xml"> | |
| 11628 <assert_contents> | |
| 11629 <is_valid_xml/> | |
| 11630 </assert_contents> | |
| 11631 </output> | |
| 11632 </test> | |
| 11633 <test expect_num_outputs="2"> | |
| 11634 <conditional name="adv_opts_cond"> | |
| 11635 <param name="adv_opts_selector" value="advanced"/> | |
| 11636 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11637 <param name="scan_regex" value=""/> | |
| 11638 <param name="no_spectra_data_override" value="false"/> | |
| 11639 <param name="no_spectra_references_override" value="false"/> | |
| 11640 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11641 <param name="force" value="false"/> | |
| 11642 <param name="test" value="true"/> | |
| 11643 </conditional> | |
| 11644 <param name="in" value="IDFileConverter_23_input.mzid"/> | |
| 11645 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11646 <param name="out_type" value="idXML"/> | |
| 11647 <param name="mz_name" value=""/> | |
| 11648 <param name="peptideprophet_analyzed" value="false"/> | |
| 11649 <param name="score_type" value="qvalue"/> | |
| 11650 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11651 <output name="ctd_out" ftype="xml"> | |
| 11652 <assert_contents> | |
| 11653 <is_valid_xml/> | |
| 11654 </assert_contents> | |
| 11655 </output> | |
| 11656 </test> | |
| 11657 <test expect_num_outputs="2"> | |
| 11658 <conditional name="adv_opts_cond"> | |
| 11659 <param name="adv_opts_selector" value="advanced"/> | |
| 11660 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11661 <param name="scan_regex" value=""/> | |
| 11662 <param name="no_spectra_data_override" value="false"/> | |
| 11663 <param name="no_spectra_references_override" value="false"/> | |
| 11664 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11665 <param name="force" value="false"/> | |
| 11666 <param name="test" value="true"/> | |
| 11667 </conditional> | |
| 11668 <param name="in" value="IDFileConverter_24_input.pep.xml"/> | |
| 11669 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11670 <param name="out_type" value="idXML"/> | |
| 11671 <param name="mz_name" value=""/> | |
| 11672 <param name="peptideprophet_analyzed" value="false"/> | |
| 11673 <param name="score_type" value="qvalue"/> | |
| 11674 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11675 <output name="ctd_out" ftype="xml"> | |
| 11676 <assert_contents> | |
| 11677 <is_valid_xml/> | |
| 11678 </assert_contents> | |
| 11679 </output> | |
| 11680 </test> | |
| 11681 <test expect_num_outputs="2"> | |
| 11682 <conditional name="adv_opts_cond"> | |
| 11683 <param name="adv_opts_selector" value="advanced"/> | |
| 11684 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11685 <param name="scan_regex" value=""/> | |
| 11686 <param name="no_spectra_data_override" value="false"/> | |
| 11687 <param name="no_spectra_references_override" value="false"/> | |
| 11688 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11689 <param name="force" value="false"/> | |
| 11690 <param name="test" value="true"/> | |
| 11691 </conditional> | |
| 11692 <param name="in" value="IDFileConverter_25_input.idXML"/> | |
| 11693 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/> | |
| 11694 <param name="out_type" value="pepXML"/> | |
| 11695 <param name="mz_name" value=""/> | |
| 11696 <param name="peptideprophet_analyzed" value="false"/> | |
| 11697 <param name="score_type" value="qvalue"/> | |
| 11698 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11699 <output name="ctd_out" ftype="xml"> | |
| 11700 <assert_contents> | |
| 11701 <is_valid_xml/> | |
| 11702 </assert_contents> | |
| 11703 </output> | |
| 11704 </test> | |
| 11705 <test expect_num_outputs="2"> | |
| 11706 <conditional name="adv_opts_cond"> | |
| 11707 <param name="adv_opts_selector" value="advanced"/> | |
| 11708 <param name="ignore_proteins_per_peptide" value="false"/> | |
| 11709 <param name="scan_regex" value=""/> | |
| 11710 <param name="no_spectra_data_override" value="false"/> | |
| 11711 <param name="no_spectra_references_override" value="false"/> | |
| 11712 <param name="add_ionmatch_annotation" value="0.0"/> | |
| 11713 <param name="force" value="false"/> | |
| 11714 <param name="test" value="true"/> | |
| 11715 </conditional> | |
| 11716 <param name="in" value="IDFileConverter_26_input.mzid"/> | |
| 11717 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11718 <param name="out_type" value="idXML"/> | |
| 11719 <param name="mz_name" value=""/> | |
| 11720 <param name="peptideprophet_analyzed" value="false"/> | |
| 11721 <param name="score_type" value="qvalue"/> | |
| 11722 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11723 <output name="ctd_out" ftype="xml"> | |
| 11724 <assert_contents> | |
| 11725 <is_valid_xml/> | |
| 11726 </assert_contents> | |
| 11727 </output> | |
| 11728 </test> | |
| 11729 </xml> | |
| 11730 <xml name="autotest_IDFilter"> | |
| 11731 <test expect_num_outputs="2"> | |
| 11732 <conditional name="adv_opts_cond"> | |
| 11733 <param name="adv_opts_selector" value="advanced"/> | |
| 11734 <param name="remove_duplicate_psm" value="false"/> | |
| 11735 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 11736 <param name="force" value="false"/> | |
| 11737 <param name="test" value="true"/> | |
| 11738 </conditional> | |
| 11739 <param name="in" value="IDFilter_1_input.idXML"/> | |
| 11740 <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11741 <param name="var_mods" value="false"/> | |
| 11742 <param name="remove_shared_peptides" value="false"/> | |
| 11743 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 11744 <param name="remove_decoys" value="false"/> | |
| 11745 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 11746 <section name="precursor"> | |
| 11747 <param name="rt" value=":"/> | |
| 11748 <param name="mz" value=":"/> | |
| 11749 <param name="length" value=":"/> | |
| 11750 <param name="charge" value=":"/> | |
| 11751 </section> | |
| 11752 <section name="score"> | |
| 11753 <param name="pep" value="0.0"/> | |
| 11754 <param name="prot" value="0.0"/> | |
| 11755 </section> | |
| 11756 <section name="whitelist"> | |
| 11757 <param name="proteins" value="IDFilter_1_input.fas"/> | |
| 11758 <param name="protein_accessions" value=""/> | |
| 11759 <param name="ignore_modifications" value="false"/> | |
| 11760 <param name="modifications" value=""/> | |
| 11761 </section> | |
| 11762 <section name="blacklist"> | |
| 11763 <param name="protein_accessions" value=""/> | |
| 11764 <param name="ignore_modifications" value="false"/> | |
| 11765 <param name="modifications" value=""/> | |
| 11766 </section> | |
| 11767 <section name="in_silico_digestion"> | |
| 11768 <param name="enzyme" value="Trypsin"/> | |
| 11769 <param name="specificity" value="full"/> | |
| 11770 <param name="missed_cleavages" value="-1"/> | |
| 11771 <param name="methionine_cleavage" value="false"/> | |
| 11772 </section> | |
| 11773 <section name="missed_cleavages"> | |
| 11774 <param name="number_of_missed_cleavages" value=":"/> | |
| 11775 <param name="enzyme" value="Trypsin"/> | |
| 11776 </section> | |
| 11777 <section name="rt"> | |
| 11778 <param name="p_value" value="0.0"/> | |
| 11779 <param name="p_value_1st_dim" value="0.0"/> | |
| 11780 </section> | |
| 11781 <section name="mz"> | |
| 11782 <param name="error" value="-1.0"/> | |
| 11783 <param name="unit" value="ppm"/> | |
| 11784 </section> | |
| 11785 <section name="best"> | |
| 11786 <param name="n_peptide_hits" value="0"/> | |
| 11787 <param name="n_protein_hits" value="0"/> | |
| 11788 <param name="strict" value="false"/> | |
| 11789 <param name="n_to_m_peptide_hits" value=":"/> | |
| 11790 </section> | |
| 11791 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11792 <output name="ctd_out" ftype="xml"> | |
| 11793 <assert_contents> | |
| 11794 <is_valid_xml/> | |
| 11795 </assert_contents> | |
| 11796 </output> | |
| 11797 </test> | |
| 11798 <test expect_num_outputs="2"> | |
| 11799 <conditional name="adv_opts_cond"> | |
| 11800 <param name="adv_opts_selector" value="advanced"/> | |
| 11801 <param name="remove_duplicate_psm" value="false"/> | |
| 11802 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 11803 <param name="force" value="false"/> | |
| 11804 <param name="test" value="true"/> | |
| 11805 </conditional> | |
| 11806 <param name="in" value="IDFilter_3_input.idXML"/> | |
| 11807 <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11808 <param name="var_mods" value="false"/> | |
| 11809 <param name="remove_shared_peptides" value="false"/> | |
| 11810 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 11811 <param name="remove_decoys" value="false"/> | |
| 11812 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 11813 <section name="precursor"> | |
| 11814 <param name="rt" value=":"/> | |
| 11815 <param name="mz" value=":"/> | |
| 11816 <param name="length" value=":"/> | |
| 11817 <param name="charge" value=":"/> | |
| 11818 </section> | |
| 11819 <section name="score"> | |
| 11820 <param name="pep" value="0.0"/> | |
| 11821 <param name="prot" value="0.0"/> | |
| 11822 </section> | |
| 11823 <section name="whitelist"> | |
| 11824 <param name="protein_accessions" value=""/> | |
| 11825 <param name="ignore_modifications" value="false"/> | |
| 11826 <param name="modifications" value=""/> | |
| 11827 </section> | |
| 11828 <section name="blacklist"> | |
| 11829 <param name="protein_accessions" value=""/> | |
| 11830 <param name="peptides" value="IDFilter_3_2_input.idXML"/> | |
| 11831 <param name="ignore_modifications" value="false"/> | |
| 11832 <param name="modifications" value=""/> | |
| 11833 </section> | |
| 11834 <section name="in_silico_digestion"> | |
| 11835 <param name="enzyme" value="Trypsin"/> | |
| 11836 <param name="specificity" value="full"/> | |
| 11837 <param name="missed_cleavages" value="-1"/> | |
| 11838 <param name="methionine_cleavage" value="false"/> | |
| 11839 </section> | |
| 11840 <section name="missed_cleavages"> | |
| 11841 <param name="number_of_missed_cleavages" value=":"/> | |
| 11842 <param name="enzyme" value="Trypsin"/> | |
| 11843 </section> | |
| 11844 <section name="rt"> | |
| 11845 <param name="p_value" value="0.0"/> | |
| 11846 <param name="p_value_1st_dim" value="0.0"/> | |
| 11847 </section> | |
| 11848 <section name="mz"> | |
| 11849 <param name="error" value="-1.0"/> | |
| 11850 <param name="unit" value="ppm"/> | |
| 11851 </section> | |
| 11852 <section name="best"> | |
| 11853 <param name="n_peptide_hits" value="0"/> | |
| 11854 <param name="n_protein_hits" value="0"/> | |
| 11855 <param name="strict" value="false"/> | |
| 11856 <param name="n_to_m_peptide_hits" value=":"/> | |
| 11857 </section> | |
| 11858 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11859 <output name="ctd_out" ftype="xml"> | |
| 11860 <assert_contents> | |
| 11861 <is_valid_xml/> | |
| 11862 </assert_contents> | |
| 11863 </output> | |
| 11864 </test> | |
| 11865 <test expect_num_outputs="2"> | |
| 11866 <conditional name="adv_opts_cond"> | |
| 11867 <param name="adv_opts_selector" value="advanced"/> | |
| 11868 <param name="remove_duplicate_psm" value="false"/> | |
| 11869 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 11870 <param name="force" value="false"/> | |
| 11871 <param name="test" value="true"/> | |
| 11872 </conditional> | |
| 11873 <param name="in" value="IDFilter_4_input.idXML"/> | |
| 11874 <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11875 <param name="var_mods" value="false"/> | |
| 11876 <param name="remove_shared_peptides" value="false"/> | |
| 11877 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 11878 <param name="remove_decoys" value="false"/> | |
| 11879 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 11880 <section name="precursor"> | |
| 11881 <param name="rt" value=":"/> | |
| 11882 <param name="mz" value=":"/> | |
| 11883 <param name="length" value=":"/> | |
| 11884 <param name="charge" value=":"/> | |
| 11885 </section> | |
| 11886 <section name="score"> | |
| 11887 <param name="pep" value="0.0"/> | |
| 11888 <param name="prot" value="0.0"/> | |
| 11889 </section> | |
| 11890 <section name="whitelist"> | |
| 11891 <param name="protein_accessions" value=""/> | |
| 11892 <param name="ignore_modifications" value="false"/> | |
| 11893 <param name="modifications" value=""/> | |
| 11894 </section> | |
| 11895 <section name="blacklist"> | |
| 11896 <param name="protein_accessions" value=""/> | |
| 11897 <param name="ignore_modifications" value="false"/> | |
| 11898 <param name="modifications" value=""/> | |
| 11899 </section> | |
| 11900 <section name="in_silico_digestion"> | |
| 11901 <param name="enzyme" value="Trypsin"/> | |
| 11902 <param name="specificity" value="full"/> | |
| 11903 <param name="missed_cleavages" value="-1"/> | |
| 11904 <param name="methionine_cleavage" value="false"/> | |
| 11905 </section> | |
| 11906 <section name="missed_cleavages"> | |
| 11907 <param name="number_of_missed_cleavages" value=":"/> | |
| 11908 <param name="enzyme" value="Trypsin"/> | |
| 11909 </section> | |
| 11910 <section name="rt"> | |
| 11911 <param name="p_value" value="0.08"/> | |
| 11912 <param name="p_value_1st_dim" value="0.0"/> | |
| 11913 </section> | |
| 11914 <section name="mz"> | |
| 11915 <param name="error" value="-1.0"/> | |
| 11916 <param name="unit" value="ppm"/> | |
| 11917 </section> | |
| 11918 <section name="best"> | |
| 11919 <param name="n_peptide_hits" value="0"/> | |
| 11920 <param name="n_protein_hits" value="0"/> | |
| 11921 <param name="strict" value="false"/> | |
| 11922 <param name="n_to_m_peptide_hits" value=":"/> | |
| 11923 </section> | |
| 11924 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11925 <output name="ctd_out" ftype="xml"> | |
| 11926 <assert_contents> | |
| 11927 <is_valid_xml/> | |
| 11928 </assert_contents> | |
| 11929 </output> | |
| 11930 </test> | |
| 11931 <test expect_num_outputs="2"> | |
| 11932 <conditional name="adv_opts_cond"> | |
| 11933 <param name="adv_opts_selector" value="advanced"/> | |
| 11934 <param name="remove_duplicate_psm" value="false"/> | |
| 11935 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 11936 <param name="force" value="false"/> | |
| 11937 <param name="test" value="true"/> | |
| 11938 </conditional> | |
| 11939 <param name="in" value="IDFilter_5_input.idXML"/> | |
| 11940 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 11941 <param name="var_mods" value="false"/> | |
| 11942 <param name="remove_shared_peptides" value="false"/> | |
| 11943 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 11944 <param name="remove_decoys" value="false"/> | |
| 11945 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 11946 <section name="precursor"> | |
| 11947 <param name="rt" value=":"/> | |
| 11948 <param name="mz" value=":"/> | |
| 11949 <param name="length" value=":"/> | |
| 11950 <param name="charge" value=":"/> | |
| 11951 </section> | |
| 11952 <section name="score"> | |
| 11953 <param name="pep" value="32.0"/> | |
| 11954 <param name="prot" value="25.0"/> | |
| 11955 </section> | |
| 11956 <section name="whitelist"> | |
| 11957 <param name="protein_accessions" value=""/> | |
| 11958 <param name="ignore_modifications" value="false"/> | |
| 11959 <param name="modifications" value=""/> | |
| 11960 </section> | |
| 11961 <section name="blacklist"> | |
| 11962 <param name="protein_accessions" value=""/> | |
| 11963 <param name="ignore_modifications" value="false"/> | |
| 11964 <param name="modifications" value=""/> | |
| 11965 </section> | |
| 11966 <section name="in_silico_digestion"> | |
| 11967 <param name="enzyme" value="Trypsin"/> | |
| 11968 <param name="specificity" value="full"/> | |
| 11969 <param name="missed_cleavages" value="-1"/> | |
| 11970 <param name="methionine_cleavage" value="false"/> | |
| 11971 </section> | |
| 11972 <section name="missed_cleavages"> | |
| 11973 <param name="number_of_missed_cleavages" value=":"/> | |
| 11974 <param name="enzyme" value="Trypsin"/> | |
| 11975 </section> | |
| 11976 <section name="rt"> | |
| 11977 <param name="p_value" value="0.0"/> | |
| 11978 <param name="p_value_1st_dim" value="0.0"/> | |
| 11979 </section> | |
| 11980 <section name="mz"> | |
| 11981 <param name="error" value="-1.0"/> | |
| 11982 <param name="unit" value="ppm"/> | |
| 11983 </section> | |
| 11984 <section name="best"> | |
| 11985 <param name="n_peptide_hits" value="0"/> | |
| 11986 <param name="n_protein_hits" value="0"/> | |
| 11987 <param name="strict" value="false"/> | |
| 11988 <param name="n_to_m_peptide_hits" value=":"/> | |
| 11989 </section> | |
| 11990 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 11991 <output name="ctd_out" ftype="xml"> | |
| 11992 <assert_contents> | |
| 11993 <is_valid_xml/> | |
| 11994 </assert_contents> | |
| 11995 </output> | |
| 11996 </test> | |
| 11997 <test expect_num_outputs="2"> | |
| 11998 <conditional name="adv_opts_cond"> | |
| 11999 <param name="adv_opts_selector" value="advanced"/> | |
| 12000 <param name="remove_duplicate_psm" value="false"/> | |
| 12001 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12002 <param name="force" value="false"/> | |
| 12003 <param name="test" value="true"/> | |
| 12004 </conditional> | |
| 12005 <param name="in" value="IDFilter_5_input.idXML"/> | |
| 12006 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12007 <param name="var_mods" value="false"/> | |
| 12008 <param name="remove_shared_peptides" value="false"/> | |
| 12009 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12010 <param name="remove_decoys" value="false"/> | |
| 12011 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12012 <section name="precursor"> | |
| 12013 <param name="rt" value=":"/> | |
| 12014 <param name="mz" value=":"/> | |
| 12015 <param name="length" value=":"/> | |
| 12016 <param name="charge" value=":"/> | |
| 12017 </section> | |
| 12018 <section name="score"> | |
| 12019 <param name="pep" value="32.0"/> | |
| 12020 <param name="prot" value="0.0"/> | |
| 12021 </section> | |
| 12022 <section name="whitelist"> | |
| 12023 <param name="protein_accessions" value=""/> | |
| 12024 <param name="ignore_modifications" value="false"/> | |
| 12025 <param name="modifications" value=""/> | |
| 12026 </section> | |
| 12027 <section name="blacklist"> | |
| 12028 <param name="protein_accessions" value=""/> | |
| 12029 <param name="ignore_modifications" value="false"/> | |
| 12030 <param name="modifications" value=""/> | |
| 12031 </section> | |
| 12032 <section name="in_silico_digestion"> | |
| 12033 <param name="enzyme" value="Trypsin"/> | |
| 12034 <param name="specificity" value="full"/> | |
| 12035 <param name="missed_cleavages" value="-1"/> | |
| 12036 <param name="methionine_cleavage" value="false"/> | |
| 12037 </section> | |
| 12038 <section name="missed_cleavages"> | |
| 12039 <param name="number_of_missed_cleavages" value=":"/> | |
| 12040 <param name="enzyme" value="Trypsin"/> | |
| 12041 </section> | |
| 12042 <section name="rt"> | |
| 12043 <param name="p_value" value="0.0"/> | |
| 12044 <param name="p_value_1st_dim" value="0.0"/> | |
| 12045 </section> | |
| 12046 <section name="mz"> | |
| 12047 <param name="error" value="-1.0"/> | |
| 12048 <param name="unit" value="ppm"/> | |
| 12049 </section> | |
| 12050 <section name="best"> | |
| 12051 <param name="n_peptide_hits" value="0"/> | |
| 12052 <param name="n_protein_hits" value="0"/> | |
| 12053 <param name="strict" value="false"/> | |
| 12054 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12055 </section> | |
| 12056 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12057 <output name="ctd_out" ftype="xml"> | |
| 12058 <assert_contents> | |
| 12059 <is_valid_xml/> | |
| 12060 </assert_contents> | |
| 12061 </output> | |
| 12062 </test> | |
| 12063 <test expect_num_outputs="2"> | |
| 12064 <conditional name="adv_opts_cond"> | |
| 12065 <param name="adv_opts_selector" value="advanced"/> | |
| 12066 <param name="remove_duplicate_psm" value="false"/> | |
| 12067 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12068 <param name="force" value="false"/> | |
| 12069 <param name="test" value="true"/> | |
| 12070 </conditional> | |
| 12071 <param name="in" value="IDFilter_5_input.idXML"/> | |
| 12072 <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12073 <param name="var_mods" value="false"/> | |
| 12074 <param name="remove_shared_peptides" value="false"/> | |
| 12075 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12076 <param name="remove_decoys" value="false"/> | |
| 12077 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12078 <section name="precursor"> | |
| 12079 <param name="rt" value=":"/> | |
| 12080 <param name="mz" value=":"/> | |
| 12081 <param name="length" value=":"/> | |
| 12082 <param name="charge" value=":"/> | |
| 12083 </section> | |
| 12084 <section name="score"> | |
| 12085 <param name="pep" value="0.0"/> | |
| 12086 <param name="prot" value="25.0"/> | |
| 12087 </section> | |
| 12088 <section name="whitelist"> | |
| 12089 <param name="protein_accessions" value=""/> | |
| 12090 <param name="ignore_modifications" value="false"/> | |
| 12091 <param name="modifications" value=""/> | |
| 12092 </section> | |
| 12093 <section name="blacklist"> | |
| 12094 <param name="protein_accessions" value=""/> | |
| 12095 <param name="ignore_modifications" value="false"/> | |
| 12096 <param name="modifications" value=""/> | |
| 12097 </section> | |
| 12098 <section name="in_silico_digestion"> | |
| 12099 <param name="enzyme" value="Trypsin"/> | |
| 12100 <param name="specificity" value="full"/> | |
| 12101 <param name="missed_cleavages" value="-1"/> | |
| 12102 <param name="methionine_cleavage" value="false"/> | |
| 12103 </section> | |
| 12104 <section name="missed_cleavages"> | |
| 12105 <param name="number_of_missed_cleavages" value=":"/> | |
| 12106 <param name="enzyme" value="Trypsin"/> | |
| 12107 </section> | |
| 12108 <section name="rt"> | |
| 12109 <param name="p_value" value="0.0"/> | |
| 12110 <param name="p_value_1st_dim" value="0.0"/> | |
| 12111 </section> | |
| 12112 <section name="mz"> | |
| 12113 <param name="error" value="-1.0"/> | |
| 12114 <param name="unit" value="ppm"/> | |
| 12115 </section> | |
| 12116 <section name="best"> | |
| 12117 <param name="n_peptide_hits" value="0"/> | |
| 12118 <param name="n_protein_hits" value="0"/> | |
| 12119 <param name="strict" value="false"/> | |
| 12120 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12121 </section> | |
| 12122 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12123 <output name="ctd_out" ftype="xml"> | |
| 12124 <assert_contents> | |
| 12125 <is_valid_xml/> | |
| 12126 </assert_contents> | |
| 12127 </output> | |
| 12128 </test> | |
| 12129 <test expect_num_outputs="2"> | |
| 12130 <conditional name="adv_opts_cond"> | |
| 12131 <param name="adv_opts_selector" value="advanced"/> | |
| 12132 <param name="remove_duplicate_psm" value="false"/> | |
| 12133 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12134 <param name="force" value="false"/> | |
| 12135 <param name="test" value="true"/> | |
| 12136 </conditional> | |
| 12137 <param name="in" value="IDFilter_5_input.idXML"/> | |
| 12138 <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12139 <param name="var_mods" value="false"/> | |
| 12140 <param name="remove_shared_peptides" value="false"/> | |
| 12141 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12142 <param name="remove_decoys" value="false"/> | |
| 12143 <param name="delete_unreferenced_peptide_hits" value="true"/> | |
| 12144 <section name="precursor"> | |
| 12145 <param name="rt" value=":"/> | |
| 12146 <param name="mz" value=":"/> | |
| 12147 <param name="length" value=":"/> | |
| 12148 <param name="charge" value=":"/> | |
| 12149 </section> | |
| 12150 <section name="score"> | |
| 12151 <param name="pep" value="0.0"/> | |
| 12152 <param name="prot" value="25.0"/> | |
| 12153 </section> | |
| 12154 <section name="whitelist"> | |
| 12155 <param name="protein_accessions" value=""/> | |
| 12156 <param name="ignore_modifications" value="false"/> | |
| 12157 <param name="modifications" value=""/> | |
| 12158 </section> | |
| 12159 <section name="blacklist"> | |
| 12160 <param name="protein_accessions" value=""/> | |
| 12161 <param name="ignore_modifications" value="false"/> | |
| 12162 <param name="modifications" value=""/> | |
| 12163 </section> | |
| 12164 <section name="in_silico_digestion"> | |
| 12165 <param name="enzyme" value="Trypsin"/> | |
| 12166 <param name="specificity" value="full"/> | |
| 12167 <param name="missed_cleavages" value="-1"/> | |
| 12168 <param name="methionine_cleavage" value="false"/> | |
| 12169 </section> | |
| 12170 <section name="missed_cleavages"> | |
| 12171 <param name="number_of_missed_cleavages" value=":"/> | |
| 12172 <param name="enzyme" value="Trypsin"/> | |
| 12173 </section> | |
| 12174 <section name="rt"> | |
| 12175 <param name="p_value" value="0.0"/> | |
| 12176 <param name="p_value_1st_dim" value="0.0"/> | |
| 12177 </section> | |
| 12178 <section name="mz"> | |
| 12179 <param name="error" value="-1.0"/> | |
| 12180 <param name="unit" value="ppm"/> | |
| 12181 </section> | |
| 12182 <section name="best"> | |
| 12183 <param name="n_peptide_hits" value="0"/> | |
| 12184 <param name="n_protein_hits" value="0"/> | |
| 12185 <param name="strict" value="false"/> | |
| 12186 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12187 </section> | |
| 12188 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12189 <output name="ctd_out" ftype="xml"> | |
| 12190 <assert_contents> | |
| 12191 <is_valid_xml/> | |
| 12192 </assert_contents> | |
| 12193 </output> | |
| 12194 </test> | |
| 12195 <test expect_num_outputs="2"> | |
| 12196 <conditional name="adv_opts_cond"> | |
| 12197 <param name="adv_opts_selector" value="advanced"/> | |
| 12198 <param name="remove_duplicate_psm" value="false"/> | |
| 12199 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12200 <param name="force" value="false"/> | |
| 12201 <param name="test" value="true"/> | |
| 12202 </conditional> | |
| 12203 <param name="in" value="IDFilter_6_input.idXML"/> | |
| 12204 <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12205 <param name="var_mods" value="false"/> | |
| 12206 <param name="remove_shared_peptides" value="false"/> | |
| 12207 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12208 <param name="remove_decoys" value="false"/> | |
| 12209 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12210 <section name="precursor"> | |
| 12211 <param name="rt" value=":"/> | |
| 12212 <param name="mz" value=":"/> | |
| 12213 <param name="length" value=":"/> | |
| 12214 <param name="charge" value=":"/> | |
| 12215 </section> | |
| 12216 <section name="score"> | |
| 12217 <param name="pep" value="0.0"/> | |
| 12218 <param name="prot" value="0.0"/> | |
| 12219 </section> | |
| 12220 <section name="whitelist"> | |
| 12221 <param name="protein_accessions" value=""/> | |
| 12222 <param name="ignore_modifications" value="false"/> | |
| 12223 <param name="modifications" value=""/> | |
| 12224 </section> | |
| 12225 <section name="blacklist"> | |
| 12226 <param name="protein_accessions" value=""/> | |
| 12227 <param name="ignore_modifications" value="false"/> | |
| 12228 <param name="modifications" value=""/> | |
| 12229 </section> | |
| 12230 <section name="in_silico_digestion"> | |
| 12231 <param name="enzyme" value="Trypsin"/> | |
| 12232 <param name="specificity" value="full"/> | |
| 12233 <param name="missed_cleavages" value="-1"/> | |
| 12234 <param name="methionine_cleavage" value="false"/> | |
| 12235 </section> | |
| 12236 <section name="missed_cleavages"> | |
| 12237 <param name="number_of_missed_cleavages" value=":"/> | |
| 12238 <param name="enzyme" value="Trypsin"/> | |
| 12239 </section> | |
| 12240 <section name="rt"> | |
| 12241 <param name="p_value" value="0.0"/> | |
| 12242 <param name="p_value_1st_dim" value="0.0"/> | |
| 12243 </section> | |
| 12244 <section name="mz"> | |
| 12245 <param name="error" value="-1.0"/> | |
| 12246 <param name="unit" value="ppm"/> | |
| 12247 </section> | |
| 12248 <section name="best"> | |
| 12249 <param name="n_peptide_hits" value="2"/> | |
| 12250 <param name="n_protein_hits" value="10"/> | |
| 12251 <param name="strict" value="false"/> | |
| 12252 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12253 </section> | |
| 12254 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12255 <output name="ctd_out" ftype="xml"> | |
| 12256 <assert_contents> | |
| 12257 <is_valid_xml/> | |
| 12258 </assert_contents> | |
| 12259 </output> | |
| 12260 </test> | |
| 12261 <test expect_num_outputs="2"> | |
| 12262 <conditional name="adv_opts_cond"> | |
| 12263 <param name="adv_opts_selector" value="advanced"/> | |
| 12264 <param name="remove_duplicate_psm" value="true"/> | |
| 12265 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12266 <param name="force" value="false"/> | |
| 12267 <param name="test" value="true"/> | |
| 12268 </conditional> | |
| 12269 <param name="in" value="IDFilter_7_input.idXML"/> | |
| 12270 <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12271 <param name="var_mods" value="false"/> | |
| 12272 <param name="remove_shared_peptides" value="false"/> | |
| 12273 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12274 <param name="remove_decoys" value="false"/> | |
| 12275 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12276 <section name="precursor"> | |
| 12277 <param name="rt" value=":"/> | |
| 12278 <param name="mz" value=":"/> | |
| 12279 <param name="length" value=":"/> | |
| 12280 <param name="charge" value=":"/> | |
| 12281 </section> | |
| 12282 <section name="score"> | |
| 12283 <param name="pep" value="0.0"/> | |
| 12284 <param name="prot" value="0.0"/> | |
| 12285 </section> | |
| 12286 <section name="whitelist"> | |
| 12287 <param name="protein_accessions" value=""/> | |
| 12288 <param name="ignore_modifications" value="false"/> | |
| 12289 <param name="modifications" value=""/> | |
| 12290 </section> | |
| 12291 <section name="blacklist"> | |
| 12292 <param name="protein_accessions" value=""/> | |
| 12293 <param name="ignore_modifications" value="false"/> | |
| 12294 <param name="modifications" value=""/> | |
| 12295 </section> | |
| 12296 <section name="in_silico_digestion"> | |
| 12297 <param name="enzyme" value="Trypsin"/> | |
| 12298 <param name="specificity" value="full"/> | |
| 12299 <param name="missed_cleavages" value="-1"/> | |
| 12300 <param name="methionine_cleavage" value="false"/> | |
| 12301 </section> | |
| 12302 <section name="missed_cleavages"> | |
| 12303 <param name="number_of_missed_cleavages" value=":"/> | |
| 12304 <param name="enzyme" value="Trypsin"/> | |
| 12305 </section> | |
| 12306 <section name="rt"> | |
| 12307 <param name="p_value" value="0.0"/> | |
| 12308 <param name="p_value_1st_dim" value="0.0"/> | |
| 12309 </section> | |
| 12310 <section name="mz"> | |
| 12311 <param name="error" value="-1.0"/> | |
| 12312 <param name="unit" value="ppm"/> | |
| 12313 </section> | |
| 12314 <section name="best"> | |
| 12315 <param name="n_peptide_hits" value="0"/> | |
| 12316 <param name="n_protein_hits" value="0"/> | |
| 12317 <param name="strict" value="false"/> | |
| 12318 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12319 </section> | |
| 12320 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12321 <output name="ctd_out" ftype="xml"> | |
| 12322 <assert_contents> | |
| 12323 <is_valid_xml/> | |
| 12324 </assert_contents> | |
| 12325 </output> | |
| 12326 </test> | |
| 12327 <test expect_num_outputs="2"> | |
| 12328 <conditional name="adv_opts_cond"> | |
| 12329 <param name="adv_opts_selector" value="advanced"/> | |
| 12330 <param name="remove_duplicate_psm" value="false"/> | |
| 12331 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12332 <param name="force" value="false"/> | |
| 12333 <param name="test" value="true"/> | |
| 12334 </conditional> | |
| 12335 <param name="in" value="IDFilter_8_input.idXML"/> | |
| 12336 <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12337 <param name="var_mods" value="false"/> | |
| 12338 <param name="remove_shared_peptides" value="false"/> | |
| 12339 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12340 <param name="remove_decoys" value="false"/> | |
| 12341 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12342 <section name="precursor"> | |
| 12343 <param name="rt" value="200:350"/> | |
| 12344 <param name="mz" value="999:1000"/> | |
| 12345 <param name="length" value=":"/> | |
| 12346 <param name="charge" value=":"/> | |
| 12347 </section> | |
| 12348 <section name="score"> | |
| 12349 <param name="pep" value="0.0"/> | |
| 12350 <param name="prot" value="0.0"/> | |
| 12351 </section> | |
| 12352 <section name="whitelist"> | |
| 12353 <param name="protein_accessions" value=""/> | |
| 12354 <param name="ignore_modifications" value="false"/> | |
| 12355 <param name="modifications" value=""/> | |
| 12356 </section> | |
| 12357 <section name="blacklist"> | |
| 12358 <param name="protein_accessions" value=""/> | |
| 12359 <param name="ignore_modifications" value="false"/> | |
| 12360 <param name="modifications" value=""/> | |
| 12361 </section> | |
| 12362 <section name="in_silico_digestion"> | |
| 12363 <param name="enzyme" value="Trypsin"/> | |
| 12364 <param name="specificity" value="full"/> | |
| 12365 <param name="missed_cleavages" value="-1"/> | |
| 12366 <param name="methionine_cleavage" value="false"/> | |
| 12367 </section> | |
| 12368 <section name="missed_cleavages"> | |
| 12369 <param name="number_of_missed_cleavages" value=":"/> | |
| 12370 <param name="enzyme" value="Trypsin"/> | |
| 12371 </section> | |
| 12372 <section name="rt"> | |
| 12373 <param name="p_value" value="0.0"/> | |
| 12374 <param name="p_value_1st_dim" value="0.0"/> | |
| 12375 </section> | |
| 12376 <section name="mz"> | |
| 12377 <param name="error" value="-1.0"/> | |
| 12378 <param name="unit" value="ppm"/> | |
| 12379 </section> | |
| 12380 <section name="best"> | |
| 12381 <param name="n_peptide_hits" value="0"/> | |
| 12382 <param name="n_protein_hits" value="0"/> | |
| 12383 <param name="strict" value="false"/> | |
| 12384 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12385 </section> | |
| 12386 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12387 <output name="ctd_out" ftype="xml"> | |
| 12388 <assert_contents> | |
| 12389 <is_valid_xml/> | |
| 12390 </assert_contents> | |
| 12391 </output> | |
| 12392 </test> | |
| 12393 <test expect_num_outputs="2"> | |
| 12394 <conditional name="adv_opts_cond"> | |
| 12395 <param name="adv_opts_selector" value="advanced"/> | |
| 12396 <param name="remove_duplicate_psm" value="false"/> | |
| 12397 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12398 <param name="force" value="false"/> | |
| 12399 <param name="test" value="true"/> | |
| 12400 </conditional> | |
| 12401 <param name="in" value="IDFilter_9_input.idXML"/> | |
| 12402 <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12403 <param name="var_mods" value="false"/> | |
| 12404 <param name="remove_shared_peptides" value="false"/> | |
| 12405 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12406 <param name="remove_decoys" value="false"/> | |
| 12407 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12408 <section name="precursor"> | |
| 12409 <param name="rt" value=":"/> | |
| 12410 <param name="mz" value=":"/> | |
| 12411 <param name="length" value=":"/> | |
| 12412 <param name="charge" value=":"/> | |
| 12413 </section> | |
| 12414 <section name="score"> | |
| 12415 <param name="pep" value="0.05"/> | |
| 12416 <param name="prot" value="0.0"/> | |
| 12417 </section> | |
| 12418 <section name="whitelist"> | |
| 12419 <param name="protein_accessions" value=""/> | |
| 12420 <param name="ignore_modifications" value="false"/> | |
| 12421 <param name="modifications" value=""/> | |
| 12422 </section> | |
| 12423 <section name="blacklist"> | |
| 12424 <param name="protein_accessions" value=""/> | |
| 12425 <param name="ignore_modifications" value="false"/> | |
| 12426 <param name="modifications" value=""/> | |
| 12427 </section> | |
| 12428 <section name="in_silico_digestion"> | |
| 12429 <param name="enzyme" value="Trypsin"/> | |
| 12430 <param name="specificity" value="full"/> | |
| 12431 <param name="missed_cleavages" value="-1"/> | |
| 12432 <param name="methionine_cleavage" value="false"/> | |
| 12433 </section> | |
| 12434 <section name="missed_cleavages"> | |
| 12435 <param name="number_of_missed_cleavages" value=":"/> | |
| 12436 <param name="enzyme" value="Trypsin"/> | |
| 12437 </section> | |
| 12438 <section name="rt"> | |
| 12439 <param name="p_value" value="0.0"/> | |
| 12440 <param name="p_value_1st_dim" value="0.0"/> | |
| 12441 </section> | |
| 12442 <section name="mz"> | |
| 12443 <param name="error" value="-1.0"/> | |
| 12444 <param name="unit" value="ppm"/> | |
| 12445 </section> | |
| 12446 <section name="best"> | |
| 12447 <param name="n_peptide_hits" value="0"/> | |
| 12448 <param name="n_protein_hits" value="0"/> | |
| 12449 <param name="strict" value="false"/> | |
| 12450 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12451 </section> | |
| 12452 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12453 <output name="ctd_out" ftype="xml"> | |
| 12454 <assert_contents> | |
| 12455 <is_valid_xml/> | |
| 12456 </assert_contents> | |
| 12457 </output> | |
| 12458 </test> | |
| 12459 <test expect_num_outputs="2"> | |
| 12460 <conditional name="adv_opts_cond"> | |
| 12461 <param name="adv_opts_selector" value="advanced"/> | |
| 12462 <param name="remove_duplicate_psm" value="false"/> | |
| 12463 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12464 <param name="force" value="false"/> | |
| 12465 <param name="test" value="true"/> | |
| 12466 </conditional> | |
| 12467 <param name="in" value="IDFilter_10_input.idXML"/> | |
| 12468 <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12469 <param name="var_mods" value="false"/> | |
| 12470 <param name="remove_shared_peptides" value="false"/> | |
| 12471 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12472 <param name="remove_decoys" value="false"/> | |
| 12473 <param name="delete_unreferenced_peptide_hits" value="true"/> | |
| 12474 <section name="precursor"> | |
| 12475 <param name="rt" value=":"/> | |
| 12476 <param name="mz" value=":"/> | |
| 12477 <param name="length" value=":"/> | |
| 12478 <param name="charge" value=":"/> | |
| 12479 </section> | |
| 12480 <section name="score"> | |
| 12481 <param name="pep" value="0.0"/> | |
| 12482 <param name="prot" value="0.3"/> | |
| 12483 </section> | |
| 12484 <section name="whitelist"> | |
| 12485 <param name="protein_accessions" value=""/> | |
| 12486 <param name="ignore_modifications" value="false"/> | |
| 12487 <param name="modifications" value=""/> | |
| 12488 </section> | |
| 12489 <section name="blacklist"> | |
| 12490 <param name="protein_accessions" value=""/> | |
| 12491 <param name="ignore_modifications" value="false"/> | |
| 12492 <param name="modifications" value=""/> | |
| 12493 </section> | |
| 12494 <section name="in_silico_digestion"> | |
| 12495 <param name="enzyme" value="Trypsin"/> | |
| 12496 <param name="specificity" value="full"/> | |
| 12497 <param name="missed_cleavages" value="-1"/> | |
| 12498 <param name="methionine_cleavage" value="false"/> | |
| 12499 </section> | |
| 12500 <section name="missed_cleavages"> | |
| 12501 <param name="number_of_missed_cleavages" value=":"/> | |
| 12502 <param name="enzyme" value="Trypsin"/> | |
| 12503 </section> | |
| 12504 <section name="rt"> | |
| 12505 <param name="p_value" value="0.0"/> | |
| 12506 <param name="p_value_1st_dim" value="0.0"/> | |
| 12507 </section> | |
| 12508 <section name="mz"> | |
| 12509 <param name="error" value="-1.0"/> | |
| 12510 <param name="unit" value="ppm"/> | |
| 12511 </section> | |
| 12512 <section name="best"> | |
| 12513 <param name="n_peptide_hits" value="0"/> | |
| 12514 <param name="n_protein_hits" value="0"/> | |
| 12515 <param name="strict" value="false"/> | |
| 12516 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12517 </section> | |
| 12518 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12519 <output name="ctd_out" ftype="xml"> | |
| 12520 <assert_contents> | |
| 12521 <is_valid_xml/> | |
| 12522 </assert_contents> | |
| 12523 </output> | |
| 12524 </test> | |
| 12525 <test expect_num_outputs="2"> | |
| 12526 <conditional name="adv_opts_cond"> | |
| 12527 <param name="adv_opts_selector" value="advanced"/> | |
| 12528 <param name="remove_duplicate_psm" value="false"/> | |
| 12529 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12530 <param name="force" value="false"/> | |
| 12531 <param name="test" value="true"/> | |
| 12532 </conditional> | |
| 12533 <param name="in" value="IDFilter_11_input.idXML"/> | |
| 12534 <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12535 <param name="var_mods" value="false"/> | |
| 12536 <param name="remove_shared_peptides" value="false"/> | |
| 12537 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12538 <param name="remove_decoys" value="true"/> | |
| 12539 <param name="delete_unreferenced_peptide_hits" value="true"/> | |
| 12540 <section name="precursor"> | |
| 12541 <param name="rt" value=":"/> | |
| 12542 <param name="mz" value=":"/> | |
| 12543 <param name="length" value=":"/> | |
| 12544 <param name="charge" value=":"/> | |
| 12545 </section> | |
| 12546 <section name="score"> | |
| 12547 <param name="pep" value="0.0"/> | |
| 12548 <param name="prot" value="0.0"/> | |
| 12549 </section> | |
| 12550 <section name="whitelist"> | |
| 12551 <param name="protein_accessions" value=""/> | |
| 12552 <param name="ignore_modifications" value="false"/> | |
| 12553 <param name="modifications" value=""/> | |
| 12554 </section> | |
| 12555 <section name="blacklist"> | |
| 12556 <param name="protein_accessions" value=""/> | |
| 12557 <param name="ignore_modifications" value="false"/> | |
| 12558 <param name="modifications" value=""/> | |
| 12559 </section> | |
| 12560 <section name="in_silico_digestion"> | |
| 12561 <param name="enzyme" value="Trypsin"/> | |
| 12562 <param name="specificity" value="full"/> | |
| 12563 <param name="missed_cleavages" value="-1"/> | |
| 12564 <param name="methionine_cleavage" value="false"/> | |
| 12565 </section> | |
| 12566 <section name="missed_cleavages"> | |
| 12567 <param name="number_of_missed_cleavages" value=":"/> | |
| 12568 <param name="enzyme" value="Trypsin"/> | |
| 12569 </section> | |
| 12570 <section name="rt"> | |
| 12571 <param name="p_value" value="0.0"/> | |
| 12572 <param name="p_value_1st_dim" value="0.0"/> | |
| 12573 </section> | |
| 12574 <section name="mz"> | |
| 12575 <param name="error" value="-1.0"/> | |
| 12576 <param name="unit" value="ppm"/> | |
| 12577 </section> | |
| 12578 <section name="best"> | |
| 12579 <param name="n_peptide_hits" value="0"/> | |
| 12580 <param name="n_protein_hits" value="0"/> | |
| 12581 <param name="strict" value="false"/> | |
| 12582 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12583 </section> | |
| 12584 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12585 <output name="ctd_out" ftype="xml"> | |
| 12586 <assert_contents> | |
| 12587 <is_valid_xml/> | |
| 12588 </assert_contents> | |
| 12589 </output> | |
| 12590 </test> | |
| 12591 <test expect_num_outputs="2"> | |
| 12592 <conditional name="adv_opts_cond"> | |
| 12593 <param name="adv_opts_selector" value="advanced"/> | |
| 12594 <param name="remove_duplicate_psm" value="false"/> | |
| 12595 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12596 <param name="force" value="false"/> | |
| 12597 <param name="test" value="true"/> | |
| 12598 </conditional> | |
| 12599 <param name="in" value="IDFilter_12_input.idXML"/> | |
| 12600 <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12601 <param name="var_mods" value="false"/> | |
| 12602 <param name="remove_shared_peptides" value="false"/> | |
| 12603 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12604 <param name="remove_decoys" value="false"/> | |
| 12605 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12606 <section name="precursor"> | |
| 12607 <param name="rt" value=":"/> | |
| 12608 <param name="mz" value=":"/> | |
| 12609 <param name="length" value=":"/> | |
| 12610 <param name="charge" value=":"/> | |
| 12611 </section> | |
| 12612 <section name="score"> | |
| 12613 <param name="pep" value="0.0"/> | |
| 12614 <param name="prot" value="0.0"/> | |
| 12615 </section> | |
| 12616 <section name="whitelist"> | |
| 12617 <param name="protein_accessions" value=""/> | |
| 12618 <param name="ignore_modifications" value="false"/> | |
| 12619 <param name="modifications" value=""/> | |
| 12620 </section> | |
| 12621 <section name="blacklist"> | |
| 12622 <param name="protein_accessions" value=""/> | |
| 12623 <param name="ignore_modifications" value="false"/> | |
| 12624 <param name="modifications" value=""/> | |
| 12625 </section> | |
| 12626 <section name="in_silico_digestion"> | |
| 12627 <param name="fasta" value="IDFilter_12_input.fasta"/> | |
| 12628 <param name="enzyme" value="Trypsin"/> | |
| 12629 <param name="specificity" value="full"/> | |
| 12630 <param name="missed_cleavages" value="-1"/> | |
| 12631 <param name="methionine_cleavage" value="false"/> | |
| 12632 </section> | |
| 12633 <section name="missed_cleavages"> | |
| 12634 <param name="number_of_missed_cleavages" value=":"/> | |
| 12635 <param name="enzyme" value="Trypsin"/> | |
| 12636 </section> | |
| 12637 <section name="rt"> | |
| 12638 <param name="p_value" value="0.0"/> | |
| 12639 <param name="p_value_1st_dim" value="0.0"/> | |
| 12640 </section> | |
| 12641 <section name="mz"> | |
| 12642 <param name="error" value="-1.0"/> | |
| 12643 <param name="unit" value="ppm"/> | |
| 12644 </section> | |
| 12645 <section name="best"> | |
| 12646 <param name="n_peptide_hits" value="0"/> | |
| 12647 <param name="n_protein_hits" value="0"/> | |
| 12648 <param name="strict" value="false"/> | |
| 12649 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12650 </section> | |
| 12651 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12652 <output name="ctd_out" ftype="xml"> | |
| 12653 <assert_contents> | |
| 12654 <is_valid_xml/> | |
| 12655 </assert_contents> | |
| 12656 </output> | |
| 12657 </test> | |
| 12658 <test expect_num_outputs="2"> | |
| 12659 <conditional name="adv_opts_cond"> | |
| 12660 <param name="adv_opts_selector" value="advanced"/> | |
| 12661 <param name="remove_duplicate_psm" value="false"/> | |
| 12662 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12663 <param name="force" value="false"/> | |
| 12664 <param name="test" value="true"/> | |
| 12665 </conditional> | |
| 12666 <param name="in" value="IDFilter_13_input.idXML"/> | |
| 12667 <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12668 <param name="var_mods" value="false"/> | |
| 12669 <param name="remove_shared_peptides" value="false"/> | |
| 12670 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12671 <param name="remove_decoys" value="false"/> | |
| 12672 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12673 <section name="precursor"> | |
| 12674 <param name="rt" value=":"/> | |
| 12675 <param name="mz" value=":"/> | |
| 12676 <param name="length" value=":"/> | |
| 12677 <param name="charge" value=":"/> | |
| 12678 </section> | |
| 12679 <section name="score"> | |
| 12680 <param name="pep" value="0.0"/> | |
| 12681 <param name="prot" value="0.0"/> | |
| 12682 </section> | |
| 12683 <section name="whitelist"> | |
| 12684 <param name="protein_accessions" value=""/> | |
| 12685 <param name="ignore_modifications" value="false"/> | |
| 12686 <param name="modifications" value=""/> | |
| 12687 </section> | |
| 12688 <section name="blacklist"> | |
| 12689 <param name="protein_accessions" value=""/> | |
| 12690 <param name="ignore_modifications" value="false"/> | |
| 12691 <param name="modifications" value=""/> | |
| 12692 </section> | |
| 12693 <section name="in_silico_digestion"> | |
| 12694 <param name="fasta" value="IDFilter_13_input.fasta"/> | |
| 12695 <param name="enzyme" value="Trypsin"/> | |
| 12696 <param name="specificity" value="full"/> | |
| 12697 <param name="missed_cleavages" value="1"/> | |
| 12698 <param name="methionine_cleavage" value="false"/> | |
| 12699 </section> | |
| 12700 <section name="missed_cleavages"> | |
| 12701 <param name="number_of_missed_cleavages" value=":"/> | |
| 12702 <param name="enzyme" value="Trypsin"/> | |
| 12703 </section> | |
| 12704 <section name="rt"> | |
| 12705 <param name="p_value" value="0.0"/> | |
| 12706 <param name="p_value_1st_dim" value="0.0"/> | |
| 12707 </section> | |
| 12708 <section name="mz"> | |
| 12709 <param name="error" value="-1.0"/> | |
| 12710 <param name="unit" value="ppm"/> | |
| 12711 </section> | |
| 12712 <section name="best"> | |
| 12713 <param name="n_peptide_hits" value="0"/> | |
| 12714 <param name="n_protein_hits" value="0"/> | |
| 12715 <param name="strict" value="false"/> | |
| 12716 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12717 </section> | |
| 12718 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12719 <output name="ctd_out" ftype="xml"> | |
| 12720 <assert_contents> | |
| 12721 <is_valid_xml/> | |
| 12722 </assert_contents> | |
| 12723 </output> | |
| 12724 </test> | |
| 12725 <test expect_num_outputs="2"> | |
| 12726 <conditional name="adv_opts_cond"> | |
| 12727 <param name="adv_opts_selector" value="advanced"/> | |
| 12728 <param name="remove_duplicate_psm" value="false"/> | |
| 12729 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12730 <param name="force" value="false"/> | |
| 12731 <param name="test" value="true"/> | |
| 12732 </conditional> | |
| 12733 <param name="in" value="IDFilter_14_input.idXML"/> | |
| 12734 <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12735 <param name="var_mods" value="false"/> | |
| 12736 <param name="remove_shared_peptides" value="false"/> | |
| 12737 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12738 <param name="remove_decoys" value="false"/> | |
| 12739 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12740 <section name="precursor"> | |
| 12741 <param name="rt" value=":"/> | |
| 12742 <param name="mz" value=":"/> | |
| 12743 <param name="length" value=":"/> | |
| 12744 <param name="charge" value=":"/> | |
| 12745 </section> | |
| 12746 <section name="score"> | |
| 12747 <param name="pep" value="0.0"/> | |
| 12748 <param name="prot" value="0.0"/> | |
| 12749 </section> | |
| 12750 <section name="whitelist"> | |
| 12751 <param name="protein_accessions" value=""/> | |
| 12752 <param name="ignore_modifications" value="false"/> | |
| 12753 <param name="modifications" value=""/> | |
| 12754 </section> | |
| 12755 <section name="blacklist"> | |
| 12756 <param name="protein_accessions" value=""/> | |
| 12757 <param name="ignore_modifications" value="false"/> | |
| 12758 <param name="modifications" value=""/> | |
| 12759 </section> | |
| 12760 <section name="in_silico_digestion"> | |
| 12761 <param name="fasta" value="IDFilter_14_input.fasta"/> | |
| 12762 <param name="enzyme" value="Trypsin/P"/> | |
| 12763 <param name="specificity" value="full"/> | |
| 12764 <param name="missed_cleavages" value="1"/> | |
| 12765 <param name="methionine_cleavage" value="false"/> | |
| 12766 </section> | |
| 12767 <section name="missed_cleavages"> | |
| 12768 <param name="number_of_missed_cleavages" value=":"/> | |
| 12769 <param name="enzyme" value="Trypsin"/> | |
| 12770 </section> | |
| 12771 <section name="rt"> | |
| 12772 <param name="p_value" value="0.0"/> | |
| 12773 <param name="p_value_1st_dim" value="0.0"/> | |
| 12774 </section> | |
| 12775 <section name="mz"> | |
| 12776 <param name="error" value="-1.0"/> | |
| 12777 <param name="unit" value="ppm"/> | |
| 12778 </section> | |
| 12779 <section name="best"> | |
| 12780 <param name="n_peptide_hits" value="0"/> | |
| 12781 <param name="n_protein_hits" value="0"/> | |
| 12782 <param name="strict" value="false"/> | |
| 12783 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12784 </section> | |
| 12785 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12786 <output name="ctd_out" ftype="xml"> | |
| 12787 <assert_contents> | |
| 12788 <is_valid_xml/> | |
| 12789 </assert_contents> | |
| 12790 </output> | |
| 12791 </test> | |
| 12792 <test expect_num_outputs="2"> | |
| 12793 <conditional name="adv_opts_cond"> | |
| 12794 <param name="adv_opts_selector" value="advanced"/> | |
| 12795 <param name="remove_duplicate_psm" value="false"/> | |
| 12796 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12797 <param name="force" value="false"/> | |
| 12798 <param name="test" value="true"/> | |
| 12799 </conditional> | |
| 12800 <param name="in" value="IDFilter_15_input.idXML"/> | |
| 12801 <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12802 <param name="var_mods" value="false"/> | |
| 12803 <param name="remove_shared_peptides" value="false"/> | |
| 12804 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12805 <param name="remove_decoys" value="false"/> | |
| 12806 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12807 <section name="precursor"> | |
| 12808 <param name="rt" value=":"/> | |
| 12809 <param name="mz" value=":"/> | |
| 12810 <param name="length" value=":"/> | |
| 12811 <param name="charge" value=":"/> | |
| 12812 </section> | |
| 12813 <section name="score"> | |
| 12814 <param name="pep" value="0.0"/> | |
| 12815 <param name="prot" value="0.0"/> | |
| 12816 </section> | |
| 12817 <section name="whitelist"> | |
| 12818 <param name="protein_accessions" value=""/> | |
| 12819 <param name="ignore_modifications" value="false"/> | |
| 12820 <param name="modifications" value=""/> | |
| 12821 </section> | |
| 12822 <section name="blacklist"> | |
| 12823 <param name="protein_accessions" value=""/> | |
| 12824 <param name="ignore_modifications" value="false"/> | |
| 12825 <param name="modifications" value=""/> | |
| 12826 </section> | |
| 12827 <section name="in_silico_digestion"> | |
| 12828 <param name="fasta" value="IDFilter_15_input.fasta"/> | |
| 12829 <param name="enzyme" value="Trypsin/P"/> | |
| 12830 <param name="specificity" value="semi"/> | |
| 12831 <param name="missed_cleavages" value="1"/> | |
| 12832 <param name="methionine_cleavage" value="false"/> | |
| 12833 </section> | |
| 12834 <section name="missed_cleavages"> | |
| 12835 <param name="number_of_missed_cleavages" value=":"/> | |
| 12836 <param name="enzyme" value="Trypsin"/> | |
| 12837 </section> | |
| 12838 <section name="rt"> | |
| 12839 <param name="p_value" value="0.0"/> | |
| 12840 <param name="p_value_1st_dim" value="0.0"/> | |
| 12841 </section> | |
| 12842 <section name="mz"> | |
| 12843 <param name="error" value="-1.0"/> | |
| 12844 <param name="unit" value="ppm"/> | |
| 12845 </section> | |
| 12846 <section name="best"> | |
| 12847 <param name="n_peptide_hits" value="0"/> | |
| 12848 <param name="n_protein_hits" value="0"/> | |
| 12849 <param name="strict" value="false"/> | |
| 12850 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12851 </section> | |
| 12852 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12853 <output name="ctd_out" ftype="xml"> | |
| 12854 <assert_contents> | |
| 12855 <is_valid_xml/> | |
| 12856 </assert_contents> | |
| 12857 </output> | |
| 12858 </test> | |
| 12859 <test expect_num_outputs="2"> | |
| 12860 <conditional name="adv_opts_cond"> | |
| 12861 <param name="adv_opts_selector" value="advanced"/> | |
| 12862 <param name="remove_duplicate_psm" value="false"/> | |
| 12863 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12864 <param name="force" value="false"/> | |
| 12865 <param name="test" value="true"/> | |
| 12866 </conditional> | |
| 12867 <param name="in" value="IDFilter_16_input.idXML"/> | |
| 12868 <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12869 <param name="var_mods" value="false"/> | |
| 12870 <param name="remove_shared_peptides" value="false"/> | |
| 12871 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12872 <param name="remove_decoys" value="false"/> | |
| 12873 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12874 <section name="precursor"> | |
| 12875 <param name="rt" value=":"/> | |
| 12876 <param name="mz" value=":"/> | |
| 12877 <param name="length" value=":"/> | |
| 12878 <param name="charge" value=":"/> | |
| 12879 </section> | |
| 12880 <section name="score"> | |
| 12881 <param name="pep" value="0.0"/> | |
| 12882 <param name="prot" value="0.0"/> | |
| 12883 </section> | |
| 12884 <section name="whitelist"> | |
| 12885 <param name="protein_accessions" value=""/> | |
| 12886 <param name="ignore_modifications" value="false"/> | |
| 12887 <param name="modifications" value=""/> | |
| 12888 </section> | |
| 12889 <section name="blacklist"> | |
| 12890 <param name="protein_accessions" value=""/> | |
| 12891 <param name="ignore_modifications" value="false"/> | |
| 12892 <param name="modifications" value=""/> | |
| 12893 </section> | |
| 12894 <section name="in_silico_digestion"> | |
| 12895 <param name="fasta" value="IDFilter_16_input.fasta"/> | |
| 12896 <param name="enzyme" value="Trypsin/P"/> | |
| 12897 <param name="specificity" value="full"/> | |
| 12898 <param name="missed_cleavages" value="1"/> | |
| 12899 <param name="methionine_cleavage" value="true"/> | |
| 12900 </section> | |
| 12901 <section name="missed_cleavages"> | |
| 12902 <param name="number_of_missed_cleavages" value=":"/> | |
| 12903 <param name="enzyme" value="Trypsin"/> | |
| 12904 </section> | |
| 12905 <section name="rt"> | |
| 12906 <param name="p_value" value="0.0"/> | |
| 12907 <param name="p_value_1st_dim" value="0.0"/> | |
| 12908 </section> | |
| 12909 <section name="mz"> | |
| 12910 <param name="error" value="-1.0"/> | |
| 12911 <param name="unit" value="ppm"/> | |
| 12912 </section> | |
| 12913 <section name="best"> | |
| 12914 <param name="n_peptide_hits" value="0"/> | |
| 12915 <param name="n_protein_hits" value="0"/> | |
| 12916 <param name="strict" value="false"/> | |
| 12917 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12918 </section> | |
| 12919 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12920 <output name="ctd_out" ftype="xml"> | |
| 12921 <assert_contents> | |
| 12922 <is_valid_xml/> | |
| 12923 </assert_contents> | |
| 12924 </output> | |
| 12925 </test> | |
| 12926 <test expect_num_outputs="2"> | |
| 12927 <conditional name="adv_opts_cond"> | |
| 12928 <param name="adv_opts_selector" value="advanced"/> | |
| 12929 <param name="remove_duplicate_psm" value="false"/> | |
| 12930 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12931 <param name="force" value="false"/> | |
| 12932 <param name="test" value="true"/> | |
| 12933 </conditional> | |
| 12934 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> | |
| 12935 <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 12936 <param name="var_mods" value="false"/> | |
| 12937 <param name="remove_shared_peptides" value="false"/> | |
| 12938 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 12939 <param name="remove_decoys" value="false"/> | |
| 12940 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 12941 <section name="precursor"> | |
| 12942 <param name="rt" value=":"/> | |
| 12943 <param name="mz" value=":"/> | |
| 12944 <param name="length" value=":"/> | |
| 12945 <param name="charge" value=":"/> | |
| 12946 </section> | |
| 12947 <section name="score"> | |
| 12948 <param name="pep" value="0.0"/> | |
| 12949 <param name="prot" value="0.0"/> | |
| 12950 </section> | |
| 12951 <section name="whitelist"> | |
| 12952 <param name="protein_accessions" value=""/> | |
| 12953 <param name="ignore_modifications" value="false"/> | |
| 12954 <param name="modifications" value=""/> | |
| 12955 </section> | |
| 12956 <section name="blacklist"> | |
| 12957 <param name="protein_accessions" value=""/> | |
| 12958 <param name="ignore_modifications" value="false"/> | |
| 12959 <param name="modifications" value=""/> | |
| 12960 </section> | |
| 12961 <section name="in_silico_digestion"> | |
| 12962 <param name="enzyme" value="Trypsin"/> | |
| 12963 <param name="specificity" value="full"/> | |
| 12964 <param name="missed_cleavages" value="-1"/> | |
| 12965 <param name="methionine_cleavage" value="false"/> | |
| 12966 </section> | |
| 12967 <section name="missed_cleavages"> | |
| 12968 <param name="number_of_missed_cleavages" value=":2"/> | |
| 12969 <param name="enzyme" value="Lys-N"/> | |
| 12970 </section> | |
| 12971 <section name="rt"> | |
| 12972 <param name="p_value" value="0.0"/> | |
| 12973 <param name="p_value_1st_dim" value="0.0"/> | |
| 12974 </section> | |
| 12975 <section name="mz"> | |
| 12976 <param name="error" value="-1.0"/> | |
| 12977 <param name="unit" value="ppm"/> | |
| 12978 </section> | |
| 12979 <section name="best"> | |
| 12980 <param name="n_peptide_hits" value="0"/> | |
| 12981 <param name="n_protein_hits" value="0"/> | |
| 12982 <param name="strict" value="false"/> | |
| 12983 <param name="n_to_m_peptide_hits" value=":"/> | |
| 12984 </section> | |
| 12985 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 12986 <output name="ctd_out" ftype="xml"> | |
| 12987 <assert_contents> | |
| 12988 <is_valid_xml/> | |
| 12989 </assert_contents> | |
| 12990 </output> | |
| 12991 </test> | |
| 12992 <test expect_num_outputs="2"> | |
| 12993 <conditional name="adv_opts_cond"> | |
| 12994 <param name="adv_opts_selector" value="advanced"/> | |
| 12995 <param name="remove_duplicate_psm" value="false"/> | |
| 12996 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 12997 <param name="force" value="false"/> | |
| 12998 <param name="test" value="true"/> | |
| 12999 </conditional> | |
| 13000 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> | |
| 13001 <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13002 <param name="var_mods" value="false"/> | |
| 13003 <param name="remove_shared_peptides" value="false"/> | |
| 13004 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 13005 <param name="remove_decoys" value="false"/> | |
| 13006 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 13007 <section name="precursor"> | |
| 13008 <param name="rt" value=":"/> | |
| 13009 <param name="mz" value=":"/> | |
| 13010 <param name="length" value=":"/> | |
| 13011 <param name="charge" value=":"/> | |
| 13012 </section> | |
| 13013 <section name="score"> | |
| 13014 <param name="pep" value="0.0"/> | |
| 13015 <param name="prot" value="0.0"/> | |
| 13016 </section> | |
| 13017 <section name="whitelist"> | |
| 13018 <param name="protein_accessions" value=""/> | |
| 13019 <param name="ignore_modifications" value="false"/> | |
| 13020 <param name="modifications" value=""/> | |
| 13021 </section> | |
| 13022 <section name="blacklist"> | |
| 13023 <param name="protein_accessions" value=""/> | |
| 13024 <param name="ignore_modifications" value="false"/> | |
| 13025 <param name="modifications" value=""/> | |
| 13026 </section> | |
| 13027 <section name="in_silico_digestion"> | |
| 13028 <param name="enzyme" value="Trypsin"/> | |
| 13029 <param name="specificity" value="full"/> | |
| 13030 <param name="missed_cleavages" value="-1"/> | |
| 13031 <param name="methionine_cleavage" value="false"/> | |
| 13032 </section> | |
| 13033 <section name="missed_cleavages"> | |
| 13034 <param name="number_of_missed_cleavages" value="2:"/> | |
| 13035 <param name="enzyme" value="Lys-N"/> | |
| 13036 </section> | |
| 13037 <section name="rt"> | |
| 13038 <param name="p_value" value="0.0"/> | |
| 13039 <param name="p_value_1st_dim" value="0.0"/> | |
| 13040 </section> | |
| 13041 <section name="mz"> | |
| 13042 <param name="error" value="-1.0"/> | |
| 13043 <param name="unit" value="ppm"/> | |
| 13044 </section> | |
| 13045 <section name="best"> | |
| 13046 <param name="n_peptide_hits" value="0"/> | |
| 13047 <param name="n_protein_hits" value="0"/> | |
| 13048 <param name="strict" value="false"/> | |
| 13049 <param name="n_to_m_peptide_hits" value=":"/> | |
| 13050 </section> | |
| 13051 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13052 <output name="ctd_out" ftype="xml"> | |
| 13053 <assert_contents> | |
| 13054 <is_valid_xml/> | |
| 13055 </assert_contents> | |
| 13056 </output> | |
| 13057 </test> | |
| 13058 <test expect_num_outputs="2"> | |
| 13059 <conditional name="adv_opts_cond"> | |
| 13060 <param name="adv_opts_selector" value="advanced"/> | |
| 13061 <param name="remove_duplicate_psm" value="false"/> | |
| 13062 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 13063 <param name="force" value="false"/> | |
| 13064 <param name="test" value="true"/> | |
| 13065 </conditional> | |
| 13066 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> | |
| 13067 <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13068 <param name="var_mods" value="false"/> | |
| 13069 <param name="remove_shared_peptides" value="false"/> | |
| 13070 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 13071 <param name="remove_decoys" value="false"/> | |
| 13072 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 13073 <section name="precursor"> | |
| 13074 <param name="rt" value=":"/> | |
| 13075 <param name="mz" value=":"/> | |
| 13076 <param name="length" value=":"/> | |
| 13077 <param name="charge" value=":"/> | |
| 13078 </section> | |
| 13079 <section name="score"> | |
| 13080 <param name="pep" value="0.0"/> | |
| 13081 <param name="prot" value="0.0"/> | |
| 13082 </section> | |
| 13083 <section name="whitelist"> | |
| 13084 <param name="protein_accessions" value=""/> | |
| 13085 <param name="ignore_modifications" value="false"/> | |
| 13086 <param name="modifications" value=""/> | |
| 13087 </section> | |
| 13088 <section name="blacklist"> | |
| 13089 <param name="protein_accessions" value=""/> | |
| 13090 <param name="ignore_modifications" value="false"/> | |
| 13091 <param name="modifications" value=""/> | |
| 13092 </section> | |
| 13093 <section name="in_silico_digestion"> | |
| 13094 <param name="enzyme" value="Trypsin"/> | |
| 13095 <param name="specificity" value="full"/> | |
| 13096 <param name="missed_cleavages" value="-1"/> | |
| 13097 <param name="methionine_cleavage" value="false"/> | |
| 13098 </section> | |
| 13099 <section name="missed_cleavages"> | |
| 13100 <param name="number_of_missed_cleavages" value="1:3"/> | |
| 13101 <param name="enzyme" value="Lys-N"/> | |
| 13102 </section> | |
| 13103 <section name="rt"> | |
| 13104 <param name="p_value" value="0.0"/> | |
| 13105 <param name="p_value_1st_dim" value="0.0"/> | |
| 13106 </section> | |
| 13107 <section name="mz"> | |
| 13108 <param name="error" value="-1.0"/> | |
| 13109 <param name="unit" value="ppm"/> | |
| 13110 </section> | |
| 13111 <section name="best"> | |
| 13112 <param name="n_peptide_hits" value="0"/> | |
| 13113 <param name="n_protein_hits" value="0"/> | |
| 13114 <param name="strict" value="false"/> | |
| 13115 <param name="n_to_m_peptide_hits" value=":"/> | |
| 13116 </section> | |
| 13117 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13118 <output name="ctd_out" ftype="xml"> | |
| 13119 <assert_contents> | |
| 13120 <is_valid_xml/> | |
| 13121 </assert_contents> | |
| 13122 </output> | |
| 13123 </test> | |
| 13124 <test expect_num_outputs="2"> | |
| 13125 <conditional name="adv_opts_cond"> | |
| 13126 <param name="adv_opts_selector" value="advanced"/> | |
| 13127 <param name="remove_duplicate_psm" value="false"/> | |
| 13128 <param name="remove_peptide_hits_by_metavalue" value=""/> | |
| 13129 <param name="force" value="false"/> | |
| 13130 <param name="test" value="true"/> | |
| 13131 </conditional> | |
| 13132 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> | |
| 13133 <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13134 <param name="var_mods" value="false"/> | |
| 13135 <param name="remove_shared_peptides" value="false"/> | |
| 13136 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 13137 <param name="remove_decoys" value="false"/> | |
| 13138 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 13139 <section name="precursor"> | |
| 13140 <param name="rt" value=":"/> | |
| 13141 <param name="mz" value=":"/> | |
| 13142 <param name="length" value=":"/> | |
| 13143 <param name="charge" value=":"/> | |
| 13144 </section> | |
| 13145 <section name="score"> | |
| 13146 <param name="pep" value="0.0"/> | |
| 13147 <param name="prot" value="0.0"/> | |
| 13148 </section> | |
| 13149 <section name="whitelist"> | |
| 13150 <param name="protein_accessions" value=""/> | |
| 13151 <param name="ignore_modifications" value="false"/> | |
| 13152 <param name="modifications" value=""/> | |
| 13153 </section> | |
| 13154 <section name="blacklist"> | |
| 13155 <param name="protein_accessions" value=""/> | |
| 13156 <param name="ignore_modifications" value="false"/> | |
| 13157 <param name="modifications" value=""/> | |
| 13158 </section> | |
| 13159 <section name="in_silico_digestion"> | |
| 13160 <param name="enzyme" value="Trypsin"/> | |
| 13161 <param name="specificity" value="full"/> | |
| 13162 <param name="missed_cleavages" value="-1"/> | |
| 13163 <param name="methionine_cleavage" value="false"/> | |
| 13164 </section> | |
| 13165 <section name="missed_cleavages"> | |
| 13166 <param name="number_of_missed_cleavages" value="1:0"/> | |
| 13167 <param name="enzyme" value="Trypsin"/> | |
| 13168 </section> | |
| 13169 <section name="rt"> | |
| 13170 <param name="p_value" value="0.0"/> | |
| 13171 <param name="p_value_1st_dim" value="0.0"/> | |
| 13172 </section> | |
| 13173 <section name="mz"> | |
| 13174 <param name="error" value="-1.0"/> | |
| 13175 <param name="unit" value="ppm"/> | |
| 13176 </section> | |
| 13177 <section name="best"> | |
| 13178 <param name="n_peptide_hits" value="0"/> | |
| 13179 <param name="n_protein_hits" value="0"/> | |
| 13180 <param name="strict" value="false"/> | |
| 13181 <param name="n_to_m_peptide_hits" value=":"/> | |
| 13182 </section> | |
| 13183 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13184 <output name="ctd_out" ftype="xml"> | |
| 13185 <assert_contents> | |
| 13186 <is_valid_xml/> | |
| 13187 </assert_contents> | |
| 13188 </output> | |
| 13189 </test> | |
| 13190 <test expect_num_outputs="2"> | |
| 13191 <conditional name="adv_opts_cond"> | |
| 13192 <param name="adv_opts_selector" value="advanced"/> | |
| 13193 <param name="remove_duplicate_psm" value="false"/> | |
| 13194 <param name="remove_peptide_hits_by_metavalue" value=""calcMZ" "gt" "750.0""/> | |
| 13195 <param name="force" value="false"/> | |
| 13196 <param name="test" value="true"/> | |
| 13197 </conditional> | |
| 13198 <param name="in" value="IDFilter_16_input.idXML"/> | |
| 13199 <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13200 <param name="var_mods" value="false"/> | |
| 13201 <param name="remove_shared_peptides" value="false"/> | |
| 13202 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 13203 <param name="remove_decoys" value="false"/> | |
| 13204 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 13205 <section name="precursor"> | |
| 13206 <param name="rt" value=":"/> | |
| 13207 <param name="mz" value=":"/> | |
| 13208 <param name="length" value=":"/> | |
| 13209 <param name="charge" value=":"/> | |
| 13210 </section> | |
| 13211 <section name="score"> | |
| 13212 <param name="pep" value="0.0"/> | |
| 13213 <param name="prot" value="0.0"/> | |
| 13214 </section> | |
| 13215 <section name="whitelist"> | |
| 13216 <param name="protein_accessions" value=""/> | |
| 13217 <param name="ignore_modifications" value="false"/> | |
| 13218 <param name="modifications" value=""/> | |
| 13219 </section> | |
| 13220 <section name="blacklist"> | |
| 13221 <param name="protein_accessions" value=""/> | |
| 13222 <param name="ignore_modifications" value="false"/> | |
| 13223 <param name="modifications" value=""/> | |
| 13224 </section> | |
| 13225 <section name="in_silico_digestion"> | |
| 13226 <param name="enzyme" value="Trypsin"/> | |
| 13227 <param name="specificity" value="full"/> | |
| 13228 <param name="missed_cleavages" value="-1"/> | |
| 13229 <param name="methionine_cleavage" value="false"/> | |
| 13230 </section> | |
| 13231 <section name="missed_cleavages"> | |
| 13232 <param name="number_of_missed_cleavages" value=":"/> | |
| 13233 <param name="enzyme" value="Trypsin"/> | |
| 13234 </section> | |
| 13235 <section name="rt"> | |
| 13236 <param name="p_value" value="0.0"/> | |
| 13237 <param name="p_value_1st_dim" value="0.0"/> | |
| 13238 </section> | |
| 13239 <section name="mz"> | |
| 13240 <param name="error" value="-1.0"/> | |
| 13241 <param name="unit" value="ppm"/> | |
| 13242 </section> | |
| 13243 <section name="best"> | |
| 13244 <param name="n_peptide_hits" value="0"/> | |
| 13245 <param name="n_protein_hits" value="0"/> | |
| 13246 <param name="strict" value="false"/> | |
| 13247 <param name="n_to_m_peptide_hits" value=":"/> | |
| 13248 </section> | |
| 13249 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13250 <output name="ctd_out" ftype="xml"> | |
| 13251 <assert_contents> | |
| 13252 <is_valid_xml/> | |
| 13253 </assert_contents> | |
| 13254 </output> | |
| 13255 </test> | |
| 13256 <test expect_num_outputs="2"> | |
| 13257 <conditional name="adv_opts_cond"> | |
| 13258 <param name="adv_opts_selector" value="advanced"/> | |
| 13259 <param name="remove_duplicate_psm" value="false"/> | |
| 13260 <param name="remove_peptide_hits_by_metavalue" value=""end" "ne" "23""/> | |
| 13261 <param name="force" value="false"/> | |
| 13262 <param name="test" value="true"/> | |
| 13263 </conditional> | |
| 13264 <param name="in" value="IDFilter_16_input.idXML"/> | |
| 13265 <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13266 <param name="var_mods" value="false"/> | |
| 13267 <param name="remove_shared_peptides" value="false"/> | |
| 13268 <param name="keep_unreferenced_protein_hits" value="false"/> | |
| 13269 <param name="remove_decoys" value="false"/> | |
| 13270 <param name="delete_unreferenced_peptide_hits" value="false"/> | |
| 13271 <section name="precursor"> | |
| 13272 <param name="rt" value=":"/> | |
| 13273 <param name="mz" value=":"/> | |
| 13274 <param name="length" value=":"/> | |
| 13275 <param name="charge" value=":"/> | |
| 13276 </section> | |
| 13277 <section name="score"> | |
| 13278 <param name="pep" value="0.0"/> | |
| 13279 <param name="prot" value="0.0"/> | |
| 13280 </section> | |
| 13281 <section name="whitelist"> | |
| 13282 <param name="protein_accessions" value=""/> | |
| 13283 <param name="ignore_modifications" value="false"/> | |
| 13284 <param name="modifications" value=""/> | |
| 13285 </section> | |
| 13286 <section name="blacklist"> | |
| 13287 <param name="protein_accessions" value=""/> | |
| 13288 <param name="ignore_modifications" value="false"/> | |
| 13289 <param name="modifications" value=""/> | |
| 13290 </section> | |
| 13291 <section name="in_silico_digestion"> | |
| 13292 <param name="enzyme" value="Trypsin"/> | |
| 13293 <param name="specificity" value="full"/> | |
| 13294 <param name="missed_cleavages" value="-1"/> | |
| 13295 <param name="methionine_cleavage" value="false"/> | |
| 13296 </section> | |
| 13297 <section name="missed_cleavages"> | |
| 13298 <param name="number_of_missed_cleavages" value=":"/> | |
| 13299 <param name="enzyme" value="Trypsin"/> | |
| 13300 </section> | |
| 13301 <section name="rt"> | |
| 13302 <param name="p_value" value="0.0"/> | |
| 13303 <param name="p_value_1st_dim" value="0.0"/> | |
| 13304 </section> | |
| 13305 <section name="mz"> | |
| 13306 <param name="error" value="-1.0"/> | |
| 13307 <param name="unit" value="ppm"/> | |
| 13308 </section> | |
| 13309 <section name="best"> | |
| 13310 <param name="n_peptide_hits" value="0"/> | |
| 13311 <param name="n_protein_hits" value="0"/> | |
| 13312 <param name="strict" value="false"/> | |
| 13313 <param name="n_to_m_peptide_hits" value=":"/> | |
| 13314 </section> | |
| 13315 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13316 <output name="ctd_out" ftype="xml"> | |
| 13317 <assert_contents> | |
| 13318 <is_valid_xml/> | |
| 13319 </assert_contents> | |
| 13320 </output> | |
| 13321 </test> | |
| 13322 </xml> | |
| 13323 <xml name="autotest_IDMapper"> | |
| 13324 <test expect_num_outputs="2"> | |
| 13325 <conditional name="adv_opts_cond"> | |
| 13326 <param name="adv_opts_selector" value="advanced"/> | |
| 13327 <param name="ignore_charge" value="true"/> | |
| 13328 <param name="force" value="false"/> | |
| 13329 <param name="test" value="true"/> | |
| 13330 </conditional> | |
| 13331 <param name="id" value="IDMapper_1_input.idXML"/> | |
| 13332 <param name="in" value="IDMapper_1_input.featureXML"/> | |
| 13333 <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 13334 <param name="rt_tolerance" value="5.0"/> | |
| 13335 <param name="mz_tolerance" value="1.0"/> | |
| 13336 <param name="mz_measure" value="Da"/> | |
| 13337 <param name="mz_reference" value="precursor"/> | |
| 13338 <section name="feature"> | |
| 13339 <param name="use_centroid_rt" value="false"/> | |
| 13340 <param name="use_centroid_mz" value="false"/> | |
| 13341 </section> | |
| 13342 <section name="consensus"> | |
| 13343 <param name="use_subelements" value="false"/> | |
| 13344 <param name="annotate_ids_with_subelements" value="false"/> | |
| 13345 </section> | |
| 13346 <section name="spectra"/> | |
| 13347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13348 <output name="ctd_out" ftype="xml"> | |
| 13349 <assert_contents> | |
| 13350 <is_valid_xml/> | |
| 13351 </assert_contents> | |
| 13352 </output> | |
| 13353 </test> | |
| 13354 <test expect_num_outputs="2"> | |
| 13355 <conditional name="adv_opts_cond"> | |
| 13356 <param name="adv_opts_selector" value="advanced"/> | |
| 13357 <param name="ignore_charge" value="false"/> | |
| 13358 <param name="force" value="false"/> | |
| 13359 <param name="test" value="true"/> | |
| 13360 </conditional> | |
| 13361 <param name="id" value="IDMapper_2_input.idXML"/> | |
| 13362 <param name="in" value="IDMapper_2_input.consensusXML"/> | |
| 13363 <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 13364 <param name="rt_tolerance" value="5.0"/> | |
| 13365 <param name="mz_tolerance" value="1.0"/> | |
| 13366 <param name="mz_measure" value="Da"/> | |
| 13367 <param name="mz_reference" value="precursor"/> | |
| 13368 <section name="feature"> | |
| 13369 <param name="use_centroid_rt" value="false"/> | |
| 13370 <param name="use_centroid_mz" value="true"/> | |
| 13371 </section> | |
| 13372 <section name="consensus"> | |
| 13373 <param name="use_subelements" value="false"/> | |
| 13374 <param name="annotate_ids_with_subelements" value="false"/> | |
| 13375 </section> | |
| 13376 <section name="spectra"/> | |
| 13377 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13378 <output name="ctd_out" ftype="xml"> | |
| 13379 <assert_contents> | |
| 13380 <is_valid_xml/> | |
| 13381 </assert_contents> | |
| 13382 </output> | |
| 13383 </test> | |
| 13384 <test expect_num_outputs="2"> | |
| 13385 <conditional name="adv_opts_cond"> | |
| 13386 <param name="adv_opts_selector" value="advanced"/> | |
| 13387 <param name="ignore_charge" value="true"/> | |
| 13388 <param name="force" value="false"/> | |
| 13389 <param name="test" value="true"/> | |
| 13390 </conditional> | |
| 13391 <param name="id" value="IDMapper_3_input.idXML"/> | |
| 13392 <param name="in" value="IDMapper_3_input.featureXML"/> | |
| 13393 <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 13394 <param name="rt_tolerance" value="4.0"/> | |
| 13395 <param name="mz_tolerance" value="3.0"/> | |
| 13396 <param name="mz_measure" value="ppm"/> | |
| 13397 <param name="mz_reference" value="precursor"/> | |
| 13398 <section name="feature"> | |
| 13399 <param name="use_centroid_rt" value="false"/> | |
| 13400 <param name="use_centroid_mz" value="true"/> | |
| 13401 </section> | |
| 13402 <section name="consensus"> | |
| 13403 <param name="use_subelements" value="false"/> | |
| 13404 <param name="annotate_ids_with_subelements" value="false"/> | |
| 13405 </section> | |
| 13406 <section name="spectra"/> | |
| 13407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13408 <output name="ctd_out" ftype="xml"> | |
| 13409 <assert_contents> | |
| 13410 <is_valid_xml/> | |
| 13411 </assert_contents> | |
| 13412 </output> | |
| 13413 </test> | |
| 13414 <test expect_num_outputs="2"> | |
| 13415 <conditional name="adv_opts_cond"> | |
| 13416 <param name="adv_opts_selector" value="advanced"/> | |
| 13417 <param name="ignore_charge" value="false"/> | |
| 13418 <param name="force" value="false"/> | |
| 13419 <param name="test" value="true"/> | |
| 13420 </conditional> | |
| 13421 <param name="id" value="IDMapper_4_input.idXML"/> | |
| 13422 <param name="in" value="IDMapper_4_input.featureXML"/> | |
| 13423 <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 13424 <param name="rt_tolerance" value="10.0"/> | |
| 13425 <param name="mz_tolerance" value="20.0"/> | |
| 13426 <param name="mz_measure" value="ppm"/> | |
| 13427 <param name="mz_reference" value="peptide"/> | |
| 13428 <section name="feature"> | |
| 13429 <param name="use_centroid_rt" value="false"/> | |
| 13430 <param name="use_centroid_mz" value="true"/> | |
| 13431 </section> | |
| 13432 <section name="consensus"> | |
| 13433 <param name="use_subelements" value="false"/> | |
| 13434 <param name="annotate_ids_with_subelements" value="false"/> | |
| 13435 </section> | |
| 13436 <section name="spectra"> | |
| 13437 <param name="_in" value="IDMapper_4_input.mzML"/> | |
| 13438 </section> | |
| 13439 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13440 <output name="ctd_out" ftype="xml"> | |
| 13441 <assert_contents> | |
| 13442 <is_valid_xml/> | |
| 13443 </assert_contents> | |
| 13444 </output> | |
| 13445 </test> | |
| 13446 <test expect_num_outputs="2"> | |
| 13447 <conditional name="adv_opts_cond"> | |
| 13448 <param name="adv_opts_selector" value="advanced"/> | |
| 13449 <param name="ignore_charge" value="false"/> | |
| 13450 <param name="force" value="false"/> | |
| 13451 <param name="test" value="true"/> | |
| 13452 </conditional> | |
| 13453 <param name="id" value="IDMapper_5_input.idXML"/> | |
| 13454 <param name="in" value="IDMapper_5_input.featureXML"/> | |
| 13455 <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 13456 <param name="rt_tolerance" value="20.0"/> | |
| 13457 <param name="mz_tolerance" value="10.0"/> | |
| 13458 <param name="mz_measure" value="ppm"/> | |
| 13459 <param name="mz_reference" value="peptide"/> | |
| 13460 <section name="feature"> | |
| 13461 <param name="use_centroid_rt" value="false"/> | |
| 13462 <param name="use_centroid_mz" value="false"/> | |
| 13463 </section> | |
| 13464 <section name="consensus"> | |
| 13465 <param name="use_subelements" value="false"/> | |
| 13466 <param name="annotate_ids_with_subelements" value="false"/> | |
| 13467 </section> | |
| 13468 <section name="spectra"> | |
| 13469 <param name="_in" value="IDMapper_5_input.mzML"/> | |
| 13470 </section> | |
| 13471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13472 <output name="ctd_out" ftype="xml"> | |
| 13473 <assert_contents> | |
| 13474 <is_valid_xml/> | |
| 13475 </assert_contents> | |
| 13476 </output> | |
| 13477 </test> | |
| 13478 </xml> | |
| 13479 <xml name="autotest_IDMassAccuracy"> | |
| 13480 <test expect_num_outputs="5"> | |
| 13481 <conditional name="adv_opts_cond"> | |
| 13482 <param name="adv_opts_selector" value="advanced"/> | |
| 13483 <param name="number_of_bins" value="10"/> | |
| 13484 <param name="force" value="false"/> | |
| 13485 <param name="test" value="true"/> | |
| 13486 </conditional> | |
| 13487 <param name="in" value="spectra.mzML"/> | |
| 13488 <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/> | |
| 13489 <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 13490 <param name="precursor_error_ppm" value="false"/> | |
| 13491 <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 13492 <param name="fragment_error_ppm" value="false"/> | |
| 13493 <param name="fragment_mass_tolerance" value="0.5"/> | |
| 13494 <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 13495 <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 13496 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/> | |
| 13497 <output name="ctd_out" ftype="xml"> | |
| 13498 <assert_contents> | |
| 13499 <is_valid_xml/> | |
| 13500 </assert_contents> | |
| 13501 </output> | |
| 13502 </test> | |
| 13503 </xml> | |
| 13504 <xml name="autotest_IDMerger"> | |
| 13505 <test expect_num_outputs="2"> | |
| 13506 <conditional name="adv_opts_cond"> | |
| 13507 <param name="adv_opts_selector" value="advanced"/> | |
| 13508 <param name="force" value="false"/> | |
| 13509 <param name="test" value="true"/> | |
| 13510 </conditional> | |
| 13511 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/> | |
| 13512 <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13513 <param name="annotate_file_origin" value="true"/> | |
| 13514 <param name="pepxml_protxml" value="false"/> | |
| 13515 <param name="merge_proteins_add_PSMs" value="false"/> | |
| 13516 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13517 <output name="ctd_out" ftype="xml"> | |
| 13518 <assert_contents> | |
| 13519 <is_valid_xml/> | |
| 13520 </assert_contents> | |
| 13521 </output> | |
| 13522 </test> | |
| 13523 <test expect_num_outputs="2"> | |
| 13524 <conditional name="adv_opts_cond"> | |
| 13525 <param name="adv_opts_selector" value="advanced"/> | |
| 13526 <param name="force" value="false"/> | |
| 13527 <param name="test" value="true"/> | |
| 13528 </conditional> | |
| 13529 <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/> | |
| 13530 <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13531 <param name="annotate_file_origin" value="false"/> | |
| 13532 <param name="pepxml_protxml" value="true"/> | |
| 13533 <param name="merge_proteins_add_PSMs" value="false"/> | |
| 13534 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13535 <output name="ctd_out" ftype="xml"> | |
| 13536 <assert_contents> | |
| 13537 <is_valid_xml/> | |
| 13538 </assert_contents> | |
| 13539 </output> | |
| 13540 </test> | |
| 13541 <test expect_num_outputs="2"> | |
| 13542 <conditional name="adv_opts_cond"> | |
| 13543 <param name="adv_opts_selector" value="advanced"/> | |
| 13544 <param name="force" value="false"/> | |
| 13545 <param name="test" value="true"/> | |
| 13546 </conditional> | |
| 13547 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/> | |
| 13548 <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13549 <param name="annotate_file_origin" value="false"/> | |
| 13550 <param name="pepxml_protxml" value="false"/> | |
| 13551 <param name="merge_proteins_add_PSMs" value="false"/> | |
| 13552 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13553 <output name="ctd_out" ftype="xml"> | |
| 13554 <assert_contents> | |
| 13555 <is_valid_xml/> | |
| 13556 </assert_contents> | |
| 13557 </output> | |
| 13558 </test> | |
| 13559 <test expect_num_outputs="2"> | |
| 13560 <conditional name="adv_opts_cond"> | |
| 13561 <param name="adv_opts_selector" value="advanced"/> | |
| 13562 <param name="force" value="false"/> | |
| 13563 <param name="test" value="true"/> | |
| 13564 </conditional> | |
| 13565 <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/> | |
| 13566 <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13567 <param name="annotate_file_origin" value="false"/> | |
| 13568 <param name="pepxml_protxml" value="false"/> | |
| 13569 <param name="merge_proteins_add_PSMs" value="false"/> | |
| 13570 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13571 <output name="ctd_out" ftype="xml"> | |
| 13572 <assert_contents> | |
| 13573 <is_valid_xml/> | |
| 13574 </assert_contents> | |
| 13575 </output> | |
| 13576 </test> | |
| 13577 <test expect_num_outputs="2"> | |
| 13578 <conditional name="adv_opts_cond"> | |
| 13579 <param name="adv_opts_selector" value="advanced"/> | |
| 13580 <param name="force" value="false"/> | |
| 13581 <param name="test" value="true"/> | |
| 13582 </conditional> | |
| 13583 <param name="in" value="IDMerger_2_input1.idXML"/> | |
| 13584 <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13585 <param name="add_to" value="IDMerger_5_input1.idXML"/> | |
| 13586 <param name="annotate_file_origin" value="false"/> | |
| 13587 <param name="pepxml_protxml" value="false"/> | |
| 13588 <param name="merge_proteins_add_PSMs" value="false"/> | |
| 13589 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13590 <output name="ctd_out" ftype="xml"> | |
| 13591 <assert_contents> | |
| 13592 <is_valid_xml/> | |
| 13593 </assert_contents> | |
| 13594 </output> | |
| 13595 </test> | |
| 13596 <test expect_num_outputs="2"> | |
| 13597 <conditional name="adv_opts_cond"> | |
| 13598 <param name="adv_opts_selector" value="advanced"/> | |
| 13599 <param name="force" value="false"/> | |
| 13600 <param name="test" value="true"/> | |
| 13601 </conditional> | |
| 13602 <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/> | |
| 13603 <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13604 <param name="annotate_file_origin" value="true"/> | |
| 13605 <param name="pepxml_protxml" value="false"/> | |
| 13606 <param name="merge_proteins_add_PSMs" value="false"/> | |
| 13607 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13608 <output name="ctd_out" ftype="xml"> | |
| 13609 <assert_contents> | |
| 13610 <is_valid_xml/> | |
| 13611 </assert_contents> | |
| 13612 </output> | |
| 13613 </test> | |
| 13614 </xml> | |
| 13615 <xml name="autotest_IDPosteriorErrorProbability"> | |
| 13616 <test expect_num_outputs="2"> | |
| 13617 <conditional name="adv_opts_cond"> | |
| 13618 <param name="adv_opts_selector" value="advanced"/> | |
| 13619 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13620 <param name="force" value="false"/> | |
| 13621 <param name="test" value="true"/> | |
| 13622 </conditional> | |
| 13623 <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/> | |
| 13624 <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13625 <param name="split_charge" value="false"/> | |
| 13626 <param name="top_hits_only" value="false"/> | |
| 13627 <param name="ignore_bad_data" value="false"/> | |
| 13628 <param name="prob_correct" value="false"/> | |
| 13629 <section name="fit_algorithm"> | |
| 13630 <param name="number_of_bins" value="100"/> | |
| 13631 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13632 <param name="max_nr_iterations" value="1000"/> | |
| 13633 <param name="neg_log_delta" value="6"/> | |
| 13634 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13635 </section> | |
| 13636 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13637 <output name="ctd_out" ftype="xml"> | |
| 13638 <assert_contents> | |
| 13639 <is_valid_xml/> | |
| 13640 </assert_contents> | |
| 13641 </output> | |
| 13642 </test> | |
| 13643 <test expect_num_outputs="2"> | |
| 13644 <conditional name="adv_opts_cond"> | |
| 13645 <param name="adv_opts_selector" value="advanced"/> | |
| 13646 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13647 <param name="force" value="false"/> | |
| 13648 <param name="test" value="true"/> | |
| 13649 </conditional> | |
| 13650 <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/> | |
| 13651 <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13652 <param name="split_charge" value="false"/> | |
| 13653 <param name="top_hits_only" value="false"/> | |
| 13654 <param name="ignore_bad_data" value="false"/> | |
| 13655 <param name="prob_correct" value="false"/> | |
| 13656 <section name="fit_algorithm"> | |
| 13657 <param name="number_of_bins" value="100"/> | |
| 13658 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13659 <param name="max_nr_iterations" value="1000"/> | |
| 13660 <param name="neg_log_delta" value="6"/> | |
| 13661 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13662 </section> | |
| 13663 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13664 <output name="ctd_out" ftype="xml"> | |
| 13665 <assert_contents> | |
| 13666 <is_valid_xml/> | |
| 13667 </assert_contents> | |
| 13668 </output> | |
| 13669 </test> | |
| 13670 <test expect_num_outputs="2"> | |
| 13671 <conditional name="adv_opts_cond"> | |
| 13672 <param name="adv_opts_selector" value="advanced"/> | |
| 13673 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13674 <param name="force" value="false"/> | |
| 13675 <param name="test" value="true"/> | |
| 13676 </conditional> | |
| 13677 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> | |
| 13678 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13679 <param name="split_charge" value="false"/> | |
| 13680 <param name="top_hits_only" value="false"/> | |
| 13681 <param name="ignore_bad_data" value="false"/> | |
| 13682 <param name="prob_correct" value="false"/> | |
| 13683 <section name="fit_algorithm"> | |
| 13684 <param name="number_of_bins" value="100"/> | |
| 13685 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13686 <param name="max_nr_iterations" value="1000"/> | |
| 13687 <param name="neg_log_delta" value="6"/> | |
| 13688 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13689 </section> | |
| 13690 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13691 <output name="ctd_out" ftype="xml"> | |
| 13692 <assert_contents> | |
| 13693 <is_valid_xml/> | |
| 13694 </assert_contents> | |
| 13695 </output> | |
| 13696 </test> | |
| 13697 <test expect_num_outputs="2"> | |
| 13698 <conditional name="adv_opts_cond"> | |
| 13699 <param name="adv_opts_selector" value="advanced"/> | |
| 13700 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13701 <param name="force" value="false"/> | |
| 13702 <param name="test" value="true"/> | |
| 13703 </conditional> | |
| 13704 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/> | |
| 13705 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13706 <param name="split_charge" value="true"/> | |
| 13707 <param name="top_hits_only" value="false"/> | |
| 13708 <param name="ignore_bad_data" value="false"/> | |
| 13709 <param name="prob_correct" value="false"/> | |
| 13710 <section name="fit_algorithm"> | |
| 13711 <param name="number_of_bins" value="100"/> | |
| 13712 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13713 <param name="max_nr_iterations" value="1000"/> | |
| 13714 <param name="neg_log_delta" value="6"/> | |
| 13715 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13716 </section> | |
| 13717 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13718 <output name="ctd_out" ftype="xml"> | |
| 13719 <assert_contents> | |
| 13720 <is_valid_xml/> | |
| 13721 </assert_contents> | |
| 13722 </output> | |
| 13723 </test> | |
| 13724 <test expect_num_outputs="2"> | |
| 13725 <conditional name="adv_opts_cond"> | |
| 13726 <param name="adv_opts_selector" value="advanced"/> | |
| 13727 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13728 <param name="force" value="false"/> | |
| 13729 <param name="test" value="true"/> | |
| 13730 </conditional> | |
| 13731 <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/> | |
| 13732 <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13733 <param name="split_charge" value="true"/> | |
| 13734 <param name="top_hits_only" value="false"/> | |
| 13735 <param name="ignore_bad_data" value="false"/> | |
| 13736 <param name="prob_correct" value="false"/> | |
| 13737 <section name="fit_algorithm"> | |
| 13738 <param name="number_of_bins" value="100"/> | |
| 13739 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13740 <param name="max_nr_iterations" value="1000"/> | |
| 13741 <param name="neg_log_delta" value="6"/> | |
| 13742 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13743 </section> | |
| 13744 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13745 <output name="ctd_out" ftype="xml"> | |
| 13746 <assert_contents> | |
| 13747 <is_valid_xml/> | |
| 13748 </assert_contents> | |
| 13749 </output> | |
| 13750 </test> | |
| 13751 <test expect_num_outputs="2"> | |
| 13752 <conditional name="adv_opts_cond"> | |
| 13753 <param name="adv_opts_selector" value="advanced"/> | |
| 13754 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13755 <param name="force" value="false"/> | |
| 13756 <param name="test" value="true"/> | |
| 13757 </conditional> | |
| 13758 <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/> | |
| 13759 <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13760 <param name="split_charge" value="true"/> | |
| 13761 <param name="top_hits_only" value="false"/> | |
| 13762 <param name="ignore_bad_data" value="false"/> | |
| 13763 <param name="prob_correct" value="false"/> | |
| 13764 <section name="fit_algorithm"> | |
| 13765 <param name="number_of_bins" value="100"/> | |
| 13766 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13767 <param name="max_nr_iterations" value="1000"/> | |
| 13768 <param name="neg_log_delta" value="6"/> | |
| 13769 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13770 </section> | |
| 13771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13772 <output name="ctd_out" ftype="xml"> | |
| 13773 <assert_contents> | |
| 13774 <is_valid_xml/> | |
| 13775 </assert_contents> | |
| 13776 </output> | |
| 13777 </test> | |
| 13778 <test expect_num_outputs="2"> | |
| 13779 <conditional name="adv_opts_cond"> | |
| 13780 <param name="adv_opts_selector" value="advanced"/> | |
| 13781 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13782 <param name="force" value="false"/> | |
| 13783 <param name="test" value="true"/> | |
| 13784 </conditional> | |
| 13785 <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/> | |
| 13786 <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13787 <param name="split_charge" value="false"/> | |
| 13788 <param name="top_hits_only" value="false"/> | |
| 13789 <param name="ignore_bad_data" value="true"/> | |
| 13790 <param name="prob_correct" value="false"/> | |
| 13791 <section name="fit_algorithm"> | |
| 13792 <param name="number_of_bins" value="100"/> | |
| 13793 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13794 <param name="max_nr_iterations" value="1000"/> | |
| 13795 <param name="neg_log_delta" value="6"/> | |
| 13796 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13797 </section> | |
| 13798 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13799 <output name="ctd_out" ftype="xml"> | |
| 13800 <assert_contents> | |
| 13801 <is_valid_xml/> | |
| 13802 </assert_contents> | |
| 13803 </output> | |
| 13804 </test> | |
| 13805 <test expect_num_outputs="2"> | |
| 13806 <conditional name="adv_opts_cond"> | |
| 13807 <param name="adv_opts_selector" value="advanced"/> | |
| 13808 <param name="fdr_for_targets_smaller" value="0.05"/> | |
| 13809 <param name="force" value="false"/> | |
| 13810 <param name="test" value="true"/> | |
| 13811 </conditional> | |
| 13812 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> | |
| 13813 <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13814 <param name="split_charge" value="false"/> | |
| 13815 <param name="top_hits_only" value="false"/> | |
| 13816 <param name="ignore_bad_data" value="false"/> | |
| 13817 <param name="prob_correct" value="true"/> | |
| 13818 <section name="fit_algorithm"> | |
| 13819 <param name="number_of_bins" value="100"/> | |
| 13820 <param name="incorrectly_assigned" value="Gumbel"/> | |
| 13821 <param name="max_nr_iterations" value="1000"/> | |
| 13822 <param name="neg_log_delta" value="6"/> | |
| 13823 <param name="outlier_handling" value="ignore_iqr_outliers"/> | |
| 13824 </section> | |
| 13825 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13826 <output name="ctd_out" ftype="xml"> | |
| 13827 <assert_contents> | |
| 13828 <is_valid_xml/> | |
| 13829 </assert_contents> | |
| 13830 </output> | |
| 13831 </test> | |
| 13832 </xml> | |
| 13833 <xml name="autotest_IDRipper"/> | |
| 13834 <xml name="autotest_IDRTCalibration"> | |
| 13835 <test expect_num_outputs="2"> | |
| 13836 <conditional name="adv_opts_cond"> | |
| 13837 <param name="adv_opts_selector" value="advanced"/> | |
| 13838 <param name="force" value="false"/> | |
| 13839 <param name="test" value="true"/> | |
| 13840 </conditional> | |
| 13841 <param name="in" value="IDRTCalibration_1_input.idXML"/> | |
| 13842 <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13843 <param name="calibrant_1_reference" value="0.1"/> | |
| 13844 <param name="calibrant_2_reference" value="0.9"/> | |
| 13845 <param name="calibrant_1_input" value="10.0"/> | |
| 13846 <param name="calibrant_2_input" value="90.0"/> | |
| 13847 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13848 <output name="ctd_out" ftype="xml"> | |
| 13849 <assert_contents> | |
| 13850 <is_valid_xml/> | |
| 13851 </assert_contents> | |
| 13852 </output> | |
| 13853 </test> | |
| 13854 <test expect_num_outputs="2"> | |
| 13855 <conditional name="adv_opts_cond"> | |
| 13856 <param name="adv_opts_selector" value="advanced"/> | |
| 13857 <param name="force" value="false"/> | |
| 13858 <param name="test" value="true"/> | |
| 13859 </conditional> | |
| 13860 <param name="in" value="degenerated_empty.idXML"/> | |
| 13861 <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13862 <param name="calibrant_1_reference" value="0.1"/> | |
| 13863 <param name="calibrant_2_reference" value="0.9"/> | |
| 13864 <param name="calibrant_1_input" value="10.0"/> | |
| 13865 <param name="calibrant_2_input" value="90.0"/> | |
| 13866 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13867 <output name="ctd_out" ftype="xml"> | |
| 13868 <assert_contents> | |
| 13869 <is_valid_xml/> | |
| 13870 </assert_contents> | |
| 13871 </output> | |
| 13872 </test> | |
| 13873 </xml> | |
| 13874 <xml name="autotest_IDScoreSwitcher"> | |
| 13875 <test expect_num_outputs="2"> | |
| 13876 <conditional name="adv_opts_cond"> | |
| 13877 <param name="adv_opts_selector" value="advanced"/> | |
| 13878 <param name="force" value="false"/> | |
| 13879 <param name="test" value="true"/> | |
| 13880 </conditional> | |
| 13881 <param name="in" value="IDFileConverter_12_output.idXML"/> | |
| 13882 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13883 <param name="new_score" value="Percolator_PEP"/> | |
| 13884 <param name="new_score_orientation" value="lower_better"/> | |
| 13885 <param name="new_score_type" value="Posterior Error Probability"/> | |
| 13886 <param name="old_score" value="Percolator_qvalue"/> | |
| 13887 <param name="proteins" value="false"/> | |
| 13888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13889 <output name="ctd_out" ftype="xml"> | |
| 13890 <assert_contents> | |
| 13891 <is_valid_xml/> | |
| 13892 </assert_contents> | |
| 13893 </output> | |
| 13894 </test> | |
| 13895 <test expect_num_outputs="2"> | |
| 13896 <conditional name="adv_opts_cond"> | |
| 13897 <param name="adv_opts_selector" value="advanced"/> | |
| 13898 <param name="force" value="false"/> | |
| 13899 <param name="test" value="true"/> | |
| 13900 </conditional> | |
| 13901 <param name="in" value="IDScoreSwitcher_2_input.idXML"/> | |
| 13902 <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13903 <param name="new_score" value="Posterior Probability_score"/> | |
| 13904 <param name="new_score_orientation" value="higher_better"/> | |
| 13905 <param name="new_score_type" value="Posterior Probability"/> | |
| 13906 <param name="old_score" value=""/> | |
| 13907 <param name="proteins" value="true"/> | |
| 13908 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 13909 <output name="ctd_out" ftype="xml"> | |
| 13910 <assert_contents> | |
| 13911 <is_valid_xml/> | |
| 13912 </assert_contents> | |
| 13913 </output> | |
| 13914 </test> | |
| 13915 </xml> | |
| 13916 <xml name="autotest_IDSplitter"> | |
| 13917 <test expect_num_outputs="3"> | |
| 13918 <conditional name="adv_opts_cond"> | |
| 13919 <param name="adv_opts_selector" value="advanced"/> | |
| 13920 <param name="force" value="false"/> | |
| 13921 <param name="test" value="true"/> | |
| 13922 </conditional> | |
| 13923 <param name="in" value="IDMapper_1_output.featureXML"/> | |
| 13924 <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 13925 <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 13926 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/> | |
| 13927 <output name="ctd_out" ftype="xml"> | |
| 13928 <assert_contents> | |
| 13929 <is_valid_xml/> | |
| 13930 </assert_contents> | |
| 13931 </output> | |
| 13932 </test> | |
| 13933 </xml> | |
| 13934 <xml name="autotest_InternalCalibration"> | |
| 13935 <test expect_num_outputs="4"> | |
| 13936 <conditional name="adv_opts_cond"> | |
| 13937 <param name="adv_opts_selector" value="advanced"/> | |
| 13938 <param name="force" value="false"/> | |
| 13939 <param name="test" value="true"/> | |
| 13940 </conditional> | |
| 13941 <param name="in" value="InternalCalibration_1_BSA1.mzML"/> | |
| 13942 <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 13943 <param name="ppm_match_tolerance" value="25.0"/> | |
| 13944 <param name="ms_level" value="1"/> | |
| 13945 <param name="RT_chunking" value="-1.0"/> | |
| 13946 <section name="cal"> | |
| 13947 <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/> | |
| 13948 <param name="lock_require_mono" value="false"/> | |
| 13949 <param name="lock_require_iso" value="false"/> | |
| 13950 <param name="model_type" value="linear"/> | |
| 13951 </section> | |
| 13952 <section name="RANSAC"> | |
| 13953 <param name="enabled" value="true"/> | |
| 13954 <param name="threshold" value="1.0"/> | |
| 13955 <param name="pc_inliers" value="30"/> | |
| 13956 <param name="iter" value="500"/> | |
| 13957 </section> | |
| 13958 <section name="goodness"> | |
| 13959 <param name="median" value="4.0"/> | |
| 13960 <param name="MAD" value="2.0"/> | |
| 13961 </section> | |
| 13962 <section name="quality_control"/> | |
| 13963 <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 13964 <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 13965 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> | |
| 13966 <output name="ctd_out" ftype="xml"> | |
| 13967 <assert_contents> | |
| 13968 <is_valid_xml/> | |
| 13969 </assert_contents> | |
| 13970 </output> | |
| 13971 </test> | |
| 13972 <test expect_num_outputs="4"> | |
| 13973 <conditional name="adv_opts_cond"> | |
| 13974 <param name="adv_opts_selector" value="advanced"/> | |
| 13975 <param name="force" value="false"/> | |
| 13976 <param name="test" value="true"/> | |
| 13977 </conditional> | |
| 13978 <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/> | |
| 13979 <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 13980 <param name="ppm_match_tolerance" value="25.0"/> | |
| 13981 <param name="ms_level" value="1 2 3"/> | |
| 13982 <param name="RT_chunking" value="60.0"/> | |
| 13983 <section name="cal"> | |
| 13984 <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/> | |
| 13985 <param name="lock_require_mono" value="true"/> | |
| 13986 <param name="lock_require_iso" value="false"/> | |
| 13987 <param name="model_type" value="linear"/> | |
| 13988 </section> | |
| 13989 <section name="RANSAC"> | |
| 13990 <param name="enabled" value="false"/> | |
| 13991 <param name="threshold" value="10.0"/> | |
| 13992 <param name="pc_inliers" value="30"/> | |
| 13993 <param name="iter" value="70"/> | |
| 13994 </section> | |
| 13995 <section name="goodness"> | |
| 13996 <param name="median" value="4.0"/> | |
| 13997 <param name="MAD" value="2.0"/> | |
| 13998 </section> | |
| 13999 <section name="quality_control"/> | |
| 14000 <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 14001 <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 14002 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> | |
| 14003 <output name="ctd_out" ftype="xml"> | |
| 14004 <assert_contents> | |
| 14005 <is_valid_xml/> | |
| 14006 </assert_contents> | |
| 14007 </output> | |
| 14008 </test> | |
| 14009 </xml> | |
| 14010 <xml name="autotest_IsobaricAnalyzer"> | |
| 14011 <test expect_num_outputs="2"> | |
| 14012 <conditional name="adv_opts_cond"> | |
| 14013 <param name="adv_opts_selector" value="advanced"/> | |
| 14014 <param name="force" value="false"/> | |
| 14015 <param name="test" value="true"/> | |
| 14016 </conditional> | |
| 14017 <param name="type" value="itraq4plex"/> | |
| 14018 <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> | |
| 14019 <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 14020 <section name="extraction"> | |
| 14021 <param name="select_activation" value=""/> | |
| 14022 <param name="reporter_mass_shift" value="0.1"/> | |
| 14023 <param name="min_precursor_intensity" value="1.0"/> | |
| 14024 <param name="keep_unannotated_precursor" value="true"/> | |
| 14025 <param name="min_reporter_intensity" value="0.0"/> | |
| 14026 <param name="discard_low_intensity_quantifications" value="false"/> | |
| 14027 <param name="min_precursor_purity" value="0.0"/> | |
| 14028 <param name="precursor_isotope_deviation" value="10.0"/> | |
| 14029 <param name="purity_interpolation" value="true"/> | |
| 14030 </section> | |
| 14031 <section name="itraq4plex"> | |
| 14032 <param name="channel_114_description" value="l1"/> | |
| 14033 <param name="channel_115_description" value="l2"/> | |
| 14034 <param name="channel_116_description" value="l3"/> | |
| 14035 <param name="channel_117_description" value="lung"/> | |
| 14036 <param name="reference_channel" value="114"/> | |
| 14037 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
| 14038 </section> | |
| 14039 <section name="itraq8plex"> | |
| 14040 <param name="channel_113_description" value=""/> | |
| 14041 <param name="channel_114_description" value=""/> | |
| 14042 <param name="channel_115_description" value=""/> | |
| 14043 <param name="channel_116_description" value=""/> | |
| 14044 <param name="channel_117_description" value=""/> | |
| 14045 <param name="channel_118_description" value=""/> | |
| 14046 <param name="channel_119_description" value=""/> | |
| 14047 <param name="channel_121_description" value=""/> | |
| 14048 <param name="reference_channel" value="113"/> | |
| 14049 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
| 14050 </section> | |
| 14051 <section name="quantification"> | |
| 14052 <param name="isotope_correction" value="true"/> | |
| 14053 <param name="normalization" value="false"/> | |
| 14054 </section> | |
| 14055 <section name="tmt10plex"> | |
| 14056 <param name="channel_126_description" value=""/> | |
| 14057 <param name="channel_127N_description" value=""/> | |
| 14058 <param name="channel_127C_description" value=""/> | |
| 14059 <param name="channel_128N_description" value=""/> | |
| 14060 <param name="channel_128C_description" value=""/> | |
| 14061 <param name="channel_129N_description" value=""/> | |
| 14062 <param name="channel_129C_description" value=""/> | |
| 14063 <param name="channel_130N_description" value=""/> | |
| 14064 <param name="channel_130C_description" value=""/> | |
| 14065 <param name="channel_131_description" value=""/> | |
| 14066 <param name="reference_channel" value="126"/> | |
| 14067 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14068 </section> | |
| 14069 <section name="tmt11plex"> | |
| 14070 <param name="channel_126_description" value=""/> | |
| 14071 <param name="channel_127N_description" value=""/> | |
| 14072 <param name="channel_127C_description" value=""/> | |
| 14073 <param name="channel_128N_description" value=""/> | |
| 14074 <param name="channel_128C_description" value=""/> | |
| 14075 <param name="channel_129N_description" value=""/> | |
| 14076 <param name="channel_129C_description" value=""/> | |
| 14077 <param name="channel_130N_description" value=""/> | |
| 14078 <param name="channel_130C_description" value=""/> | |
| 14079 <param name="channel_131N_description" value=""/> | |
| 14080 <param name="channel_131C_description" value=""/> | |
| 14081 <param name="reference_channel" value="126"/> | |
| 14082 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14083 </section> | |
| 14084 <section name="tmt16plex"> | |
| 14085 <param name="channel_126_description" value=""/> | |
| 14086 <param name="channel_127N_description" value=""/> | |
| 14087 <param name="channel_127C_description" value=""/> | |
| 14088 <param name="channel_128N_description" value=""/> | |
| 14089 <param name="channel_128C_description" value=""/> | |
| 14090 <param name="channel_129N_description" value=""/> | |
| 14091 <param name="channel_129C_description" value=""/> | |
| 14092 <param name="channel_130N_description" value=""/> | |
| 14093 <param name="channel_130C_description" value=""/> | |
| 14094 <param name="channel_131N_description" value=""/> | |
| 14095 <param name="channel_131C_description" value=""/> | |
| 14096 <param name="channel_132N_description" value=""/> | |
| 14097 <param name="channel_132C_description" value=""/> | |
| 14098 <param name="channel_133N_description" value=""/> | |
| 14099 <param name="channel_133C_description" value=""/> | |
| 14100 <param name="channel_134N_description" value=""/> | |
| 14101 <param name="reference_channel" value="126"/> | |
| 14102 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
| 14103 </section> | |
| 14104 <section name="tmt6plex"> | |
| 14105 <param name="channel_126_description" value=""/> | |
| 14106 <param name="channel_127_description" value=""/> | |
| 14107 <param name="channel_128_description" value=""/> | |
| 14108 <param name="channel_129_description" value=""/> | |
| 14109 <param name="channel_130_description" value=""/> | |
| 14110 <param name="channel_131_description" value=""/> | |
| 14111 <param name="reference_channel" value="126"/> | |
| 14112 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14113 </section> | |
| 14114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 14115 <output name="ctd_out" ftype="xml"> | |
| 14116 <assert_contents> | |
| 14117 <is_valid_xml/> | |
| 14118 </assert_contents> | |
| 14119 </output> | |
| 14120 </test> | |
| 14121 <test expect_num_outputs="2"> | |
| 14122 <conditional name="adv_opts_cond"> | |
| 14123 <param name="adv_opts_selector" value="advanced"/> | |
| 14124 <param name="force" value="false"/> | |
| 14125 <param name="test" value="true"/> | |
| 14126 </conditional> | |
| 14127 <param name="type" value="itraq4plex"/> | |
| 14128 <param name="in" value="TMTTenPlexMethod_test.mzML"/> | |
| 14129 <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 14130 <section name="extraction"> | |
| 14131 <param name="select_activation" value="High-energy collision-induced dissociation"/> | |
| 14132 <param name="reporter_mass_shift" value="0.002"/> | |
| 14133 <param name="min_precursor_intensity" value="1.0"/> | |
| 14134 <param name="keep_unannotated_precursor" value="true"/> | |
| 14135 <param name="min_reporter_intensity" value="0.0"/> | |
| 14136 <param name="discard_low_intensity_quantifications" value="false"/> | |
| 14137 <param name="min_precursor_purity" value="0.0"/> | |
| 14138 <param name="precursor_isotope_deviation" value="10.0"/> | |
| 14139 <param name="purity_interpolation" value="true"/> | |
| 14140 </section> | |
| 14141 <section name="itraq4plex"> | |
| 14142 <param name="channel_114_description" value=""/> | |
| 14143 <param name="channel_115_description" value=""/> | |
| 14144 <param name="channel_116_description" value=""/> | |
| 14145 <param name="channel_117_description" value=""/> | |
| 14146 <param name="reference_channel" value="114"/> | |
| 14147 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
| 14148 </section> | |
| 14149 <section name="itraq8plex"> | |
| 14150 <param name="channel_113_description" value=""/> | |
| 14151 <param name="channel_114_description" value=""/> | |
| 14152 <param name="channel_115_description" value=""/> | |
| 14153 <param name="channel_116_description" value=""/> | |
| 14154 <param name="channel_117_description" value=""/> | |
| 14155 <param name="channel_118_description" value=""/> | |
| 14156 <param name="channel_119_description" value=""/> | |
| 14157 <param name="channel_121_description" value=""/> | |
| 14158 <param name="reference_channel" value="113"/> | |
| 14159 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
| 14160 </section> | |
| 14161 <section name="quantification"> | |
| 14162 <param name="isotope_correction" value="true"/> | |
| 14163 <param name="normalization" value="false"/> | |
| 14164 </section> | |
| 14165 <section name="tmt10plex"> | |
| 14166 <param name="channel_126_description" value=""/> | |
| 14167 <param name="channel_127N_description" value=""/> | |
| 14168 <param name="channel_127C_description" value=""/> | |
| 14169 <param name="channel_128N_description" value=""/> | |
| 14170 <param name="channel_128C_description" value=""/> | |
| 14171 <param name="channel_129N_description" value=""/> | |
| 14172 <param name="channel_129C_description" value=""/> | |
| 14173 <param name="channel_130N_description" value=""/> | |
| 14174 <param name="channel_130C_description" value=""/> | |
| 14175 <param name="channel_131_description" value=""/> | |
| 14176 <param name="reference_channel" value="126"/> | |
| 14177 <param name="correction_matrix" value=""0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0""/> | |
| 14178 </section> | |
| 14179 <section name="tmt11plex"> | |
| 14180 <param name="channel_126_description" value=""/> | |
| 14181 <param name="channel_127N_description" value=""/> | |
| 14182 <param name="channel_127C_description" value=""/> | |
| 14183 <param name="channel_128N_description" value=""/> | |
| 14184 <param name="channel_128C_description" value=""/> | |
| 14185 <param name="channel_129N_description" value=""/> | |
| 14186 <param name="channel_129C_description" value=""/> | |
| 14187 <param name="channel_130N_description" value=""/> | |
| 14188 <param name="channel_130C_description" value=""/> | |
| 14189 <param name="channel_131N_description" value=""/> | |
| 14190 <param name="channel_131C_description" value=""/> | |
| 14191 <param name="reference_channel" value="126"/> | |
| 14192 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14193 </section> | |
| 14194 <section name="tmt16plex"> | |
| 14195 <param name="channel_126_description" value=""/> | |
| 14196 <param name="channel_127N_description" value=""/> | |
| 14197 <param name="channel_127C_description" value=""/> | |
| 14198 <param name="channel_128N_description" value=""/> | |
| 14199 <param name="channel_128C_description" value=""/> | |
| 14200 <param name="channel_129N_description" value=""/> | |
| 14201 <param name="channel_129C_description" value=""/> | |
| 14202 <param name="channel_130N_description" value=""/> | |
| 14203 <param name="channel_130C_description" value=""/> | |
| 14204 <param name="channel_131N_description" value=""/> | |
| 14205 <param name="channel_131C_description" value=""/> | |
| 14206 <param name="channel_132N_description" value=""/> | |
| 14207 <param name="channel_132C_description" value=""/> | |
| 14208 <param name="channel_133N_description" value=""/> | |
| 14209 <param name="channel_133C_description" value=""/> | |
| 14210 <param name="channel_134N_description" value=""/> | |
| 14211 <param name="reference_channel" value="126"/> | |
| 14212 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
| 14213 </section> | |
| 14214 <section name="tmt6plex"> | |
| 14215 <param name="channel_126_description" value=""/> | |
| 14216 <param name="channel_127_description" value=""/> | |
| 14217 <param name="channel_128_description" value=""/> | |
| 14218 <param name="channel_129_description" value=""/> | |
| 14219 <param name="channel_130_description" value=""/> | |
| 14220 <param name="channel_131_description" value=""/> | |
| 14221 <param name="reference_channel" value="126"/> | |
| 14222 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14223 </section> | |
| 14224 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 14225 <output name="ctd_out" ftype="xml"> | |
| 14226 <assert_contents> | |
| 14227 <is_valid_xml/> | |
| 14228 </assert_contents> | |
| 14229 </output> | |
| 14230 </test> | |
| 14231 <test expect_num_outputs="2"> | |
| 14232 <conditional name="adv_opts_cond"> | |
| 14233 <param name="adv_opts_selector" value="advanced"/> | |
| 14234 <param name="force" value="false"/> | |
| 14235 <param name="test" value="true"/> | |
| 14236 </conditional> | |
| 14237 <param name="type" value="itraq4plex"/> | |
| 14238 <param name="in" value="TMTTenPlexMethod_test.mzML"/> | |
| 14239 <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 14240 <section name="extraction"> | |
| 14241 <param name="select_activation" value="High-energy collision-induced dissociation"/> | |
| 14242 <param name="reporter_mass_shift" value="0.002"/> | |
| 14243 <param name="min_precursor_intensity" value="1.0"/> | |
| 14244 <param name="keep_unannotated_precursor" value="true"/> | |
| 14245 <param name="min_reporter_intensity" value="0.0"/> | |
| 14246 <param name="discard_low_intensity_quantifications" value="false"/> | |
| 14247 <param name="min_precursor_purity" value="0.0"/> | |
| 14248 <param name="precursor_isotope_deviation" value="10.0"/> | |
| 14249 <param name="purity_interpolation" value="true"/> | |
| 14250 </section> | |
| 14251 <section name="itraq4plex"> | |
| 14252 <param name="channel_114_description" value=""/> | |
| 14253 <param name="channel_115_description" value=""/> | |
| 14254 <param name="channel_116_description" value=""/> | |
| 14255 <param name="channel_117_description" value=""/> | |
| 14256 <param name="reference_channel" value="114"/> | |
| 14257 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
| 14258 </section> | |
| 14259 <section name="itraq8plex"> | |
| 14260 <param name="channel_113_description" value=""/> | |
| 14261 <param name="channel_114_description" value=""/> | |
| 14262 <param name="channel_115_description" value=""/> | |
| 14263 <param name="channel_116_description" value=""/> | |
| 14264 <param name="channel_117_description" value=""/> | |
| 14265 <param name="channel_118_description" value=""/> | |
| 14266 <param name="channel_119_description" value=""/> | |
| 14267 <param name="channel_121_description" value=""/> | |
| 14268 <param name="reference_channel" value="113"/> | |
| 14269 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
| 14270 </section> | |
| 14271 <section name="quantification"> | |
| 14272 <param name="isotope_correction" value="true"/> | |
| 14273 <param name="normalization" value="false"/> | |
| 14274 </section> | |
| 14275 <section name="tmt10plex"> | |
| 14276 <param name="channel_126_description" value=""/> | |
| 14277 <param name="channel_127N_description" value=""/> | |
| 14278 <param name="channel_127C_description" value=""/> | |
| 14279 <param name="channel_128N_description" value=""/> | |
| 14280 <param name="channel_128C_description" value=""/> | |
| 14281 <param name="channel_129N_description" value=""/> | |
| 14282 <param name="channel_129C_description" value=""/> | |
| 14283 <param name="channel_130N_description" value=""/> | |
| 14284 <param name="channel_130C_description" value=""/> | |
| 14285 <param name="channel_131_description" value=""/> | |
| 14286 <param name="reference_channel" value="126"/> | |
| 14287 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14288 </section> | |
| 14289 <section name="tmt11plex"> | |
| 14290 <param name="channel_126_description" value=""/> | |
| 14291 <param name="channel_127N_description" value=""/> | |
| 14292 <param name="channel_127C_description" value=""/> | |
| 14293 <param name="channel_128N_description" value=""/> | |
| 14294 <param name="channel_128C_description" value=""/> | |
| 14295 <param name="channel_129N_description" value=""/> | |
| 14296 <param name="channel_129C_description" value=""/> | |
| 14297 <param name="channel_130N_description" value=""/> | |
| 14298 <param name="channel_130C_description" value=""/> | |
| 14299 <param name="channel_131N_description" value=""/> | |
| 14300 <param name="channel_131C_description" value=""/> | |
| 14301 <param name="reference_channel" value="126"/> | |
| 14302 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14303 </section> | |
| 14304 <section name="tmt16plex"> | |
| 14305 <param name="channel_126_description" value=""/> | |
| 14306 <param name="channel_127N_description" value=""/> | |
| 14307 <param name="channel_127C_description" value=""/> | |
| 14308 <param name="channel_128N_description" value=""/> | |
| 14309 <param name="channel_128C_description" value=""/> | |
| 14310 <param name="channel_129N_description" value=""/> | |
| 14311 <param name="channel_129C_description" value=""/> | |
| 14312 <param name="channel_130N_description" value=""/> | |
| 14313 <param name="channel_130C_description" value=""/> | |
| 14314 <param name="channel_131N_description" value=""/> | |
| 14315 <param name="channel_131C_description" value=""/> | |
| 14316 <param name="channel_132N_description" value=""/> | |
| 14317 <param name="channel_132C_description" value=""/> | |
| 14318 <param name="channel_133N_description" value=""/> | |
| 14319 <param name="channel_133C_description" value=""/> | |
| 14320 <param name="channel_134N_description" value=""/> | |
| 14321 <param name="reference_channel" value="126"/> | |
| 14322 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
| 14323 </section> | |
| 14324 <section name="tmt6plex"> | |
| 14325 <param name="channel_126_description" value=""/> | |
| 14326 <param name="channel_127_description" value=""/> | |
| 14327 <param name="channel_128_description" value=""/> | |
| 14328 <param name="channel_129_description" value=""/> | |
| 14329 <param name="channel_130_description" value=""/> | |
| 14330 <param name="channel_131_description" value=""/> | |
| 14331 <param name="reference_channel" value="126"/> | |
| 14332 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14333 </section> | |
| 14334 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 14335 <output name="ctd_out" ftype="xml"> | |
| 14336 <assert_contents> | |
| 14337 <is_valid_xml/> | |
| 14338 </assert_contents> | |
| 14339 </output> | |
| 14340 </test> | |
| 14341 <test expect_num_outputs="2"> | |
| 14342 <conditional name="adv_opts_cond"> | |
| 14343 <param name="adv_opts_selector" value="advanced"/> | |
| 14344 <param name="force" value="false"/> | |
| 14345 <param name="test" value="true"/> | |
| 14346 </conditional> | |
| 14347 <param name="type" value="tmt10plex"/> | |
| 14348 <param name="in" value="MS3_nonHierarchical.mzML"/> | |
| 14349 <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 14350 <section name="extraction"> | |
| 14351 <param name="select_activation" value="Collision-induced dissociation"/> | |
| 14352 <param name="reporter_mass_shift" value="0.002"/> | |
| 14353 <param name="min_precursor_intensity" value="1.0"/> | |
| 14354 <param name="keep_unannotated_precursor" value="true"/> | |
| 14355 <param name="min_reporter_intensity" value="0.0"/> | |
| 14356 <param name="discard_low_intensity_quantifications" value="false"/> | |
| 14357 <param name="min_precursor_purity" value="0.0"/> | |
| 14358 <param name="precursor_isotope_deviation" value="10.0"/> | |
| 14359 <param name="purity_interpolation" value="true"/> | |
| 14360 </section> | |
| 14361 <section name="itraq4plex"> | |
| 14362 <param name="channel_114_description" value=""/> | |
| 14363 <param name="channel_115_description" value=""/> | |
| 14364 <param name="channel_116_description" value=""/> | |
| 14365 <param name="channel_117_description" value=""/> | |
| 14366 <param name="reference_channel" value="114"/> | |
| 14367 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
| 14368 </section> | |
| 14369 <section name="itraq8plex"> | |
| 14370 <param name="channel_113_description" value=""/> | |
| 14371 <param name="channel_114_description" value=""/> | |
| 14372 <param name="channel_115_description" value=""/> | |
| 14373 <param name="channel_116_description" value=""/> | |
| 14374 <param name="channel_117_description" value=""/> | |
| 14375 <param name="channel_118_description" value=""/> | |
| 14376 <param name="channel_119_description" value=""/> | |
| 14377 <param name="channel_121_description" value=""/> | |
| 14378 <param name="reference_channel" value="113"/> | |
| 14379 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
| 14380 </section> | |
| 14381 <section name="quantification"> | |
| 14382 <param name="isotope_correction" value="true"/> | |
| 14383 <param name="normalization" value="false"/> | |
| 14384 </section> | |
| 14385 <section name="tmt10plex"> | |
| 14386 <param name="channel_126_description" value=""/> | |
| 14387 <param name="channel_127N_description" value=""/> | |
| 14388 <param name="channel_127C_description" value=""/> | |
| 14389 <param name="channel_128N_description" value=""/> | |
| 14390 <param name="channel_128C_description" value=""/> | |
| 14391 <param name="channel_129N_description" value=""/> | |
| 14392 <param name="channel_129C_description" value=""/> | |
| 14393 <param name="channel_130N_description" value=""/> | |
| 14394 <param name="channel_130C_description" value=""/> | |
| 14395 <param name="channel_131_description" value=""/> | |
| 14396 <param name="reference_channel" value="126"/> | |
| 14397 <param name="correction_matrix" value=""0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0""/> | |
| 14398 </section> | |
| 14399 <section name="tmt11plex"> | |
| 14400 <param name="channel_126_description" value=""/> | |
| 14401 <param name="channel_127N_description" value=""/> | |
| 14402 <param name="channel_127C_description" value=""/> | |
| 14403 <param name="channel_128N_description" value=""/> | |
| 14404 <param name="channel_128C_description" value=""/> | |
| 14405 <param name="channel_129N_description" value=""/> | |
| 14406 <param name="channel_129C_description" value=""/> | |
| 14407 <param name="channel_130N_description" value=""/> | |
| 14408 <param name="channel_130C_description" value=""/> | |
| 14409 <param name="channel_131N_description" value=""/> | |
| 14410 <param name="channel_131C_description" value=""/> | |
| 14411 <param name="reference_channel" value="126"/> | |
| 14412 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14413 </section> | |
| 14414 <section name="tmt16plex"> | |
| 14415 <param name="channel_126_description" value=""/> | |
| 14416 <param name="channel_127N_description" value=""/> | |
| 14417 <param name="channel_127C_description" value=""/> | |
| 14418 <param name="channel_128N_description" value=""/> | |
| 14419 <param name="channel_128C_description" value=""/> | |
| 14420 <param name="channel_129N_description" value=""/> | |
| 14421 <param name="channel_129C_description" value=""/> | |
| 14422 <param name="channel_130N_description" value=""/> | |
| 14423 <param name="channel_130C_description" value=""/> | |
| 14424 <param name="channel_131N_description" value=""/> | |
| 14425 <param name="channel_131C_description" value=""/> | |
| 14426 <param name="channel_132N_description" value=""/> | |
| 14427 <param name="channel_132C_description" value=""/> | |
| 14428 <param name="channel_133N_description" value=""/> | |
| 14429 <param name="channel_133C_description" value=""/> | |
| 14430 <param name="channel_134N_description" value=""/> | |
| 14431 <param name="reference_channel" value="126"/> | |
| 14432 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
| 14433 </section> | |
| 14434 <section name="tmt6plex"> | |
| 14435 <param name="channel_126_description" value=""/> | |
| 14436 <param name="channel_127_description" value=""/> | |
| 14437 <param name="channel_128_description" value=""/> | |
| 14438 <param name="channel_129_description" value=""/> | |
| 14439 <param name="channel_130_description" value=""/> | |
| 14440 <param name="channel_131_description" value=""/> | |
| 14441 <param name="reference_channel" value="126"/> | |
| 14442 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
| 14443 </section> | |
| 14444 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 14445 <output name="ctd_out" ftype="xml"> | |
| 14446 <assert_contents> | |
| 14447 <is_valid_xml/> | |
| 14448 </assert_contents> | |
| 14449 </output> | |
| 14450 </test> | |
| 14451 </xml> | |
| 14452 <xml name="autotest_LabeledEval"> | |
| 14453 </xml> | |
| 14454 <xml name="autotest_LowMemPeakPickerHiResRandomAccess"> | |
| 14455 <test expect_num_outputs="2"> | |
| 14456 <conditional name="adv_opts_cond"> | |
| 14457 <param name="adv_opts_selector" value="advanced"/> | |
| 14458 <param name="force" value="false"/> | |
| 14459 <param name="test" value="true"/> | |
| 14460 </conditional> | |
| 14461 <param name="in" value="PeakPickerHiRes_RandomAccess_input.mzML"/> | |
| 14462 <output name="out" file="LowMemPeakPickerHiRes_RandomAccess_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 14463 <section name="algorithm"> | |
| 14464 <param name="signal_to_noise" value="1.0"/> | |
| 14465 <param name="spacing_difference_gap" value="4.0"/> | |
| 14466 <param name="spacing_difference" value="1.5"/> | |
| 14467 <param name="missing" value="1"/> | |
| 14468 <param name="ms_levels" value="1"/> | |
| 14469 <param name="report_FWHM" value="false"/> | |
| 14470 <param name="report_FWHM_unit" value="relative"/> | |
| 14471 <section name="SignalToNoise"> | |
| 14472 <param name="max_intensity" value="-1"/> | |
| 14473 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 14474 <param name="auto_max_percentile" value="95"/> | |
| 14475 <param name="auto_mode" value="0"/> | |
| 14476 <param name="win_len" value="200.0"/> | |
| 14477 <param name="bin_count" value="30"/> | |
| 14478 <param name="min_required_elements" value="10"/> | |
| 14479 <param name="noise_for_empty_window" value="1e+20"/> | |
| 14480 <param name="write_log_messages" value="true"/> | |
| 14481 </section> | |
| 14482 </section> | |
| 14483 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 14484 <output name="ctd_out" ftype="xml"> | |
| 14485 <assert_contents> | |
| 14486 <is_valid_xml/> | |
| 14487 </assert_contents> | |
| 14488 </output> | |
| 14489 </test> | |
| 14490 </xml> | |
| 14491 <xml name="autotest_LowMemPeakPickerHiRes"> | |
| 14492 <test expect_num_outputs="2"> | |
| 14493 <conditional name="adv_opts_cond"> | |
| 14494 <param name="adv_opts_selector" value="advanced"/> | |
| 14495 <param name="force" value="false"/> | |
| 14496 <param name="test" value="true"/> | |
| 14497 </conditional> | |
| 14498 <param name="in" value="PeakPickerHiRes_input.mzML"/> | |
| 14499 <output name="out" file="LowMemPeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 14500 <section name="algorithm"> | |
| 14501 <param name="signal_to_noise" value="1.0"/> | |
| 14502 <param name="spacing_difference_gap" value="4.0"/> | |
| 14503 <param name="spacing_difference" value="1.5"/> | |
| 14504 <param name="missing" value="1"/> | |
| 14505 <param name="ms_levels" value="1"/> | |
| 14506 <param name="report_FWHM" value="false"/> | |
| 14507 <param name="report_FWHM_unit" value="relative"/> | |
| 14508 <section name="SignalToNoise"> | |
| 14509 <param name="max_intensity" value="-1"/> | |
| 14510 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 14511 <param name="auto_max_percentile" value="95"/> | |
| 14512 <param name="auto_mode" value="0"/> | |
| 14513 <param name="win_len" value="200.0"/> | |
| 14514 <param name="bin_count" value="30"/> | |
| 14515 <param name="min_required_elements" value="10"/> | |
| 14516 <param name="noise_for_empty_window" value="1e+20"/> | |
| 14517 <param name="write_log_messages" value="true"/> | |
| 14518 </section> | |
| 14519 </section> | |
| 14520 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 14521 <output name="ctd_out" ftype="xml"> | |
| 14522 <assert_contents> | |
| 14523 <is_valid_xml/> | |
| 14524 </assert_contents> | |
| 14525 </output> | |
| 14526 </test> | |
| 14527 </xml> | |
| 14528 <xml name="autotest_LuciphorAdapter"> | |
| 14529 <test expect_num_outputs="2"> | |
| 14530 <conditional name="adv_opts_cond"> | |
| 14531 <param name="adv_opts_selector" value="advanced"/> | |
| 14532 <param name="force" value="false"/> | |
| 14533 <param name="test" value="true"/> | |
| 14534 </conditional> | |
| 14535 <param name="in" value="LuciphorAdapter_1_input.mzML"/> | |
| 14536 <param name="id" value="LuciphorAdapter_1_input.idXML"/> | |
| 14537 <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 14538 <param name="fragment_method" value="CID"/> | |
| 14539 <param name="fragment_mass_tolerance" value="0.5"/> | |
| 14540 <param name="fragment_error_units" value="Da"/> | |
| 14541 <param name="min_mz" value="150.0"/> | |
| 14542 <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/> | |
| 14543 <param name="neutral_losses" value=""sty -H3PO4 -97.97690""/> | |
| 14544 <param name="decoy_mass" value="79.966331"/> | |
| 14545 <param name="decoy_neutral_losses" value=""X -H3PO4 -97.97690""/> | |
| 14546 <param name="max_charge_state" value="5"/> | |
| 14547 <param name="max_peptide_length" value="40"/> | |
| 14548 <param name="max_num_perm" value="16384"/> | |
| 14549 <param name="modeling_score_threshold" value="0.95"/> | |
| 14550 <param name="scoring_threshold" value="0.0"/> | |
| 14551 <param name="min_num_psms_model" value="1"/> | |
| 14552 <param name="run_mode" value="0"/> | |
| 14553 <param name="rt_tolerance" value="0.01"/> | |
| 14554 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 14555 <output name="ctd_out" ftype="xml"> | |
| 14556 <assert_contents> | |
| 14557 <is_valid_xml/> | |
| 14558 </assert_contents> | |
| 14559 </output> | |
| 14560 </test> | |
| 14561 </xml> | |
| 14562 <xml name="autotest_MapAlignerIdentification"> | |
| 14563 <test expect_num_outputs="2"> | |
| 14564 <conditional name="adv_opts_cond"> | |
| 14565 <param name="adv_opts_selector" value="advanced"/> | |
| 14566 <param name="force" value="false"/> | |
| 14567 <param name="test" value="true"/> | |
| 14568 </conditional> | |
| 14569 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> | |
| 14570 <output_collection name="out" count="2"/> | |
| 14571 <section name="reference"> | |
| 14572 <param name="index" value="0"/> | |
| 14573 </section> | |
| 14574 <section name="algorithm"> | |
| 14575 <param name="score_cutoff" value="false"/> | |
| 14576 <param name="min_score" value="0.05"/> | |
| 14577 <param name="min_run_occur" value="2"/> | |
| 14578 <param name="max_rt_shift" value="0.0"/> | |
| 14579 <param name="use_unassigned_peptides" value="true"/> | |
| 14580 <param name="use_feature_rt" value="false"/> | |
| 14581 </section> | |
| 14582 <section name="model"> | |
| 14583 <param name="type" value="b_spline"/> | |
| 14584 <section name="linear"> | |
| 14585 <param name="symmetric_regression" value="false"/> | |
| 14586 <param name="x_weight" value=""/> | |
| 14587 <param name="y_weight" value=""/> | |
| 14588 <param name="x_datum_min" value="1e-15"/> | |
| 14589 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 14590 <param name="y_datum_min" value="1e-15"/> | |
| 14591 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 14592 </section> | |
| 14593 <section name="b_spline"> | |
| 14594 <param name="wavelength" value="0.0"/> | |
| 14595 <param name="num_nodes" value="5"/> | |
| 14596 <param name="extrapolate" value="linear"/> | |
| 14597 <param name="boundary_condition" value="2"/> | |
| 14598 </section> | |
| 14599 <section name="lowess"> | |
| 14600 <param name="span" value="0.666666666666667"/> | |
| 14601 <param name="num_iterations" value="3"/> | |
| 14602 <param name="delta" value="-1.0"/> | |
| 14603 <param name="interpolation_type" value="cspline"/> | |
| 14604 <param name="extrapolation_type" value="four-point-linear"/> | |
| 14605 </section> | |
| 14606 <section name="interpolated"> | |
| 14607 <param name="interpolation_type" value="cspline"/> | |
| 14608 <param name="extrapolation_type" value="two-point-linear"/> | |
| 14609 </section> | |
| 14610 </section> | |
| 14611 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 14612 <output name="ctd_out" ftype="xml"> | |
| 14613 <assert_contents> | |
| 14614 <is_valid_xml/> | |
| 14615 </assert_contents> | |
| 14616 </output> | |
| 14617 </test> | |
| 14618 <test expect_num_outputs="2"> | |
| 14619 <conditional name="adv_opts_cond"> | |
| 14620 <param name="adv_opts_selector" value="advanced"/> | |
| 14621 <param name="force" value="false"/> | |
| 14622 <param name="test" value="true"/> | |
| 14623 </conditional> | |
| 14624 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> | |
| 14625 <output_collection name="out" count="1"/> | |
| 14626 <section name="reference"> | |
| 14627 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> | |
| 14628 <param name="index" value="0"/> | |
| 14629 </section> | |
| 14630 <section name="algorithm"> | |
| 14631 <param name="score_cutoff" value="false"/> | |
| 14632 <param name="min_score" value="0.05"/> | |
| 14633 <param name="min_run_occur" value="2"/> | |
| 14634 <param name="max_rt_shift" value="0.0"/> | |
| 14635 <param name="use_unassigned_peptides" value="true"/> | |
| 14636 <param name="use_feature_rt" value="false"/> | |
| 14637 </section> | |
| 14638 <section name="model"> | |
| 14639 <param name="type" value="b_spline"/> | |
| 14640 <section name="linear"> | |
| 14641 <param name="symmetric_regression" value="false"/> | |
| 14642 <param name="x_weight" value=""/> | |
| 14643 <param name="y_weight" value=""/> | |
| 14644 <param name="x_datum_min" value="1e-15"/> | |
| 14645 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 14646 <param name="y_datum_min" value="1e-15"/> | |
| 14647 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 14648 </section> | |
| 14649 <section name="b_spline"> | |
| 14650 <param name="wavelength" value="0.0"/> | |
| 14651 <param name="num_nodes" value="5"/> | |
| 14652 <param name="extrapolate" value="linear"/> | |
| 14653 <param name="boundary_condition" value="2"/> | |
| 14654 </section> | |
| 14655 <section name="lowess"> | |
| 14656 <param name="span" value="0.666666666666667"/> | |
| 14657 <param name="num_iterations" value="3"/> | |
| 14658 <param name="delta" value="-1.0"/> | |
| 14659 <param name="interpolation_type" value="cspline"/> | |
| 14660 <param name="extrapolation_type" value="four-point-linear"/> | |
| 14661 </section> | |
| 14662 <section name="interpolated"> | |
| 14663 <param name="interpolation_type" value="cspline"/> | |
| 14664 <param name="extrapolation_type" value="two-point-linear"/> | |
| 14665 </section> | |
| 14666 </section> | |
| 14667 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 14668 <output name="ctd_out" ftype="xml"> | |
| 14669 <assert_contents> | |
| 14670 <is_valid_xml/> | |
| 14671 </assert_contents> | |
| 14672 </output> | |
| 14673 </test> | |
| 14674 <test expect_num_outputs="2"> | |
| 14675 <conditional name="adv_opts_cond"> | |
| 14676 <param name="adv_opts_selector" value="advanced"/> | |
| 14677 <param name="force" value="false"/> | |
| 14678 <param name="test" value="true"/> | |
| 14679 </conditional> | |
| 14680 <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/> | |
| 14681 <output_collection name="out" count="2"/> | |
| 14682 <section name="reference"> | |
| 14683 <param name="index" value="1"/> | |
| 14684 </section> | |
| 14685 <section name="algorithm"> | |
| 14686 <param name="score_cutoff" value="false"/> | |
| 14687 <param name="min_score" value="0.05"/> | |
| 14688 <param name="min_run_occur" value="2"/> | |
| 14689 <param name="max_rt_shift" value="0.0"/> | |
| 14690 <param name="use_unassigned_peptides" value="true"/> | |
| 14691 <param name="use_feature_rt" value="false"/> | |
| 14692 </section> | |
| 14693 <section name="model"> | |
| 14694 <param name="type" value="b_spline"/> | |
| 14695 <section name="linear"> | |
| 14696 <param name="symmetric_regression" value="false"/> | |
| 14697 <param name="x_weight" value=""/> | |
| 14698 <param name="y_weight" value=""/> | |
| 14699 <param name="x_datum_min" value="1e-15"/> | |
| 14700 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 14701 <param name="y_datum_min" value="1e-15"/> | |
| 14702 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 14703 </section> | |
| 14704 <section name="b_spline"> | |
| 14705 <param name="wavelength" value="0.0"/> | |
| 14706 <param name="num_nodes" value="5"/> | |
| 14707 <param name="extrapolate" value="linear"/> | |
| 14708 <param name="boundary_condition" value="2"/> | |
| 14709 </section> | |
| 14710 <section name="lowess"> | |
| 14711 <param name="span" value="0.666666666666667"/> | |
| 14712 <param name="num_iterations" value="3"/> | |
| 14713 <param name="delta" value="-1.0"/> | |
| 14714 <param name="interpolation_type" value="cspline"/> | |
| 14715 <param name="extrapolation_type" value="four-point-linear"/> | |
| 14716 </section> | |
| 14717 <section name="interpolated"> | |
| 14718 <param name="interpolation_type" value="cspline"/> | |
| 14719 <param name="extrapolation_type" value="two-point-linear"/> | |
| 14720 </section> | |
| 14721 </section> | |
| 14722 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 14723 <output name="ctd_out" ftype="xml"> | |
| 14724 <assert_contents> | |
| 14725 <is_valid_xml/> | |
| 14726 </assert_contents> | |
| 14727 </output> | |
| 14728 </test> | |
| 14729 <test expect_num_outputs="2"> | |
| 14730 <conditional name="adv_opts_cond"> | |
| 14731 <param name="adv_opts_selector" value="advanced"/> | |
| 14732 <param name="force" value="false"/> | |
| 14733 <param name="test" value="true"/> | |
| 14734 </conditional> | |
| 14735 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> | |
| 14736 <output_collection name="out" count="2"/> | |
| 14737 <section name="reference"> | |
| 14738 <param name="index" value="2"/> | |
| 14739 </section> | |
| 14740 <section name="algorithm"> | |
| 14741 <param name="score_cutoff" value="false"/> | |
| 14742 <param name="min_score" value="0.05"/> | |
| 14743 <param name="min_run_occur" value="2"/> | |
| 14744 <param name="max_rt_shift" value="0.0"/> | |
| 14745 <param name="use_unassigned_peptides" value="true"/> | |
| 14746 <param name="use_feature_rt" value="false"/> | |
| 14747 </section> | |
| 14748 <section name="model"> | |
| 14749 <param name="type" value="b_spline"/> | |
| 14750 <section name="linear"> | |
| 14751 <param name="symmetric_regression" value="false"/> | |
| 14752 <param name="x_weight" value=""/> | |
| 14753 <param name="y_weight" value=""/> | |
| 14754 <param name="x_datum_min" value="1e-15"/> | |
| 14755 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 14756 <param name="y_datum_min" value="1e-15"/> | |
| 14757 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 14758 </section> | |
| 14759 <section name="b_spline"> | |
| 14760 <param name="wavelength" value="0.0"/> | |
| 14761 <param name="num_nodes" value="5"/> | |
| 14762 <param name="extrapolate" value="linear"/> | |
| 14763 <param name="boundary_condition" value="2"/> | |
| 14764 </section> | |
| 14765 <section name="lowess"> | |
| 14766 <param name="span" value="0.666666666666667"/> | |
| 14767 <param name="num_iterations" value="3"/> | |
| 14768 <param name="delta" value="-1.0"/> | |
| 14769 <param name="interpolation_type" value="cspline"/> | |
| 14770 <param name="extrapolation_type" value="four-point-linear"/> | |
| 14771 </section> | |
| 14772 <section name="interpolated"> | |
| 14773 <param name="interpolation_type" value="cspline"/> | |
| 14774 <param name="extrapolation_type" value="two-point-linear"/> | |
| 14775 </section> | |
| 14776 </section> | |
| 14777 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 14778 <output name="ctd_out" ftype="xml"> | |
| 14779 <assert_contents> | |
| 14780 <is_valid_xml/> | |
| 14781 </assert_contents> | |
| 14782 </output> | |
| 14783 </test> | |
| 14784 <test expect_num_outputs="2"> | |
| 14785 <conditional name="adv_opts_cond"> | |
| 14786 <param name="adv_opts_selector" value="advanced"/> | |
| 14787 <param name="force" value="false"/> | |
| 14788 <param name="test" value="true"/> | |
| 14789 </conditional> | |
| 14790 <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/> | |
| 14791 <output_collection name="out" count="2"/> | |
| 14792 <section name="reference"> | |
| 14793 <param name="index" value="0"/> | |
| 14794 </section> | |
| 14795 <section name="algorithm"> | |
| 14796 <param name="score_cutoff" value="false"/> | |
| 14797 <param name="min_score" value="0.05"/> | |
| 14798 <param name="min_run_occur" value="2"/> | |
| 14799 <param name="max_rt_shift" value="0.0"/> | |
| 14800 <param name="use_unassigned_peptides" value="true"/> | |
| 14801 <param name="use_feature_rt" value="false"/> | |
| 14802 </section> | |
| 14803 <section name="model"> | |
| 14804 <param name="type" value="b_spline"/> | |
| 14805 <section name="linear"> | |
| 14806 <param name="symmetric_regression" value="false"/> | |
| 14807 <param name="x_weight" value=""/> | |
| 14808 <param name="y_weight" value=""/> | |
| 14809 <param name="x_datum_min" value="1e-15"/> | |
| 14810 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 14811 <param name="y_datum_min" value="1e-15"/> | |
| 14812 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 14813 </section> | |
| 14814 <section name="b_spline"> | |
| 14815 <param name="wavelength" value="0.0"/> | |
| 14816 <param name="num_nodes" value="5"/> | |
| 14817 <param name="extrapolate" value="linear"/> | |
| 14818 <param name="boundary_condition" value="2"/> | |
| 14819 </section> | |
| 14820 <section name="lowess"> | |
| 14821 <param name="span" value="0.666666666666667"/> | |
| 14822 <param name="num_iterations" value="3"/> | |
| 14823 <param name="delta" value="-1.0"/> | |
| 14824 <param name="interpolation_type" value="cspline"/> | |
| 14825 <param name="extrapolation_type" value="four-point-linear"/> | |
| 14826 </section> | |
| 14827 <section name="interpolated"> | |
| 14828 <param name="interpolation_type" value="cspline"/> | |
| 14829 <param name="extrapolation_type" value="two-point-linear"/> | |
| 14830 </section> | |
| 14831 </section> | |
| 14832 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 14833 <output name="ctd_out" ftype="xml"> | |
| 14834 <assert_contents> | |
| 14835 <is_valid_xml/> | |
| 14836 </assert_contents> | |
| 14837 </output> | |
| 14838 </test> | |
| 14839 <test expect_num_outputs="2"> | |
| 14840 <conditional name="adv_opts_cond"> | |
| 14841 <param name="adv_opts_selector" value="advanced"/> | |
| 14842 <param name="force" value="false"/> | |
| 14843 <param name="test" value="true"/> | |
| 14844 </conditional> | |
| 14845 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> | |
| 14846 <output_collection name="trafo_out" count="1"/> | |
| 14847 <section name="reference"> | |
| 14848 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> | |
| 14849 <param name="index" value="0"/> | |
| 14850 </section> | |
| 14851 <section name="algorithm"> | |
| 14852 <param name="score_cutoff" value="false"/> | |
| 14853 <param name="min_score" value="0.05"/> | |
| 14854 <param name="min_run_occur" value="2"/> | |
| 14855 <param name="max_rt_shift" value="0.0"/> | |
| 14856 <param name="use_unassigned_peptides" value="true"/> | |
| 14857 <param name="use_feature_rt" value="false"/> | |
| 14858 </section> | |
| 14859 <section name="model"> | |
| 14860 <param name="type" value="b_spline"/> | |
| 14861 <section name="linear"> | |
| 14862 <param name="symmetric_regression" value="false"/> | |
| 14863 <param name="x_weight" value=""/> | |
| 14864 <param name="y_weight" value=""/> | |
| 14865 <param name="x_datum_min" value="1e-15"/> | |
| 14866 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 14867 <param name="y_datum_min" value="1e-15"/> | |
| 14868 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 14869 </section> | |
| 14870 <section name="b_spline"> | |
| 14871 <param name="wavelength" value="0.0"/> | |
| 14872 <param name="num_nodes" value="5"/> | |
| 14873 <param name="extrapolate" value="linear"/> | |
| 14874 <param name="boundary_condition" value="2"/> | |
| 14875 </section> | |
| 14876 <section name="lowess"> | |
| 14877 <param name="span" value="0.666666666666667"/> | |
| 14878 <param name="num_iterations" value="3"/> | |
| 14879 <param name="delta" value="-1.0"/> | |
| 14880 <param name="interpolation_type" value="cspline"/> | |
| 14881 <param name="extrapolation_type" value="four-point-linear"/> | |
| 14882 </section> | |
| 14883 <section name="interpolated"> | |
| 14884 <param name="interpolation_type" value="cspline"/> | |
| 14885 <param name="extrapolation_type" value="two-point-linear"/> | |
| 14886 </section> | |
| 14887 </section> | |
| 14888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> | |
| 14889 <output name="ctd_out" ftype="xml"> | |
| 14890 <assert_contents> | |
| 14891 <is_valid_xml/> | |
| 14892 </assert_contents> | |
| 14893 </output> | |
| 14894 </test> | |
| 14895 </xml> | |
| 14896 <xml name="autotest_MapAlignerPoseClustering"> | |
| 14897 <test expect_num_outputs="3"> | |
| 14898 <conditional name="adv_opts_cond"> | |
| 14899 <param name="adv_opts_selector" value="advanced"/> | |
| 14900 <param name="force" value="false"/> | |
| 14901 <param name="test" value="true"/> | |
| 14902 </conditional> | |
| 14903 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> | |
| 14904 <output_collection name="out" count="3"/> | |
| 14905 <output_collection name="trafo_out" count="3"/> | |
| 14906 <section name="reference"> | |
| 14907 <param name="index" value="0"/> | |
| 14908 </section> | |
| 14909 <section name="algorithm"> | |
| 14910 <param name="max_num_peaks_considered" value="400"/> | |
| 14911 <section name="superimposer"> | |
| 14912 <param name="mz_pair_max_distance" value="0.5"/> | |
| 14913 <param name="rt_pair_distance_fraction" value="0.1"/> | |
| 14914 <param name="num_used_points" value="2000"/> | |
| 14915 <param name="scaling_bucket_size" value="0.005"/> | |
| 14916 <param name="shift_bucket_size" value="3.0"/> | |
| 14917 <param name="max_shift" value="1000.0"/> | |
| 14918 <param name="max_scaling" value="2.0"/> | |
| 14919 <param name="dump_buckets" value=""/> | |
| 14920 <param name="dump_pairs" value=""/> | |
| 14921 </section> | |
| 14922 <section name="pairfinder"> | |
| 14923 <param name="second_nearest_gap" value="2.0"/> | |
| 14924 <param name="use_identifications" value="false"/> | |
| 14925 <param name="ignore_charge" value="true"/> | |
| 14926 <param name="ignore_adduct" value="true"/> | |
| 14927 <section name="distance_RT"> | |
| 14928 <param name="max_difference" value="30.0"/> | |
| 14929 <param name="exponent" value="1.0"/> | |
| 14930 <param name="weight" value="1.0"/> | |
| 14931 </section> | |
| 14932 <section name="distance_MZ"> | |
| 14933 <param name="max_difference" value="0.3"/> | |
| 14934 <param name="unit" value="Da"/> | |
| 14935 <param name="exponent" value="2.0"/> | |
| 14936 <param name="weight" value="1.0"/> | |
| 14937 </section> | |
| 14938 <section name="distance_intensity"> | |
| 14939 <param name="exponent" value="1.0"/> | |
| 14940 <param name="weight" value="0.0"/> | |
| 14941 <param name="log_transform" value="disabled"/> | |
| 14942 </section> | |
| 14943 </section> | |
| 14944 </section> | |
| 14945 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> | |
| 14946 <output name="ctd_out" ftype="xml"> | |
| 14947 <assert_contents> | |
| 14948 <is_valid_xml/> | |
| 14949 </assert_contents> | |
| 14950 </output> | |
| 14951 </test> | |
| 14952 <test expect_num_outputs="2"> | |
| 14953 <conditional name="adv_opts_cond"> | |
| 14954 <param name="adv_opts_selector" value="advanced"/> | |
| 14955 <param name="force" value="false"/> | |
| 14956 <param name="test" value="true"/> | |
| 14957 </conditional> | |
| 14958 <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/> | |
| 14959 <output_collection name="out" count="3"/> | |
| 14960 <section name="reference"> | |
| 14961 <param name="index" value="0"/> | |
| 14962 </section> | |
| 14963 <section name="algorithm"> | |
| 14964 <param name="max_num_peaks_considered" value="400"/> | |
| 14965 <section name="superimposer"> | |
| 14966 <param name="mz_pair_max_distance" value="0.5"/> | |
| 14967 <param name="rt_pair_distance_fraction" value="0.1"/> | |
| 14968 <param name="num_used_points" value="2000"/> | |
| 14969 <param name="scaling_bucket_size" value="0.005"/> | |
| 14970 <param name="shift_bucket_size" value="3.0"/> | |
| 14971 <param name="max_shift" value="1000.0"/> | |
| 14972 <param name="max_scaling" value="2.0"/> | |
| 14973 <param name="dump_buckets" value=""/> | |
| 14974 <param name="dump_pairs" value=""/> | |
| 14975 </section> | |
| 14976 <section name="pairfinder"> | |
| 14977 <param name="second_nearest_gap" value="2.0"/> | |
| 14978 <param name="use_identifications" value="false"/> | |
| 14979 <param name="ignore_charge" value="false"/> | |
| 14980 <param name="ignore_adduct" value="true"/> | |
| 14981 <section name="distance_RT"> | |
| 14982 <param name="max_difference" value="100.0"/> | |
| 14983 <param name="exponent" value="1.0"/> | |
| 14984 <param name="weight" value="1.0"/> | |
| 14985 </section> | |
| 14986 <section name="distance_MZ"> | |
| 14987 <param name="max_difference" value="0.3"/> | |
| 14988 <param name="unit" value="Da"/> | |
| 14989 <param name="exponent" value="2.0"/> | |
| 14990 <param name="weight" value="1.0"/> | |
| 14991 </section> | |
| 14992 <section name="distance_intensity"> | |
| 14993 <param name="exponent" value="1.0"/> | |
| 14994 <param name="weight" value="0.0"/> | |
| 14995 <param name="log_transform" value="disabled"/> | |
| 14996 </section> | |
| 14997 </section> | |
| 14998 </section> | |
| 14999 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15000 <output name="ctd_out" ftype="xml"> | |
| 15001 <assert_contents> | |
| 15002 <is_valid_xml/> | |
| 15003 </assert_contents> | |
| 15004 </output> | |
| 15005 </test> | |
| 15006 <test expect_num_outputs="2"> | |
| 15007 <conditional name="adv_opts_cond"> | |
| 15008 <param name="adv_opts_selector" value="advanced"/> | |
| 15009 <param name="force" value="false"/> | |
| 15010 <param name="test" value="true"/> | |
| 15011 </conditional> | |
| 15012 <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> | |
| 15013 <output_collection name="out" count="2"/> | |
| 15014 <section name="reference"> | |
| 15015 <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/> | |
| 15016 <param name="index" value="0"/> | |
| 15017 </section> | |
| 15018 <section name="algorithm"> | |
| 15019 <param name="max_num_peaks_considered" value="400"/> | |
| 15020 <section name="superimposer"> | |
| 15021 <param name="mz_pair_max_distance" value="0.5"/> | |
| 15022 <param name="rt_pair_distance_fraction" value="0.1"/> | |
| 15023 <param name="num_used_points" value="2000"/> | |
| 15024 <param name="scaling_bucket_size" value="0.005"/> | |
| 15025 <param name="shift_bucket_size" value="3.0"/> | |
| 15026 <param name="max_shift" value="1000.0"/> | |
| 15027 <param name="max_scaling" value="2.0"/> | |
| 15028 <param name="dump_buckets" value=""/> | |
| 15029 <param name="dump_pairs" value=""/> | |
| 15030 </section> | |
| 15031 <section name="pairfinder"> | |
| 15032 <param name="second_nearest_gap" value="2.0"/> | |
| 15033 <param name="use_identifications" value="false"/> | |
| 15034 <param name="ignore_charge" value="true"/> | |
| 15035 <param name="ignore_adduct" value="true"/> | |
| 15036 <section name="distance_RT"> | |
| 15037 <param name="max_difference" value="30.0"/> | |
| 15038 <param name="exponent" value="1.0"/> | |
| 15039 <param name="weight" value="1.0"/> | |
| 15040 </section> | |
| 15041 <section name="distance_MZ"> | |
| 15042 <param name="max_difference" value="0.3"/> | |
| 15043 <param name="unit" value="Da"/> | |
| 15044 <param name="exponent" value="2.0"/> | |
| 15045 <param name="weight" value="1.0"/> | |
| 15046 </section> | |
| 15047 <section name="distance_intensity"> | |
| 15048 <param name="exponent" value="1.0"/> | |
| 15049 <param name="weight" value="0.0"/> | |
| 15050 <param name="log_transform" value="disabled"/> | |
| 15051 </section> | |
| 15052 </section> | |
| 15053 </section> | |
| 15054 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15055 <output name="ctd_out" ftype="xml"> | |
| 15056 <assert_contents> | |
| 15057 <is_valid_xml/> | |
| 15058 </assert_contents> | |
| 15059 </output> | |
| 15060 </test> | |
| 15061 <test expect_num_outputs="2"> | |
| 15062 <conditional name="adv_opts_cond"> | |
| 15063 <param name="adv_opts_selector" value="advanced"/> | |
| 15064 <param name="force" value="false"/> | |
| 15065 <param name="test" value="true"/> | |
| 15066 </conditional> | |
| 15067 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/> | |
| 15068 <output_collection name="trafo_out" count="2"/> | |
| 15069 <section name="reference"> | |
| 15070 <param name="index" value="2"/> | |
| 15071 </section> | |
| 15072 <section name="algorithm"> | |
| 15073 <param name="max_num_peaks_considered" value="400"/> | |
| 15074 <section name="superimposer"> | |
| 15075 <param name="mz_pair_max_distance" value="0.5"/> | |
| 15076 <param name="rt_pair_distance_fraction" value="0.1"/> | |
| 15077 <param name="num_used_points" value="2000"/> | |
| 15078 <param name="scaling_bucket_size" value="0.005"/> | |
| 15079 <param name="shift_bucket_size" value="3.0"/> | |
| 15080 <param name="max_shift" value="1000.0"/> | |
| 15081 <param name="max_scaling" value="2.0"/> | |
| 15082 <param name="dump_buckets" value=""/> | |
| 15083 <param name="dump_pairs" value=""/> | |
| 15084 </section> | |
| 15085 <section name="pairfinder"> | |
| 15086 <param name="second_nearest_gap" value="2.0"/> | |
| 15087 <param name="use_identifications" value="false"/> | |
| 15088 <param name="ignore_charge" value="true"/> | |
| 15089 <param name="ignore_adduct" value="true"/> | |
| 15090 <section name="distance_RT"> | |
| 15091 <param name="max_difference" value="30.0"/> | |
| 15092 <param name="exponent" value="1.0"/> | |
| 15093 <param name="weight" value="1.0"/> | |
| 15094 </section> | |
| 15095 <section name="distance_MZ"> | |
| 15096 <param name="max_difference" value="0.3"/> | |
| 15097 <param name="unit" value="Da"/> | |
| 15098 <param name="exponent" value="2.0"/> | |
| 15099 <param name="weight" value="1.0"/> | |
| 15100 </section> | |
| 15101 <section name="distance_intensity"> | |
| 15102 <param name="exponent" value="1.0"/> | |
| 15103 <param name="weight" value="0.0"/> | |
| 15104 <param name="log_transform" value="disabled"/> | |
| 15105 </section> | |
| 15106 </section> | |
| 15107 </section> | |
| 15108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> | |
| 15109 <output name="ctd_out" ftype="xml"> | |
| 15110 <assert_contents> | |
| 15111 <is_valid_xml/> | |
| 15112 </assert_contents> | |
| 15113 </output> | |
| 15114 </test> | |
| 15115 </xml> | |
| 15116 <xml name="autotest_MapAlignerSpectrum"> | |
| 15117 <test expect_num_outputs="2"> | |
| 15118 <conditional name="adv_opts_cond"> | |
| 15119 <param name="adv_opts_selector" value="advanced"/> | |
| 15120 <param name="force" value="false"/> | |
| 15121 <param name="test" value="true"/> | |
| 15122 </conditional> | |
| 15123 <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/> | |
| 15124 <output_collection name="out" count="3"/> | |
| 15125 <section name="algorithm"> | |
| 15126 <param name="gapcost" value="1.0"/> | |
| 15127 <param name="affinegapcost" value="0.5"/> | |
| 15128 <param name="cutoff_score" value="0.7"/> | |
| 15129 <param name="bucketsize" value="100"/> | |
| 15130 <param name="anchorpoints" value="100"/> | |
| 15131 <param name="mismatchscore" value="-5.0"/> | |
| 15132 <param name="scorefunction" value="SteinScottImproveScore"/> | |
| 15133 </section> | |
| 15134 <section name="model"> | |
| 15135 <param name="type" value="interpolated"/> | |
| 15136 <section name="linear"> | |
| 15137 <param name="symmetric_regression" value="false"/> | |
| 15138 <param name="x_weight" value=""/> | |
| 15139 <param name="y_weight" value=""/> | |
| 15140 <param name="x_datum_min" value="1e-15"/> | |
| 15141 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15142 <param name="y_datum_min" value="1e-15"/> | |
| 15143 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15144 </section> | |
| 15145 <section name="b_spline"> | |
| 15146 <param name="wavelength" value="0.0"/> | |
| 15147 <param name="num_nodes" value="5"/> | |
| 15148 <param name="extrapolate" value="linear"/> | |
| 15149 <param name="boundary_condition" value="2"/> | |
| 15150 </section> | |
| 15151 <section name="lowess"> | |
| 15152 <param name="span" value="0.666666666666667"/> | |
| 15153 <param name="num_iterations" value="3"/> | |
| 15154 <param name="delta" value="-1.0"/> | |
| 15155 <param name="interpolation_type" value="cspline"/> | |
| 15156 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15157 </section> | |
| 15158 <section name="interpolated"> | |
| 15159 <param name="interpolation_type" value="cspline"/> | |
| 15160 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15161 </section> | |
| 15162 </section> | |
| 15163 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15164 <output name="ctd_out" ftype="xml"> | |
| 15165 <assert_contents> | |
| 15166 <is_valid_xml/> | |
| 15167 </assert_contents> | |
| 15168 </output> | |
| 15169 </test> | |
| 15170 </xml> | |
| 15171 <xml name="autotest_MapAlignerTreeGuided"> | |
| 15172 <test expect_num_outputs="2"> | |
| 15173 <conditional name="adv_opts_cond"> | |
| 15174 <param name="adv_opts_selector" value="advanced"/> | |
| 15175 <param name="force" value="false"/> | |
| 15176 <param name="test" value="true"/> | |
| 15177 </conditional> | |
| 15178 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> | |
| 15179 <output_collection name="out" count="3"/> | |
| 15180 <section name="algorithm"> | |
| 15181 <param name="model_type" value="b_spline"/> | |
| 15182 <section name="model"> | |
| 15183 <param name="type" value="b_spline"/> | |
| 15184 <section name="linear"> | |
| 15185 <param name="symmetric_regression" value="false"/> | |
| 15186 <param name="x_weight" value=""/> | |
| 15187 <param name="y_weight" value=""/> | |
| 15188 <param name="x_datum_min" value="1e-15"/> | |
| 15189 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15190 <param name="y_datum_min" value="1e-15"/> | |
| 15191 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15192 </section> | |
| 15193 <section name="b_spline"> | |
| 15194 <param name="wavelength" value="0.0"/> | |
| 15195 <param name="num_nodes" value="5"/> | |
| 15196 <param name="extrapolate" value="linear"/> | |
| 15197 <param name="boundary_condition" value="2"/> | |
| 15198 </section> | |
| 15199 <section name="lowess"> | |
| 15200 <param name="span" value="0.666666666666667"/> | |
| 15201 <param name="num_iterations" value="3"/> | |
| 15202 <param name="delta" value="-1.0"/> | |
| 15203 <param name="interpolation_type" value="cspline"/> | |
| 15204 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15205 </section> | |
| 15206 <section name="interpolated"> | |
| 15207 <param name="interpolation_type" value="cspline"/> | |
| 15208 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15209 </section> | |
| 15210 </section> | |
| 15211 <section name="align_algorithm"> | |
| 15212 <param name="score_cutoff" value="false"/> | |
| 15213 <param name="min_score" value="0.05"/> | |
| 15214 <param name="min_run_occur" value="2"/> | |
| 15215 <param name="max_rt_shift" value="0.5"/> | |
| 15216 <param name="use_unassigned_peptides" value="true"/> | |
| 15217 <param name="use_feature_rt" value="true"/> | |
| 15218 </section> | |
| 15219 </section> | |
| 15220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15221 <output name="ctd_out" ftype="xml"> | |
| 15222 <assert_contents> | |
| 15223 <is_valid_xml/> | |
| 15224 </assert_contents> | |
| 15225 </output> | |
| 15226 </test> | |
| 15227 <test expect_num_outputs="2"> | |
| 15228 <conditional name="adv_opts_cond"> | |
| 15229 <param name="adv_opts_selector" value="advanced"/> | |
| 15230 <param name="force" value="false"/> | |
| 15231 <param name="test" value="true"/> | |
| 15232 </conditional> | |
| 15233 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> | |
| 15234 <output_collection name="trafo_out" count="3"/> | |
| 15235 <section name="algorithm"> | |
| 15236 <param name="model_type" value="b_spline"/> | |
| 15237 <section name="model"> | |
| 15238 <param name="type" value="b_spline"/> | |
| 15239 <section name="linear"> | |
| 15240 <param name="symmetric_regression" value="false"/> | |
| 15241 <param name="x_weight" value=""/> | |
| 15242 <param name="y_weight" value=""/> | |
| 15243 <param name="x_datum_min" value="1e-15"/> | |
| 15244 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15245 <param name="y_datum_min" value="1e-15"/> | |
| 15246 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15247 </section> | |
| 15248 <section name="b_spline"> | |
| 15249 <param name="wavelength" value="0.0"/> | |
| 15250 <param name="num_nodes" value="5"/> | |
| 15251 <param name="extrapolate" value="linear"/> | |
| 15252 <param name="boundary_condition" value="2"/> | |
| 15253 </section> | |
| 15254 <section name="lowess"> | |
| 15255 <param name="span" value="0.666666666666667"/> | |
| 15256 <param name="num_iterations" value="3"/> | |
| 15257 <param name="delta" value="-1.0"/> | |
| 15258 <param name="interpolation_type" value="cspline"/> | |
| 15259 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15260 </section> | |
| 15261 <section name="interpolated"> | |
| 15262 <param name="interpolation_type" value="cspline"/> | |
| 15263 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15264 </section> | |
| 15265 </section> | |
| 15266 <section name="align_algorithm"> | |
| 15267 <param name="score_cutoff" value="false"/> | |
| 15268 <param name="min_score" value="0.05"/> | |
| 15269 <param name="min_run_occur" value="2"/> | |
| 15270 <param name="max_rt_shift" value="0.5"/> | |
| 15271 <param name="use_unassigned_peptides" value="true"/> | |
| 15272 <param name="use_feature_rt" value="true"/> | |
| 15273 </section> | |
| 15274 </section> | |
| 15275 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> | |
| 15276 <output name="ctd_out" ftype="xml"> | |
| 15277 <assert_contents> | |
| 15278 <is_valid_xml/> | |
| 15279 </assert_contents> | |
| 15280 </output> | |
| 15281 </test> | |
| 15282 </xml> | |
| 15283 <xml name="autotest_MapNormalizer"> | |
| 15284 <test expect_num_outputs="2"> | |
| 15285 <conditional name="adv_opts_cond"> | |
| 15286 <param name="adv_opts_selector" value="advanced"/> | |
| 15287 <param name="force" value="false"/> | |
| 15288 <param name="test" value="true"/> | |
| 15289 </conditional> | |
| 15290 <param name="in" value="MapNormalizer_input.mzML"/> | |
| 15291 <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 15292 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15293 <output name="ctd_out" ftype="xml"> | |
| 15294 <assert_contents> | |
| 15295 <is_valid_xml/> | |
| 15296 </assert_contents> | |
| 15297 </output> | |
| 15298 </test> | |
| 15299 </xml> | |
| 15300 <xml name="autotest_MapRTTransformer"> | |
| 15301 <test expect_num_outputs="2"> | |
| 15302 <conditional name="adv_opts_cond"> | |
| 15303 <param name="adv_opts_selector" value="advanced"/> | |
| 15304 <param name="force" value="false"/> | |
| 15305 <param name="test" value="true"/> | |
| 15306 </conditional> | |
| 15307 <param name="in" value="MapRTTransformer_1_input.featureXML"/> | |
| 15308 <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 15309 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> | |
| 15310 <param name="invert" value="false"/> | |
| 15311 <param name="store_original_rt" value="false"/> | |
| 15312 <section name="model"> | |
| 15313 <param name="type" value="none"/> | |
| 15314 <section name="linear"> | |
| 15315 <param name="symmetric_regression" value="false"/> | |
| 15316 <param name="x_weight" value=""/> | |
| 15317 <param name="y_weight" value=""/> | |
| 15318 <param name="x_datum_min" value="1e-15"/> | |
| 15319 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15320 <param name="y_datum_min" value="1e-15"/> | |
| 15321 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15322 </section> | |
| 15323 <section name="b_spline"> | |
| 15324 <param name="wavelength" value="0.0"/> | |
| 15325 <param name="num_nodes" value="5"/> | |
| 15326 <param name="extrapolate" value="linear"/> | |
| 15327 <param name="boundary_condition" value="2"/> | |
| 15328 </section> | |
| 15329 <section name="lowess"> | |
| 15330 <param name="span" value="0.666666666666667"/> | |
| 15331 <param name="num_iterations" value="3"/> | |
| 15332 <param name="delta" value="-1.0"/> | |
| 15333 <param name="interpolation_type" value="cspline"/> | |
| 15334 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15335 </section> | |
| 15336 <section name="interpolated"> | |
| 15337 <param name="interpolation_type" value="cspline"/> | |
| 15338 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15339 </section> | |
| 15340 </section> | |
| 15341 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15342 <output name="ctd_out" ftype="xml"> | |
| 15343 <assert_contents> | |
| 15344 <is_valid_xml/> | |
| 15345 </assert_contents> | |
| 15346 </output> | |
| 15347 </test> | |
| 15348 <test expect_num_outputs="2"> | |
| 15349 <conditional name="adv_opts_cond"> | |
| 15350 <param name="adv_opts_selector" value="advanced"/> | |
| 15351 <param name="force" value="false"/> | |
| 15352 <param name="test" value="true"/> | |
| 15353 </conditional> | |
| 15354 <param name="in" value="MapRTTransformer_2_input.mzML"/> | |
| 15355 <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 15356 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> | |
| 15357 <param name="invert" value="false"/> | |
| 15358 <param name="store_original_rt" value="false"/> | |
| 15359 <section name="model"> | |
| 15360 <param name="type" value="none"/> | |
| 15361 <section name="linear"> | |
| 15362 <param name="symmetric_regression" value="false"/> | |
| 15363 <param name="x_weight" value=""/> | |
| 15364 <param name="y_weight" value=""/> | |
| 15365 <param name="x_datum_min" value="1e-15"/> | |
| 15366 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15367 <param name="y_datum_min" value="1e-15"/> | |
| 15368 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15369 </section> | |
| 15370 <section name="b_spline"> | |
| 15371 <param name="wavelength" value="0.0"/> | |
| 15372 <param name="num_nodes" value="5"/> | |
| 15373 <param name="extrapolate" value="linear"/> | |
| 15374 <param name="boundary_condition" value="2"/> | |
| 15375 </section> | |
| 15376 <section name="lowess"> | |
| 15377 <param name="span" value="0.666666666666667"/> | |
| 15378 <param name="num_iterations" value="3"/> | |
| 15379 <param name="delta" value="-1.0"/> | |
| 15380 <param name="interpolation_type" value="cspline"/> | |
| 15381 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15382 </section> | |
| 15383 <section name="interpolated"> | |
| 15384 <param name="interpolation_type" value="cspline"/> | |
| 15385 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15386 </section> | |
| 15387 </section> | |
| 15388 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15389 <output name="ctd_out" ftype="xml"> | |
| 15390 <assert_contents> | |
| 15391 <is_valid_xml/> | |
| 15392 </assert_contents> | |
| 15393 </output> | |
| 15394 </test> | |
| 15395 <test expect_num_outputs="2"> | |
| 15396 <conditional name="adv_opts_cond"> | |
| 15397 <param name="adv_opts_selector" value="advanced"/> | |
| 15398 <param name="force" value="false"/> | |
| 15399 <param name="test" value="true"/> | |
| 15400 </conditional> | |
| 15401 <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/> | |
| 15402 <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> | |
| 15403 <param name="invert" value="true"/> | |
| 15404 <param name="store_original_rt" value="false"/> | |
| 15405 <section name="model"> | |
| 15406 <param name="type" value="none"/> | |
| 15407 <section name="linear"> | |
| 15408 <param name="symmetric_regression" value="false"/> | |
| 15409 <param name="x_weight" value=""/> | |
| 15410 <param name="y_weight" value=""/> | |
| 15411 <param name="x_datum_min" value="1e-15"/> | |
| 15412 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15413 <param name="y_datum_min" value="1e-15"/> | |
| 15414 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15415 </section> | |
| 15416 <section name="b_spline"> | |
| 15417 <param name="wavelength" value="0.0"/> | |
| 15418 <param name="num_nodes" value="5"/> | |
| 15419 <param name="extrapolate" value="linear"/> | |
| 15420 <param name="boundary_condition" value="2"/> | |
| 15421 </section> | |
| 15422 <section name="lowess"> | |
| 15423 <param name="span" value="0.666666666666667"/> | |
| 15424 <param name="num_iterations" value="3"/> | |
| 15425 <param name="delta" value="-1.0"/> | |
| 15426 <param name="interpolation_type" value="cspline"/> | |
| 15427 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15428 </section> | |
| 15429 <section name="interpolated"> | |
| 15430 <param name="interpolation_type" value="cspline"/> | |
| 15431 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15432 </section> | |
| 15433 </section> | |
| 15434 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> | |
| 15435 <output name="ctd_out" ftype="xml"> | |
| 15436 <assert_contents> | |
| 15437 <is_valid_xml/> | |
| 15438 </assert_contents> | |
| 15439 </output> | |
| 15440 </test> | |
| 15441 <test expect_num_outputs="2"> | |
| 15442 <conditional name="adv_opts_cond"> | |
| 15443 <param name="adv_opts_selector" value="advanced"/> | |
| 15444 <param name="force" value="false"/> | |
| 15445 <param name="test" value="true"/> | |
| 15446 </conditional> | |
| 15447 <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/> | |
| 15448 <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 15449 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> | |
| 15450 <param name="invert" value="false"/> | |
| 15451 <param name="store_original_rt" value="false"/> | |
| 15452 <section name="model"> | |
| 15453 <param name="type" value="none"/> | |
| 15454 <section name="linear"> | |
| 15455 <param name="symmetric_regression" value="false"/> | |
| 15456 <param name="x_weight" value=""/> | |
| 15457 <param name="y_weight" value=""/> | |
| 15458 <param name="x_datum_min" value="1e-15"/> | |
| 15459 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15460 <param name="y_datum_min" value="1e-15"/> | |
| 15461 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15462 </section> | |
| 15463 <section name="b_spline"> | |
| 15464 <param name="wavelength" value="0.0"/> | |
| 15465 <param name="num_nodes" value="5"/> | |
| 15466 <param name="extrapolate" value="linear"/> | |
| 15467 <param name="boundary_condition" value="2"/> | |
| 15468 </section> | |
| 15469 <section name="lowess"> | |
| 15470 <param name="span" value="0.666666666666667"/> | |
| 15471 <param name="num_iterations" value="3"/> | |
| 15472 <param name="delta" value="-1.0"/> | |
| 15473 <param name="interpolation_type" value="cspline"/> | |
| 15474 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15475 </section> | |
| 15476 <section name="interpolated"> | |
| 15477 <param name="interpolation_type" value="cspline"/> | |
| 15478 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15479 </section> | |
| 15480 </section> | |
| 15481 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15482 <output name="ctd_out" ftype="xml"> | |
| 15483 <assert_contents> | |
| 15484 <is_valid_xml/> | |
| 15485 </assert_contents> | |
| 15486 </output> | |
| 15487 </test> | |
| 15488 <test expect_num_outputs="2"> | |
| 15489 <conditional name="adv_opts_cond"> | |
| 15490 <param name="adv_opts_selector" value="advanced"/> | |
| 15491 <param name="force" value="false"/> | |
| 15492 <param name="test" value="true"/> | |
| 15493 </conditional> | |
| 15494 <param name="in" value="MapRTTransformer_1_input.featureXML"/> | |
| 15495 <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 15496 <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/> | |
| 15497 <param name="invert" value="false"/> | |
| 15498 <param name="store_original_rt" value="false"/> | |
| 15499 <section name="model"> | |
| 15500 <param name="type" value="none"/> | |
| 15501 <section name="linear"> | |
| 15502 <param name="symmetric_regression" value="false"/> | |
| 15503 <param name="x_weight" value=""/> | |
| 15504 <param name="y_weight" value=""/> | |
| 15505 <param name="x_datum_min" value="1e-15"/> | |
| 15506 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15507 <param name="y_datum_min" value="1e-15"/> | |
| 15508 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15509 </section> | |
| 15510 <section name="b_spline"> | |
| 15511 <param name="wavelength" value="0.0"/> | |
| 15512 <param name="num_nodes" value="5"/> | |
| 15513 <param name="extrapolate" value="linear"/> | |
| 15514 <param name="boundary_condition" value="2"/> | |
| 15515 </section> | |
| 15516 <section name="lowess"> | |
| 15517 <param name="span" value="0.666666666666667"/> | |
| 15518 <param name="num_iterations" value="3"/> | |
| 15519 <param name="delta" value="-1.0"/> | |
| 15520 <param name="interpolation_type" value="cspline"/> | |
| 15521 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15522 </section> | |
| 15523 <section name="interpolated"> | |
| 15524 <param name="interpolation_type" value="cspline"/> | |
| 15525 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15526 </section> | |
| 15527 </section> | |
| 15528 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15529 <output name="ctd_out" ftype="xml"> | |
| 15530 <assert_contents> | |
| 15531 <is_valid_xml/> | |
| 15532 </assert_contents> | |
| 15533 </output> | |
| 15534 </test> | |
| 15535 <test expect_num_outputs="2"> | |
| 15536 <conditional name="adv_opts_cond"> | |
| 15537 <param name="adv_opts_selector" value="advanced"/> | |
| 15538 <param name="force" value="false"/> | |
| 15539 <param name="test" value="true"/> | |
| 15540 </conditional> | |
| 15541 <param name="in" value="MapRTTransformer_1_input.featureXML"/> | |
| 15542 <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 15543 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> | |
| 15544 <param name="invert" value="false"/> | |
| 15545 <param name="store_original_rt" value="true"/> | |
| 15546 <section name="model"> | |
| 15547 <param name="type" value="none"/> | |
| 15548 <section name="linear"> | |
| 15549 <param name="symmetric_regression" value="false"/> | |
| 15550 <param name="x_weight" value=""/> | |
| 15551 <param name="y_weight" value=""/> | |
| 15552 <param name="x_datum_min" value="1e-15"/> | |
| 15553 <param name="x_datum_max" value="1000000000000000.0"/> | |
| 15554 <param name="y_datum_min" value="1e-15"/> | |
| 15555 <param name="y_datum_max" value="1000000000000000.0"/> | |
| 15556 </section> | |
| 15557 <section name="b_spline"> | |
| 15558 <param name="wavelength" value="0.0"/> | |
| 15559 <param name="num_nodes" value="5"/> | |
| 15560 <param name="extrapolate" value="linear"/> | |
| 15561 <param name="boundary_condition" value="2"/> | |
| 15562 </section> | |
| 15563 <section name="lowess"> | |
| 15564 <param name="span" value="0.666666666666667"/> | |
| 15565 <param name="num_iterations" value="3"/> | |
| 15566 <param name="delta" value="-1.0"/> | |
| 15567 <param name="interpolation_type" value="cspline"/> | |
| 15568 <param name="extrapolation_type" value="four-point-linear"/> | |
| 15569 </section> | |
| 15570 <section name="interpolated"> | |
| 15571 <param name="interpolation_type" value="cspline"/> | |
| 15572 <param name="extrapolation_type" value="two-point-linear"/> | |
| 15573 </section> | |
| 15574 </section> | |
| 15575 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15576 <output name="ctd_out" ftype="xml"> | |
| 15577 <assert_contents> | |
| 15578 <is_valid_xml/> | |
| 15579 </assert_contents> | |
| 15580 </output> | |
| 15581 </test> | |
| 15582 </xml> | |
| 15583 <xml name="autotest_MapStatistics"> | |
| 15584 </xml> | |
| 15585 <xml name="autotest_MaRaClusterAdapter"/> | |
| 15586 <xml name="autotest_MascotAdapterOnline"> | |
| 15587 <test expect_num_outputs="2"> | |
| 15588 <conditional name="adv_opts_cond"> | |
| 15589 <param name="adv_opts_selector" value="advanced"/> | |
| 15590 <param name="keep_protein_links" value="true"/> | |
| 15591 <param name="force" value="false"/> | |
| 15592 <param name="test" value="true"/> | |
| 15593 </conditional> | |
| 15594 <param name="in" value="spectra_comet.mzML"/> | |
| 15595 <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 15596 <section name="Mascot_parameters"> | |
| 15597 <param name="database" value="SwissProt"/> | |
| 15598 <param name="search_type" value="MIS"/> | |
| 15599 <param name="enzyme" value="Trypsin"/> | |
| 15600 <param name="instrument" value="Default"/> | |
| 15601 <param name="missed_cleavages" value="1"/> | |
| 15602 <param name="precursor_mass_tolerance" value="3.0"/> | |
| 15603 <param name="precursor_error_units" value="Da"/> | |
| 15604 <param name="fragment_mass_tolerance" value="0.3"/> | |
| 15605 <param name="fragment_error_units" value="Da"/> | |
| 15606 <param name="charges" value="1,2,3"/> | |
| 15607 <param name="taxonomy" value="All entries"/> | |
| 15608 <param name="fixed_modifications" value=""/> | |
| 15609 <param name="variable_modifications" value=""/> | |
| 15610 <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/> | |
| 15611 <param name="mass_type" value="monoisotopic"/> | |
| 15612 <param name="number_of_hits" value="0"/> | |
| 15613 <param name="skip_spectrum_charges" value="false"/> | |
| 15614 <param name="search_title" value="OpenMS_search"/> | |
| 15615 <param name="username" value="OpenMS"/> | |
| 15616 <param name="email" value="openmsjenkins@gmail.com"/> | |
| 15617 </section> | |
| 15618 <section name="Mascot_server"> | |
| 15619 <param name="hostname" value="www.matrixscience.com"/> | |
| 15620 <param name="host_port" value="80"/> | |
| 15621 <param name="server_path" value=""/> | |
| 15622 <param name="timeout" value="1500"/> | |
| 15623 <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/> | |
| 15624 <param name="use_proxy" value="false"/> | |
| 15625 <param name="proxy_host" value=""/> | |
| 15626 <param name="proxy_port" value="0"/> | |
| 15627 <param name="proxy_username" value=""/> | |
| 15628 <param name="proxy_password" value=""/> | |
| 15629 <param name="login" value="false"/> | |
| 15630 <param name="username" value=""/> | |
| 15631 <param name="password" value=""/> | |
| 15632 <param name="use_ssl" value="false"/> | |
| 15633 <param name="export_params" value="_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0"/> | |
| 15634 <param name="skip_export" value="false"/> | |
| 15635 </section> | |
| 15636 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15637 <output name="ctd_out" ftype="xml"> | |
| 15638 <assert_contents> | |
| 15639 <is_valid_xml/> | |
| 15640 </assert_contents> | |
| 15641 </output> | |
| 15642 </test> | |
| 15643 </xml> | |
| 15644 <xml name="autotest_MascotAdapter"> | |
| 15645 <test expect_num_outputs="2"> | |
| 15646 <conditional name="adv_opts_cond"> | |
| 15647 <param name="adv_opts_selector" value="advanced"/> | |
| 15648 <param name="force" value="false"/> | |
| 15649 <param name="test" value="true"/> | |
| 15650 </conditional> | |
| 15651 <param name="in" value="MascotAdapter_1_input.mzData"/> | |
| 15652 <output name="out" file="output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 15653 <param name="mascot_in" value="true"/> | |
| 15654 <param name="mascot_out" value="false"/> | |
| 15655 <param name="instrument" value="ESI-TRAP"/> | |
| 15656 <param name="precursor_mass_tolerance" value="1.3"/> | |
| 15657 <param name="peak_mass_tolerance" value="0.3"/> | |
| 15658 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> | |
| 15659 <param name="modifications" value=""Carboxymethyl (C)""/> | |
| 15660 <param name="variable_modifications" value=""Variable_Modifications_TEST_1""/> | |
| 15661 <param name="charges" value=""1+" "2+" "3+""/> | |
| 15662 <param name="db" value="MSDB"/> | |
| 15663 <param name="hits" value="AUTO"/> | |
| 15664 <param name="cleavage" value="Trypsin"/> | |
| 15665 <param name="missed_cleavages" value="1"/> | |
| 15666 <param name="sig_threshold" value="0.05"/> | |
| 15667 <param name="pep_homol" value="1.0"/> | |
| 15668 <param name="pep_ident" value="1.0"/> | |
| 15669 <param name="pep_rank" value="1"/> | |
| 15670 <param name="prot_score" value="1.0"/> | |
| 15671 <param name="pep_score" value="1.0"/> | |
| 15672 <param name="pep_exp_z" value="1"/> | |
| 15673 <param name="show_unassigned" value="1"/> | |
| 15674 <param name="first_dim_rt" value="0.0"/> | |
| 15675 <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/> | |
| 15676 <param name="mass_type" value="Monoisotopic"/> | |
| 15677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15678 <output name="ctd_out" ftype="xml"> | |
| 15679 <assert_contents> | |
| 15680 <is_valid_xml/> | |
| 15681 </assert_contents> | |
| 15682 </output> | |
| 15683 </test> | |
| 15684 <test expect_num_outputs="2"> | |
| 15685 <conditional name="adv_opts_cond"> | |
| 15686 <param name="adv_opts_selector" value="advanced"/> | |
| 15687 <param name="force" value="false"/> | |
| 15688 <param name="test" value="true"/> | |
| 15689 </conditional> | |
| 15690 <param name="in" value="MascotAdapter_2_input.mascotXML"/> | |
| 15691 <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 15692 <param name="mascot_in" value="false"/> | |
| 15693 <param name="mascot_out" value="true"/> | |
| 15694 <param name="instrument" value="Default"/> | |
| 15695 <param name="precursor_mass_tolerance" value="2.0"/> | |
| 15696 <param name="peak_mass_tolerance" value="1.0"/> | |
| 15697 <param name="taxonomy" value="All entries"/> | |
| 15698 <param name="modifications" value=""/> | |
| 15699 <param name="variable_modifications" value=""/> | |
| 15700 <param name="charges" value=""1+" "2+" "3+""/> | |
| 15701 <param name="db" value="MSDB"/> | |
| 15702 <param name="hits" value="AUTO"/> | |
| 15703 <param name="cleavage" value="Trypsin"/> | |
| 15704 <param name="missed_cleavages" value="0"/> | |
| 15705 <param name="sig_threshold" value="0.05"/> | |
| 15706 <param name="pep_homol" value="1.0"/> | |
| 15707 <param name="pep_ident" value="1.0"/> | |
| 15708 <param name="pep_rank" value="1"/> | |
| 15709 <param name="prot_score" value="1.0"/> | |
| 15710 <param name="pep_score" value="1.0"/> | |
| 15711 <param name="pep_exp_z" value="1"/> | |
| 15712 <param name="show_unassigned" value="1"/> | |
| 15713 <param name="first_dim_rt" value="0.0"/> | |
| 15714 <param name="boundary" value=""/> | |
| 15715 <param name="mass_type" value="Monoisotopic"/> | |
| 15716 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15717 <output name="ctd_out" ftype="xml"> | |
| 15718 <assert_contents> | |
| 15719 <is_valid_xml/> | |
| 15720 </assert_contents> | |
| 15721 </output> | |
| 15722 </test> | |
| 15723 </xml> | |
| 15724 <xml name="autotest_MassCalculator"> | |
| 15725 <test expect_num_outputs="2"> | |
| 15726 <conditional name="adv_opts_cond"> | |
| 15727 <param name="adv_opts_selector" value="advanced"/> | |
| 15728 <param name="force" value="false"/> | |
| 15729 <param name="test" value="true"/> | |
| 15730 </conditional> | |
| 15731 <param name="in" value="MassCalculator_1_input.txt" ftype="txt"/> | |
| 15732 <param name="in_seq" value=""/> | |
| 15733 <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="txt"/> | |
| 15734 <param name="charge" value="0 1"/> | |
| 15735 <param name="format" value="table"/> | |
| 15736 <param name="average_mass" value="false"/> | |
| 15737 <param name="fragment_type" value="full"/> | |
| 15738 <param name="separator" value=","/> | |
| 15739 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15740 <output name="ctd_out" ftype="xml"> | |
| 15741 <assert_contents> | |
| 15742 <is_valid_xml/> | |
| 15743 </assert_contents> | |
| 15744 </output> | |
| 15745 </test> | |
| 15746 <test expect_num_outputs="2"> | |
| 15747 <conditional name="adv_opts_cond"> | |
| 15748 <param name="adv_opts_selector" value="advanced"/> | |
| 15749 <param name="force" value="false"/> | |
| 15750 <param name="test" value="true"/> | |
| 15751 </conditional> | |
| 15752 <param name="in_seq" value=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> | |
| 15753 <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 15754 <param name="charge" value="1 2 3"/> | |
| 15755 <param name="format" value="list"/> | |
| 15756 <param name="average_mass" value="false"/> | |
| 15757 <param name="fragment_type" value="full"/> | |
| 15758 <param name="separator" value=""/> | |
| 15759 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 15760 <output name="ctd_out" ftype="xml"> | |
| 15761 <assert_contents> | |
| 15762 <is_valid_xml/> | |
| 15763 </assert_contents> | |
| 15764 </output> | |
| 15765 </test> | |
| 15766 </xml> | |
| 15767 <xml name="autotest_MassTraceExtractor"> | |
| 15768 <test expect_num_outputs="2"> | |
| 15769 <conditional name="adv_opts_cond"> | |
| 15770 <param name="adv_opts_selector" value="advanced"/> | |
| 15771 <param name="force" value="false"/> | |
| 15772 <param name="test" value="true"/> | |
| 15773 </conditional> | |
| 15774 <param name="in" value="MassTraceExtractor_1_input.mzML"/> | |
| 15775 <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 15776 <param name="out_type" value="featurexml"/> | |
| 15777 <section name="algorithm"> | |
| 15778 <section name="common"> | |
| 15779 <param name="noise_threshold_int" value="10.0"/> | |
| 15780 <param name="chrom_peak_snr" value="3.0"/> | |
| 15781 <param name="chrom_fwhm" value="5.0"/> | |
| 15782 </section> | |
| 15783 <section name="mtd"> | |
| 15784 <param name="mass_error_ppm" value="20.0"/> | |
| 15785 <param name="reestimate_mt_sd" value="true"/> | |
| 15786 <param name="quant_method" value="area"/> | |
| 15787 <param name="trace_termination_criterion" value="outlier"/> | |
| 15788 <param name="trace_termination_outliers" value="5"/> | |
| 15789 <param name="min_sample_rate" value="0.5"/> | |
| 15790 <param name="min_trace_length" value="5.0"/> | |
| 15791 <param name="max_trace_length" value="-1.0"/> | |
| 15792 </section> | |
| 15793 <section name="epd"> | |
| 15794 <param name="width_filtering" value="off"/> | |
| 15795 <param name="min_fwhm" value="3.0"/> | |
| 15796 <param name="max_fwhm" value="60.0"/> | |
| 15797 <param name="masstrace_snr_filtering" value="false"/> | |
| 15798 <param name="enabled" value="true"/> | |
| 15799 </section> | |
| 15800 </section> | |
| 15801 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15802 <output name="ctd_out" ftype="xml"> | |
| 15803 <assert_contents> | |
| 15804 <is_valid_xml/> | |
| 15805 </assert_contents> | |
| 15806 </output> | |
| 15807 </test> | |
| 15808 <test expect_num_outputs="2"> | |
| 15809 <conditional name="adv_opts_cond"> | |
| 15810 <param name="adv_opts_selector" value="advanced"/> | |
| 15811 <param name="force" value="false"/> | |
| 15812 <param name="test" value="true"/> | |
| 15813 </conditional> | |
| 15814 <param name="in" value="MassTraceExtractor_1_input.mzML"/> | |
| 15815 <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 15816 <param name="out_type" value="featurexml"/> | |
| 15817 <section name="algorithm"> | |
| 15818 <section name="common"> | |
| 15819 <param name="noise_threshold_int" value="10.0"/> | |
| 15820 <param name="chrom_peak_snr" value="3.0"/> | |
| 15821 <param name="chrom_fwhm" value="5.0"/> | |
| 15822 </section> | |
| 15823 <section name="mtd"> | |
| 15824 <param name="mass_error_ppm" value="20.0"/> | |
| 15825 <param name="reestimate_mt_sd" value="true"/> | |
| 15826 <param name="quant_method" value="area"/> | |
| 15827 <param name="trace_termination_criterion" value="outlier"/> | |
| 15828 <param name="trace_termination_outliers" value="5"/> | |
| 15829 <param name="min_sample_rate" value="0.5"/> | |
| 15830 <param name="min_trace_length" value="6.0"/> | |
| 15831 <param name="max_trace_length" value="12.0"/> | |
| 15832 </section> | |
| 15833 <section name="epd"> | |
| 15834 <param name="width_filtering" value="off"/> | |
| 15835 <param name="min_fwhm" value="3.0"/> | |
| 15836 <param name="max_fwhm" value="60.0"/> | |
| 15837 <param name="masstrace_snr_filtering" value="false"/> | |
| 15838 <param name="enabled" value="true"/> | |
| 15839 </section> | |
| 15840 </section> | |
| 15841 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15842 <output name="ctd_out" ftype="xml"> | |
| 15843 <assert_contents> | |
| 15844 <is_valid_xml/> | |
| 15845 </assert_contents> | |
| 15846 </output> | |
| 15847 </test> | |
| 15848 </xml> | |
| 15849 <xml name="autotest_MetaboliteAdductDecharger"> | |
| 15850 </xml> | |
| 15851 <xml name="autotest_MetaboliteSpectralMatcher"> | |
| 15852 </xml> | |
| 15853 <xml name="autotest_MetaProSIP"> | |
| 15854 <test expect_num_outputs="3"> | |
| 15855 <conditional name="adv_opts_cond"> | |
| 15856 <param name="adv_opts_selector" value="advanced"/> | |
| 15857 <param name="min_correlation_distance_to_averagine" value="-1.0"/> | |
| 15858 <param name="pattern_15N_TIC_threshold" value="0.95"/> | |
| 15859 <param name="pattern_13C_TIC_threshold" value="0.95"/> | |
| 15860 <param name="pattern_2H_TIC_threshold" value="0.95"/> | |
| 15861 <param name="pattern_18O_TIC_threshold" value="0.95"/> | |
| 15862 <param name="heatmap_bins" value="20"/> | |
| 15863 <param name="observed_peak_fraction" value="0.5"/> | |
| 15864 <param name="min_consecutive_isotopes" value="2"/> | |
| 15865 <param name="score_plot_yaxis_min" value="0.0"/> | |
| 15866 <param name="collect_method" value="correlation_maximum"/> | |
| 15867 <param name="lowRIA_correlation_threshold" value="-1.0"/> | |
| 15868 <param name="force" value="false"/> | |
| 15869 <param name="test" value="true"/> | |
| 15870 </conditional> | |
| 15871 <param name="in_mzML" value="MetaProSIP_1_input.mzML"/> | |
| 15872 <param name="in_fasta" value="MetaProSIP_1_input.fasta"/> | |
| 15873 <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 15874 <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 15875 <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/> | |
| 15876 <param name="mz_tolerance_ppm" value="10.0"/> | |
| 15877 <param name="rt_tolerance_s" value="30.0"/> | |
| 15878 <param name="intensity_threshold" value="10.0"/> | |
| 15879 <param name="correlation_threshold" value="0.7"/> | |
| 15880 <param name="xic_threshold" value="0.7"/> | |
| 15881 <param name="decomposition_threshold" value="0.7"/> | |
| 15882 <param name="weight_merge_window" value="5.0"/> | |
| 15883 <param name="plot_extension" value="png"/> | |
| 15884 <param name="qc_output_directory" value=""/> | |
| 15885 <param name="labeling_element" value="C"/> | |
| 15886 <param name="use_unassigned_ids" value="false"/> | |
| 15887 <param name="use_averagine_ids" value="false"/> | |
| 15888 <param name="report_natural_peptides" value="false"/> | |
| 15889 <param name="filter_monoisotopic" value="false"/> | |
| 15890 <param name="cluster" value="false"/> | |
| 15891 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15892 <output name="ctd_out" ftype="xml"> | |
| 15893 <assert_contents> | |
| 15894 <is_valid_xml/> | |
| 15895 </assert_contents> | |
| 15896 </output> | |
| 15897 </test> | |
| 15898 </xml> | |
| 15899 <xml name="autotest_MRMMapper"> | |
| 15900 <test expect_num_outputs="2"> | |
| 15901 <conditional name="adv_opts_cond"> | |
| 15902 <param name="adv_opts_selector" value="advanced"/> | |
| 15903 <param name="force" value="false"/> | |
| 15904 <param name="test" value="true"/> | |
| 15905 </conditional> | |
| 15906 <param name="in" value="MRMMapping_input.chrom.mzML"/> | |
| 15907 <param name="tr" value="MRMMapping_input.TraML"/> | |
| 15908 <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 15909 <section name="algorithm"> | |
| 15910 <param name="precursor_tolerance" value="0.3"/> | |
| 15911 <param name="product_tolerance" value="0.3"/> | |
| 15912 <param name="map_multiple_assays" value="false"/> | |
| 15913 <param name="error_on_unmapped" value="false"/> | |
| 15914 </section> | |
| 15915 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15916 <output name="ctd_out" ftype="xml"> | |
| 15917 <assert_contents> | |
| 15918 <is_valid_xml/> | |
| 15919 </assert_contents> | |
| 15920 </output> | |
| 15921 </test> | |
| 15922 <test expect_num_outputs="2"> | |
| 15923 <conditional name="adv_opts_cond"> | |
| 15924 <param name="adv_opts_selector" value="advanced"/> | |
| 15925 <param name="force" value="false"/> | |
| 15926 <param name="test" value="true"/> | |
| 15927 </conditional> | |
| 15928 <param name="in" value="MRMMapping_input.chrom.mzML"/> | |
| 15929 <param name="tr" value="MRMMapping_input_2.TraML"/> | |
| 15930 <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 15931 <section name="algorithm"> | |
| 15932 <param name="precursor_tolerance" value="0.01"/> | |
| 15933 <param name="product_tolerance" value="0.01"/> | |
| 15934 <param name="map_multiple_assays" value="false"/> | |
| 15935 <param name="error_on_unmapped" value="false"/> | |
| 15936 </section> | |
| 15937 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15938 <output name="ctd_out" ftype="xml"> | |
| 15939 <assert_contents> | |
| 15940 <is_valid_xml/> | |
| 15941 </assert_contents> | |
| 15942 </output> | |
| 15943 </test> | |
| 15944 </xml> | |
| 15945 <xml name="autotest_MRMPairFinder"> | |
| 15946 </xml> | |
| 15947 <xml name="autotest_MRMTransitionGroupPicker"> | |
| 15948 <test expect_num_outputs="2"> | |
| 15949 <conditional name="adv_opts_cond"> | |
| 15950 <param name="adv_opts_selector" value="advanced"/> | |
| 15951 <param name="force" value="false"/> | |
| 15952 <param name="test" value="true"/> | |
| 15953 </conditional> | |
| 15954 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> | |
| 15955 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> | |
| 15956 <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 15957 <section name="algorithm"> | |
| 15958 <param name="stop_after_feature" value="-1"/> | |
| 15959 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 15960 <param name="min_peak_width" value="-1.0"/> | |
| 15961 <param name="peak_integration" value="original"/> | |
| 15962 <param name="background_subtraction" value="none"/> | |
| 15963 <param name="recalculate_peaks" value="false"/> | |
| 15964 <param name="use_precursors" value="false"/> | |
| 15965 <param name="use_consensus" value="true"/> | |
| 15966 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 15967 <param name="minimal_quality" value="-10000.0"/> | |
| 15968 <param name="resample_boundary" value="15.0"/> | |
| 15969 <param name="compute_peak_quality" value="false"/> | |
| 15970 <param name="compute_peak_shape_metrics" value="false"/> | |
| 15971 <param name="compute_total_mi" value="false"/> | |
| 15972 <param name="boundary_selection_method" value="largest"/> | |
| 15973 <section name="PeakPickerMRM"> | |
| 15974 <param name="sgolay_frame_length" value="15"/> | |
| 15975 <param name="sgolay_polynomial_order" value="3"/> | |
| 15976 <param name="gauss_width" value="50.0"/> | |
| 15977 <param name="use_gauss" value="true"/> | |
| 15978 <param name="peak_width" value="40.0"/> | |
| 15979 <param name="signal_to_noise" value="1.0"/> | |
| 15980 <param name="sn_win_len" value="1000.0"/> | |
| 15981 <param name="sn_bin_count" value="30"/> | |
| 15982 <param name="write_sn_log_messages" value="false"/> | |
| 15983 <param name="remove_overlapping_peaks" value="true"/> | |
| 15984 <param name="method" value="legacy"/> | |
| 15985 </section> | |
| 15986 <section name="PeakIntegrator"> | |
| 15987 <param name="integration_type" value="intensity_sum"/> | |
| 15988 <param name="baseline_type" value="base_to_base"/> | |
| 15989 <param name="fit_EMG" value="false"/> | |
| 15990 </section> | |
| 15991 </section> | |
| 15992 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 15993 <output name="ctd_out" ftype="xml"> | |
| 15994 <assert_contents> | |
| 15995 <is_valid_xml/> | |
| 15996 </assert_contents> | |
| 15997 </output> | |
| 15998 </test> | |
| 15999 <test expect_num_outputs="2"> | |
| 16000 <conditional name="adv_opts_cond"> | |
| 16001 <param name="adv_opts_selector" value="advanced"/> | |
| 16002 <param name="force" value="false"/> | |
| 16003 <param name="test" value="true"/> | |
| 16004 </conditional> | |
| 16005 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> | |
| 16006 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> | |
| 16007 <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 16008 <section name="algorithm"> | |
| 16009 <param name="stop_after_feature" value="-1"/> | |
| 16010 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 16011 <param name="min_peak_width" value="-1.0"/> | |
| 16012 <param name="peak_integration" value="original"/> | |
| 16013 <param name="background_subtraction" value="none"/> | |
| 16014 <param name="recalculate_peaks" value="false"/> | |
| 16015 <param name="use_precursors" value="false"/> | |
| 16016 <param name="use_consensus" value="true"/> | |
| 16017 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 16018 <param name="minimal_quality" value="-10000.0"/> | |
| 16019 <param name="resample_boundary" value="15.0"/> | |
| 16020 <param name="compute_peak_quality" value="false"/> | |
| 16021 <param name="compute_peak_shape_metrics" value="false"/> | |
| 16022 <param name="compute_total_mi" value="true"/> | |
| 16023 <param name="boundary_selection_method" value="largest"/> | |
| 16024 <section name="PeakPickerMRM"> | |
| 16025 <param name="sgolay_frame_length" value="15"/> | |
| 16026 <param name="sgolay_polynomial_order" value="3"/> | |
| 16027 <param name="gauss_width" value="50.0"/> | |
| 16028 <param name="use_gauss" value="true"/> | |
| 16029 <param name="peak_width" value="40.0"/> | |
| 16030 <param name="signal_to_noise" value="1.0"/> | |
| 16031 <param name="sn_win_len" value="1000.0"/> | |
| 16032 <param name="sn_bin_count" value="30"/> | |
| 16033 <param name="write_sn_log_messages" value="false"/> | |
| 16034 <param name="remove_overlapping_peaks" value="true"/> | |
| 16035 <param name="method" value="legacy"/> | |
| 16036 </section> | |
| 16037 <section name="PeakIntegrator"> | |
| 16038 <param name="integration_type" value="intensity_sum"/> | |
| 16039 <param name="baseline_type" value="base_to_base"/> | |
| 16040 <param name="fit_EMG" value="false"/> | |
| 16041 </section> | |
| 16042 </section> | |
| 16043 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16044 <output name="ctd_out" ftype="xml"> | |
| 16045 <assert_contents> | |
| 16046 <is_valid_xml/> | |
| 16047 </assert_contents> | |
| 16048 </output> | |
| 16049 </test> | |
| 16050 </xml> | |
| 16051 <xml name="autotest_MSFraggerAdapter"/> | |
| 16052 <xml name="autotest_MSGFPlusAdapter"> | |
| 16053 <test expect_num_outputs="3"> | |
| 16054 <conditional name="adv_opts_cond"> | |
| 16055 <param name="adv_opts_selector" value="advanced"/> | |
| 16056 <param name="legacy_conversion" value="false"/> | |
| 16057 <param name="force" value="false"/> | |
| 16058 <param name="test" value="true"/> | |
| 16059 </conditional> | |
| 16060 <param name="in" value="spectra.mzML"/> | |
| 16061 <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 16062 <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 16063 <param name="database" value="proteins.fasta"/> | |
| 16064 <param name="add_decoys" value="false"/> | |
| 16065 <param name="precursor_mass_tolerance" value="10.0"/> | |
| 16066 <param name="precursor_error_units" value="ppm"/> | |
| 16067 <param name="isotope_error_range" value="0,1"/> | |
| 16068 <param name="fragment_method" value="from_spectrum"/> | |
| 16069 <param name="instrument" value="high_res"/> | |
| 16070 <param name="enzyme" value="Trypsin/P"/> | |
| 16071 <param name="protocol" value="none"/> | |
| 16072 <param name="tryptic" value="fully"/> | |
| 16073 <param name="min_precursor_charge" value="1"/> | |
| 16074 <param name="max_precursor_charge" value="3"/> | |
| 16075 <param name="min_peptide_length" value="6"/> | |
| 16076 <param name="max_peptide_length" value="40"/> | |
| 16077 <param name="matches_per_spec" value="1"/> | |
| 16078 <param name="add_features" value="false"/> | |
| 16079 <param name="max_mods" value="2"/> | |
| 16080 <param name="fixed_modifications" value=""/> | |
| 16081 <param name="variable_modifications" value="Oxidation (M)"/> | |
| 16082 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/> | |
| 16083 <output name="ctd_out" ftype="xml"> | |
| 16084 <assert_contents> | |
| 16085 <is_valid_xml/> | |
| 16086 </assert_contents> | |
| 16087 </output> | |
| 16088 </test> | |
| 16089 </xml> | |
| 16090 <xml name="autotest_MSSimulator"> | |
| 16091 </xml> | |
| 16092 <xml name="autotest_MSstatsConverter"> | |
| 16093 <test expect_num_outputs="2"> | |
| 16094 <conditional name="adv_opts_cond"> | |
| 16095 <param name="adv_opts_selector" value="advanced"/> | |
| 16096 <param name="retention_time_summarization_method" value="max"/> | |
| 16097 <param name="force" value="false"/> | |
| 16098 <param name="test" value="true"/> | |
| 16099 </conditional> | |
| 16100 <param name="in" value="MSstatsConverter_1_in.consensusXML"/> | |
| 16101 <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/> | |
| 16102 <param name="method" value="LFQ"/> | |
| 16103 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> | |
| 16104 <param name="msstats_condition" value="MSstats_Condition"/> | |
| 16105 <param name="msstats_mixture" value="MSstats_Mixture"/> | |
| 16106 <param name="labeled_reference_peptides" value="false"/> | |
| 16107 <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 16108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16109 <output name="ctd_out" ftype="xml"> | |
| 16110 <assert_contents> | |
| 16111 <is_valid_xml/> | |
| 16112 </assert_contents> | |
| 16113 </output> | |
| 16114 </test> | |
| 16115 <test expect_num_outputs="2"> | |
| 16116 <conditional name="adv_opts_cond"> | |
| 16117 <param name="adv_opts_selector" value="advanced"/> | |
| 16118 <param name="retention_time_summarization_method" value="manual"/> | |
| 16119 <param name="force" value="false"/> | |
| 16120 <param name="test" value="true"/> | |
| 16121 </conditional> | |
| 16122 <param name="in" value="MSstatsConverter_2_in.consensusXML"/> | |
| 16123 <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/> | |
| 16124 <param name="method" value="ISO"/> | |
| 16125 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> | |
| 16126 <param name="msstats_condition" value="MSstats_Condition"/> | |
| 16127 <param name="msstats_mixture" value="MSstats_Mixture"/> | |
| 16128 <param name="labeled_reference_peptides" value="false"/> | |
| 16129 <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 16130 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16131 <output name="ctd_out" ftype="xml"> | |
| 16132 <assert_contents> | |
| 16133 <is_valid_xml/> | |
| 16134 </assert_contents> | |
| 16135 </output> | |
| 16136 </test> | |
| 16137 <test expect_num_outputs="2"> | |
| 16138 <conditional name="adv_opts_cond"> | |
| 16139 <param name="adv_opts_selector" value="advanced"/> | |
| 16140 <param name="retention_time_summarization_method" value="manual"/> | |
| 16141 <param name="force" value="false"/> | |
| 16142 <param name="test" value="true"/> | |
| 16143 </conditional> | |
| 16144 <param name="in" value="MSstatsConverter_3_in.consensusXML"/> | |
| 16145 <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/> | |
| 16146 <param name="method" value="ISO"/> | |
| 16147 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> | |
| 16148 <param name="msstats_condition" value="MSstats_Condition"/> | |
| 16149 <param name="msstats_mixture" value="MSstats_Mixture"/> | |
| 16150 <param name="labeled_reference_peptides" value="false"/> | |
| 16151 <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 16152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16153 <output name="ctd_out" ftype="xml"> | |
| 16154 <assert_contents> | |
| 16155 <is_valid_xml/> | |
| 16156 </assert_contents> | |
| 16157 </output> | |
| 16158 </test> | |
| 16159 </xml> | |
| 16160 <xml name="autotest_MultiplexResolver"> | |
| 16161 <test expect_num_outputs="3"> | |
| 16162 <conditional name="adv_opts_cond"> | |
| 16163 <param name="adv_opts_selector" value="advanced"/> | |
| 16164 <param name="force" value="false"/> | |
| 16165 <param name="test" value="true"/> | |
| 16166 </conditional> | |
| 16167 <param name="in" value="MultiplexResolver_1_input.consensusXML"/> | |
| 16168 <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16169 <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16170 <section name="algorithm"> | |
| 16171 <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/> | |
| 16172 <param name="missed_cleavages" value="1"/> | |
| 16173 <param name="mass_tolerance" value="0.1"/> | |
| 16174 <param name="mz_tolerance" value="10"/> | |
| 16175 <param name="rt_tolerance" value="5"/> | |
| 16176 </section> | |
| 16177 <section name="labels"> | |
| 16178 <param name="Arg6" value="6.0201290268"/> | |
| 16179 <param name="Arg10" value="10.0082686"/> | |
| 16180 <param name="Lys4" value="4.0251069836"/> | |
| 16181 <param name="Lys6" value="6.0201290268"/> | |
| 16182 <param name="Lys8" value="8.0141988132"/> | |
| 16183 <param name="Leu3" value="3.01883"/> | |
| 16184 <param name="Dimethyl0" value="28.0313"/> | |
| 16185 <param name="Dimethyl4" value="32.056407"/> | |
| 16186 <param name="Dimethyl6" value="34.063117"/> | |
| 16187 <param name="Dimethyl8" value="36.07567"/> | |
| 16188 <param name="ICPL0" value="105.021464"/> | |
| 16189 <param name="ICPL4" value="109.046571"/> | |
| 16190 <param name="ICPL6" value="111.041593"/> | |
| 16191 <param name="ICPL10" value="115.0667"/> | |
| 16192 </section> | |
| 16193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> | |
| 16194 <output name="ctd_out" ftype="xml"> | |
| 16195 <assert_contents> | |
| 16196 <is_valid_xml/> | |
| 16197 </assert_contents> | |
| 16198 </output> | |
| 16199 </test> | |
| 16200 <test expect_num_outputs="3"> | |
| 16201 <conditional name="adv_opts_cond"> | |
| 16202 <param name="adv_opts_selector" value="advanced"/> | |
| 16203 <param name="force" value="false"/> | |
| 16204 <param name="test" value="true"/> | |
| 16205 </conditional> | |
| 16206 <param name="in" value="MultiplexResolver_2_input.consensusXML"/> | |
| 16207 <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16208 <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16209 <section name="algorithm"> | |
| 16210 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> | |
| 16211 <param name="missed_cleavages" value="4"/> | |
| 16212 <param name="mass_tolerance" value="0.1"/> | |
| 16213 <param name="mz_tolerance" value="10"/> | |
| 16214 <param name="rt_tolerance" value="5"/> | |
| 16215 </section> | |
| 16216 <section name="labels"> | |
| 16217 <param name="Arg6" value="6.0201290268"/> | |
| 16218 <param name="Arg10" value="10.0082686"/> | |
| 16219 <param name="Lys4" value="4.0251069836"/> | |
| 16220 <param name="Lys6" value="6.0201290268"/> | |
| 16221 <param name="Lys8" value="8.0141988132"/> | |
| 16222 <param name="Leu3" value="3.01883"/> | |
| 16223 <param name="Dimethyl0" value="28.0313"/> | |
| 16224 <param name="Dimethyl4" value="32.056407"/> | |
| 16225 <param name="Dimethyl6" value="34.063117"/> | |
| 16226 <param name="Dimethyl8" value="36.07567"/> | |
| 16227 <param name="ICPL0" value="105.021464"/> | |
| 16228 <param name="ICPL4" value="109.046571"/> | |
| 16229 <param name="ICPL6" value="111.041593"/> | |
| 16230 <param name="ICPL10" value="115.0667"/> | |
| 16231 </section> | |
| 16232 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> | |
| 16233 <output name="ctd_out" ftype="xml"> | |
| 16234 <assert_contents> | |
| 16235 <is_valid_xml/> | |
| 16236 </assert_contents> | |
| 16237 </output> | |
| 16238 </test> | |
| 16239 <test expect_num_outputs="3"> | |
| 16240 <conditional name="adv_opts_cond"> | |
| 16241 <param name="adv_opts_selector" value="advanced"/> | |
| 16242 <param name="force" value="false"/> | |
| 16243 <param name="test" value="true"/> | |
| 16244 </conditional> | |
| 16245 <param name="in" value="MultiplexResolver_3_input.consensusXML"/> | |
| 16246 <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16247 <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16248 <section name="algorithm"> | |
| 16249 <param name="labels" value="[][Leu3]"/> | |
| 16250 <param name="missed_cleavages" value="2"/> | |
| 16251 <param name="mass_tolerance" value="0.1"/> | |
| 16252 <param name="mz_tolerance" value="10"/> | |
| 16253 <param name="rt_tolerance" value="5"/> | |
| 16254 </section> | |
| 16255 <section name="labels"> | |
| 16256 <param name="Arg6" value="6.0201290268"/> | |
| 16257 <param name="Arg10" value="10.0082686"/> | |
| 16258 <param name="Lys4" value="4.0251069836"/> | |
| 16259 <param name="Lys6" value="6.0201290268"/> | |
| 16260 <param name="Lys8" value="8.0141988132"/> | |
| 16261 <param name="Leu3" value="3.01883"/> | |
| 16262 <param name="Dimethyl0" value="28.0313"/> | |
| 16263 <param name="Dimethyl4" value="32.056407"/> | |
| 16264 <param name="Dimethyl6" value="34.063117"/> | |
| 16265 <param name="Dimethyl8" value="36.07567"/> | |
| 16266 <param name="ICPL0" value="105.021464"/> | |
| 16267 <param name="ICPL4" value="109.046571"/> | |
| 16268 <param name="ICPL6" value="111.041593"/> | |
| 16269 <param name="ICPL10" value="115.0667"/> | |
| 16270 </section> | |
| 16271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> | |
| 16272 <output name="ctd_out" ftype="xml"> | |
| 16273 <assert_contents> | |
| 16274 <is_valid_xml/> | |
| 16275 </assert_contents> | |
| 16276 </output> | |
| 16277 </test> | |
| 16278 <test expect_num_outputs="3"> | |
| 16279 <conditional name="adv_opts_cond"> | |
| 16280 <param name="adv_opts_selector" value="advanced"/> | |
| 16281 <param name="force" value="false"/> | |
| 16282 <param name="test" value="true"/> | |
| 16283 </conditional> | |
| 16284 <param name="in" value="MultiplexResolver_4_input.consensusXML"/> | |
| 16285 <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/> | |
| 16286 <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16287 <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 16288 <section name="algorithm"> | |
| 16289 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> | |
| 16290 <param name="missed_cleavages" value="3"/> | |
| 16291 <param name="mass_tolerance" value="0.1"/> | |
| 16292 <param name="mz_tolerance" value="10"/> | |
| 16293 <param name="rt_tolerance" value="10"/> | |
| 16294 </section> | |
| 16295 <section name="labels"> | |
| 16296 <param name="Arg6" value="6.0201290268"/> | |
| 16297 <param name="Arg10" value="10.0082686"/> | |
| 16298 <param name="Lys4" value="4.0251069836"/> | |
| 16299 <param name="Lys6" value="6.0201290268"/> | |
| 16300 <param name="Lys8" value="8.0141988132"/> | |
| 16301 <param name="Leu3" value="3.01883"/> | |
| 16302 <param name="Dimethyl0" value="28.0313"/> | |
| 16303 <param name="Dimethyl4" value="32.056407"/> | |
| 16304 <param name="Dimethyl6" value="34.063117"/> | |
| 16305 <param name="Dimethyl8" value="36.07567"/> | |
| 16306 <param name="ICPL0" value="105.021464"/> | |
| 16307 <param name="ICPL4" value="109.046571"/> | |
| 16308 <param name="ICPL6" value="111.041593"/> | |
| 16309 <param name="ICPL10" value="115.0667"/> | |
| 16310 </section> | |
| 16311 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> | |
| 16312 <output name="ctd_out" ftype="xml"> | |
| 16313 <assert_contents> | |
| 16314 <is_valid_xml/> | |
| 16315 </assert_contents> | |
| 16316 </output> | |
| 16317 </test> | |
| 16318 </xml> | |
| 16319 <xml name="autotest_MyriMatchAdapter"> | |
| 16320 <test expect_num_outputs="2"> | |
| 16321 <conditional name="adv_opts_cond"> | |
| 16322 <param name="adv_opts_selector" value="advanced"/> | |
| 16323 <param name="MinPeptideMass" value="0.0"/> | |
| 16324 <param name="MaxPeptideMass" value="10000.0"/> | |
| 16325 <param name="MinPeptideLength" value="5"/> | |
| 16326 <param name="MaxPeptideLength" value="75"/> | |
| 16327 <param name="UseSmartPlusThreeModel" value="false"/> | |
| 16328 <param name="NumIntensityClasses" value="3"/> | |
| 16329 <param name="ClassSizeMultiplier" value="2.0"/> | |
| 16330 <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/> | |
| 16331 <param name="SpectrumListFilters" value=""/> | |
| 16332 <param name="ignoreConfigErrors" value="false"/> | |
| 16333 <param name="force" value="false"/> | |
| 16334 <param name="test" value="true"/> | |
| 16335 </conditional> | |
| 16336 <param name="in" value="spectra.mzML"/> | |
| 16337 <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 16338 <param name="precursor_mass_tolerance" value="5.0"/> | |
| 16339 <param name="precursor_mass_tolerance_unit" value="ppm"/> | |
| 16340 <param name="precursor_mass_tolerance_avg" value="false"/> | |
| 16341 <param name="fragment_mass_tolerance" value="0.3"/> | |
| 16342 <param name="fragment_mass_tolerance_unit" value="Da"/> | |
| 16343 <param name="database" value="proteins.fasta"/> | |
| 16344 <param name="fixed_modifications" value=""/> | |
| 16345 <param name="variable_modifications" value="Oxidation (M)"/> | |
| 16346 <param name="NumChargeStates" value="3"/> | |
| 16347 <param name="TicCutoffPercentage" value="0.98"/> | |
| 16348 <param name="MaxDynamicMods" value="2"/> | |
| 16349 <param name="MaxResultRank" value="5"/> | |
| 16350 <param name="CleavageRules" value=""/> | |
| 16351 <param name="MinTerminiCleavages" value="2"/> | |
| 16352 <param name="MaxMissedCleavages" value="-1"/> | |
| 16353 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16354 <output name="ctd_out" ftype="xml"> | |
| 16355 <assert_contents> | |
| 16356 <is_valid_xml/> | |
| 16357 </assert_contents> | |
| 16358 </output> | |
| 16359 </test> | |
| 16360 </xml> | |
| 16361 <xml name="autotest_MzMLSplitter"/> | |
| 16362 <xml name="autotest_MzTabExporter"> | |
| 16363 <test expect_num_outputs="2"> | |
| 16364 <conditional name="adv_opts_cond"> | |
| 16365 <param name="adv_opts_selector" value="advanced"/> | |
| 16366 <param name="first_run_inference_only" value="false"/> | |
| 16367 <param name="force" value="false"/> | |
| 16368 <param name="test" value="true"/> | |
| 16369 </conditional> | |
| 16370 <param name="in" value="MzTabExporter_1_input.consensusXML"/> | |
| 16371 <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 16372 <param name="opt_columns" value="subfeatures"/> | |
| 16373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16374 <output name="ctd_out" ftype="xml"> | |
| 16375 <assert_contents> | |
| 16376 <is_valid_xml/> | |
| 16377 </assert_contents> | |
| 16378 </output> | |
| 16379 </test> | |
| 16380 <test expect_num_outputs="2"> | |
| 16381 <conditional name="adv_opts_cond"> | |
| 16382 <param name="adv_opts_selector" value="advanced"/> | |
| 16383 <param name="first_run_inference_only" value="false"/> | |
| 16384 <param name="force" value="false"/> | |
| 16385 <param name="test" value="true"/> | |
| 16386 </conditional> | |
| 16387 <param name="in" value="MzTabExporter_2_input.idXML"/> | |
| 16388 <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 16389 <param name="opt_columns" value="subfeatures"/> | |
| 16390 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16391 <output name="ctd_out" ftype="xml"> | |
| 16392 <assert_contents> | |
| 16393 <is_valid_xml/> | |
| 16394 </assert_contents> | |
| 16395 </output> | |
| 16396 </test> | |
| 16397 <test expect_num_outputs="2"> | |
| 16398 <conditional name="adv_opts_cond"> | |
| 16399 <param name="adv_opts_selector" value="advanced"/> | |
| 16400 <param name="first_run_inference_only" value="false"/> | |
| 16401 <param name="force" value="false"/> | |
| 16402 <param name="test" value="true"/> | |
| 16403 </conditional> | |
| 16404 <param name="in" value="MzTabExporter_3_input.featureXML"/> | |
| 16405 <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 16406 <param name="opt_columns" value="subfeatures"/> | |
| 16407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16408 <output name="ctd_out" ftype="xml"> | |
| 16409 <assert_contents> | |
| 16410 <is_valid_xml/> | |
| 16411 </assert_contents> | |
| 16412 </output> | |
| 16413 </test> | |
| 16414 </xml> | |
| 16415 <xml name="autotest_NoiseFilterGaussian"> | |
| 16416 <test expect_num_outputs="2"> | |
| 16417 <conditional name="adv_opts_cond"> | |
| 16418 <param name="adv_opts_selector" value="advanced"/> | |
| 16419 <param name="processOption" value="inmemory"/> | |
| 16420 <param name="force" value="false"/> | |
| 16421 <param name="test" value="true"/> | |
| 16422 </conditional> | |
| 16423 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> | |
| 16424 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16425 <section name="algorithm"> | |
| 16426 <param name="gaussian_width" value="1.0"/> | |
| 16427 <param name="ppm_tolerance" value="10.0"/> | |
| 16428 <param name="use_ppm_tolerance" value="false"/> | |
| 16429 </section> | |
| 16430 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16431 <output name="ctd_out" ftype="xml"> | |
| 16432 <assert_contents> | |
| 16433 <is_valid_xml/> | |
| 16434 </assert_contents> | |
| 16435 </output> | |
| 16436 </test> | |
| 16437 <test expect_num_outputs="2"> | |
| 16438 <conditional name="adv_opts_cond"> | |
| 16439 <param name="adv_opts_selector" value="advanced"/> | |
| 16440 <param name="processOption" value="inmemory"/> | |
| 16441 <param name="force" value="false"/> | |
| 16442 <param name="test" value="true"/> | |
| 16443 </conditional> | |
| 16444 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> | |
| 16445 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16446 <section name="algorithm"> | |
| 16447 <param name="gaussian_width" value="50.0"/> | |
| 16448 <param name="ppm_tolerance" value="10.0"/> | |
| 16449 <param name="use_ppm_tolerance" value="false"/> | |
| 16450 </section> | |
| 16451 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16452 <output name="ctd_out" ftype="xml"> | |
| 16453 <assert_contents> | |
| 16454 <is_valid_xml/> | |
| 16455 </assert_contents> | |
| 16456 </output> | |
| 16457 </test> | |
| 16458 <test expect_num_outputs="2"> | |
| 16459 <conditional name="adv_opts_cond"> | |
| 16460 <param name="adv_opts_selector" value="advanced"/> | |
| 16461 <param name="processOption" value="lowmemory"/> | |
| 16462 <param name="force" value="false"/> | |
| 16463 <param name="test" value="true"/> | |
| 16464 </conditional> | |
| 16465 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> | |
| 16466 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16467 <section name="algorithm"> | |
| 16468 <param name="gaussian_width" value="1.0"/> | |
| 16469 <param name="ppm_tolerance" value="10.0"/> | |
| 16470 <param name="use_ppm_tolerance" value="false"/> | |
| 16471 </section> | |
| 16472 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16473 <output name="ctd_out" ftype="xml"> | |
| 16474 <assert_contents> | |
| 16475 <is_valid_xml/> | |
| 16476 </assert_contents> | |
| 16477 </output> | |
| 16478 </test> | |
| 16479 <test expect_num_outputs="2"> | |
| 16480 <conditional name="adv_opts_cond"> | |
| 16481 <param name="adv_opts_selector" value="advanced"/> | |
| 16482 <param name="processOption" value="lowmemory"/> | |
| 16483 <param name="force" value="false"/> | |
| 16484 <param name="test" value="true"/> | |
| 16485 </conditional> | |
| 16486 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> | |
| 16487 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16488 <section name="algorithm"> | |
| 16489 <param name="gaussian_width" value="50.0"/> | |
| 16490 <param name="ppm_tolerance" value="10.0"/> | |
| 16491 <param name="use_ppm_tolerance" value="false"/> | |
| 16492 </section> | |
| 16493 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16494 <output name="ctd_out" ftype="xml"> | |
| 16495 <assert_contents> | |
| 16496 <is_valid_xml/> | |
| 16497 </assert_contents> | |
| 16498 </output> | |
| 16499 </test> | |
| 16500 </xml> | |
| 16501 <xml name="autotest_NoiseFilterSGolay"> | |
| 16502 <test expect_num_outputs="2"> | |
| 16503 <conditional name="adv_opts_cond"> | |
| 16504 <param name="adv_opts_selector" value="advanced"/> | |
| 16505 <param name="processOption" value="inmemory"/> | |
| 16506 <param name="force" value="false"/> | |
| 16507 <param name="test" value="true"/> | |
| 16508 </conditional> | |
| 16509 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> | |
| 16510 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16511 <section name="algorithm"> | |
| 16512 <param name="frame_length" value="9"/> | |
| 16513 <param name="polynomial_order" value="4"/> | |
| 16514 </section> | |
| 16515 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16516 <output name="ctd_out" ftype="xml"> | |
| 16517 <assert_contents> | |
| 16518 <is_valid_xml/> | |
| 16519 </assert_contents> | |
| 16520 </output> | |
| 16521 </test> | |
| 16522 <test expect_num_outputs="2"> | |
| 16523 <conditional name="adv_opts_cond"> | |
| 16524 <param name="adv_opts_selector" value="advanced"/> | |
| 16525 <param name="processOption" value="inmemory"/> | |
| 16526 <param name="force" value="false"/> | |
| 16527 <param name="test" value="true"/> | |
| 16528 </conditional> | |
| 16529 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> | |
| 16530 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16531 <section name="algorithm"> | |
| 16532 <param name="frame_length" value="11"/> | |
| 16533 <param name="polynomial_order" value="4"/> | |
| 16534 </section> | |
| 16535 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16536 <output name="ctd_out" ftype="xml"> | |
| 16537 <assert_contents> | |
| 16538 <is_valid_xml/> | |
| 16539 </assert_contents> | |
| 16540 </output> | |
| 16541 </test> | |
| 16542 <test expect_num_outputs="2"> | |
| 16543 <conditional name="adv_opts_cond"> | |
| 16544 <param name="adv_opts_selector" value="advanced"/> | |
| 16545 <param name="processOption" value="lowmemory"/> | |
| 16546 <param name="force" value="false"/> | |
| 16547 <param name="test" value="true"/> | |
| 16548 </conditional> | |
| 16549 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> | |
| 16550 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16551 <section name="algorithm"> | |
| 16552 <param name="frame_length" value="9"/> | |
| 16553 <param name="polynomial_order" value="4"/> | |
| 16554 </section> | |
| 16555 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16556 <output name="ctd_out" ftype="xml"> | |
| 16557 <assert_contents> | |
| 16558 <is_valid_xml/> | |
| 16559 </assert_contents> | |
| 16560 </output> | |
| 16561 </test> | |
| 16562 <test expect_num_outputs="2"> | |
| 16563 <conditional name="adv_opts_cond"> | |
| 16564 <param name="adv_opts_selector" value="advanced"/> | |
| 16565 <param name="processOption" value="lowmemory"/> | |
| 16566 <param name="force" value="false"/> | |
| 16567 <param name="test" value="true"/> | |
| 16568 </conditional> | |
| 16569 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> | |
| 16570 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 16571 <section name="algorithm"> | |
| 16572 <param name="frame_length" value="11"/> | |
| 16573 <param name="polynomial_order" value="4"/> | |
| 16574 </section> | |
| 16575 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16576 <output name="ctd_out" ftype="xml"> | |
| 16577 <assert_contents> | |
| 16578 <is_valid_xml/> | |
| 16579 </assert_contents> | |
| 16580 </output> | |
| 16581 </test> | |
| 16582 </xml> | |
| 16583 <xml name="autotest_NovorAdapter"/> | |
| 16584 <xml name="autotest_NucleicAcidSearchEngine"> | |
| 16585 <test expect_num_outputs="3"> | |
| 16586 <conditional name="adv_opts_cond"> | |
| 16587 <param name="adv_opts_selector" value="advanced"/> | |
| 16588 <param name="decharge_ms2" value="false"/> | |
| 16589 <param name="force" value="false"/> | |
| 16590 <param name="test" value="true"/> | |
| 16591 </conditional> | |
| 16592 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> | |
| 16593 <param name="database" value="NucleicAcidSearchEngine_1.fasta"/> | |
| 16594 <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 16595 <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 16596 <section name="precursor"> | |
| 16597 <param name="mass_tolerance" value="5.0"/> | |
| 16598 <param name="mass_tolerance_unit" value="ppm"/> | |
| 16599 <param name="min_charge" value="-2"/> | |
| 16600 <param name="max_charge" value="-14"/> | |
| 16601 <param name="include_unknown_charge" value="true"/> | |
| 16602 <param name="use_avg_mass" value="false"/> | |
| 16603 <param name="use_adducts" value="false"/> | |
| 16604 <param name="potential_adducts" value=""K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++""/> | |
| 16605 <param name="isotopes" value="0 1 2"/> | |
| 16606 </section> | |
| 16607 <section name="fragment"> | |
| 16608 <param name="mass_tolerance" value="5.0"/> | |
| 16609 <param name="mass_tolerance_unit" value="ppm"/> | |
| 16610 <param name="ions" value="a-B,c,w,y"/> | |
| 16611 </section> | |
| 16612 <section name="modifications"> | |
| 16613 <param name="variable" value=""/> | |
| 16614 <param name="variable_max_per_oligo" value="2"/> | |
| 16615 <param name="resolve_ambiguities" value="false"/> | |
| 16616 </section> | |
| 16617 <section name="oligo"> | |
| 16618 <param name="min_size" value="5"/> | |
| 16619 <param name="max_size" value="0"/> | |
| 16620 <param name="missed_cleavages" value="22"/> | |
| 16621 <param name="enzyme" value="no cleavage"/> | |
| 16622 </section> | |
| 16623 <section name="report"> | |
| 16624 <param name="top_hits" value="1"/> | |
| 16625 </section> | |
| 16626 <section name="fdr"> | |
| 16627 <param name="decoy_pattern" value="DECOY_"/> | |
| 16628 <param name="cutoff" value="0.05"/> | |
| 16629 <param name="remove_decoys" value="true"/> | |
| 16630 </section> | |
| 16631 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/> | |
| 16632 <output name="ctd_out" ftype="xml"> | |
| 16633 <assert_contents> | |
| 16634 <is_valid_xml/> | |
| 16635 </assert_contents> | |
| 16636 </output> | |
| 16637 </test> | |
| 16638 </xml> | |
| 16639 <xml name="autotest_OMSSAAdapter"> | |
| 16640 <test expect_num_outputs="2"> | |
| 16641 <conditional name="adv_opts_cond"> | |
| 16642 <param name="adv_opts_selector" value="advanced"/> | |
| 16643 <param name="pc" value="1"/> | |
| 16644 <param name="hs" value="4"/> | |
| 16645 <param name="tez" value="1"/> | |
| 16646 <param name="tom" value="0"/> | |
| 16647 <param name="tem" value="0"/> | |
| 16648 <param name="tex" value="1446.94"/> | |
| 16649 <param name="zt" value="3"/> | |
| 16650 <param name="z1" value="0.95"/> | |
| 16651 <param name="zc" value="1"/> | |
| 16652 <param name="zcc" value="2"/> | |
| 16653 <param name="zoh" value="2"/> | |
| 16654 <param name="no" value="4"/> | |
| 16655 <param name="nox" value="40"/> | |
| 16656 <param name="i" value="1,4"/> | |
| 16657 <param name="sp" value="100"/> | |
| 16658 <param name="sb1" value="1"/> | |
| 16659 <param name="sct" value="0"/> | |
| 16660 <param name="x" value="0"/> | |
| 16661 <param name="hm" value="2"/> | |
| 16662 <param name="ht" value="6"/> | |
| 16663 <param name="mm" value="128"/> | |
| 16664 <param name="mnm" value="false"/> | |
| 16665 <param name="is" value="0.0"/> | |
| 16666 <param name="ir" value="0.0"/> | |
| 16667 <param name="ii" value="0.0"/> | |
| 16668 <param name="chunk_size" value="0"/> | |
| 16669 <param name="force" value="false"/> | |
| 16670 <param name="test" value="true"/> | |
| 16671 </conditional> | |
| 16672 <param name="in" value="spectra.mzML"/> | |
| 16673 <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 16674 <param name="precursor_mass_tolerance" value="5.0"/> | |
| 16675 <param name="precursor_error_units" value="ppm"/> | |
| 16676 <param name="fragment_mass_tolerance" value="0.3"/> | |
| 16677 <param name="database" value="proteins.fasta"/> | |
| 16678 <param name="min_precursor_charge" value="1"/> | |
| 16679 <param name="max_precursor_charge" value="3"/> | |
| 16680 <param name="fixed_modifications" value=""/> | |
| 16681 <param name="variable_modifications" value="Oxidation (M)"/> | |
| 16682 <param name="v" value="1"/> | |
| 16683 <param name="enzyme" value="Trypsin"/> | |
| 16684 <param name="hl" value="30"/> | |
| 16685 <param name="he" value="1.0"/> | |
| 16686 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16687 <output name="ctd_out" ftype="xml"> | |
| 16688 <assert_contents> | |
| 16689 <is_valid_xml/> | |
| 16690 </assert_contents> | |
| 16691 </output> | |
| 16692 </test> | |
| 16693 </xml> | |
| 16694 <xml name="autotest_OpenPepXLLF"> | |
| 16695 <test expect_num_outputs="5"> | |
| 16696 <conditional name="adv_opts_cond"> | |
| 16697 <param name="adv_opts_selector" value="advanced"/> | |
| 16698 <param name="force" value="false"/> | |
| 16699 <param name="test" value="true"/> | |
| 16700 </conditional> | |
| 16701 <param name="in" value="OpenPepXLLF_input.mzML"/> | |
| 16702 <param name="database" value="OpenPepXLLF_input.fasta"/> | |
| 16703 <param name="decoy_string" value="decoy"/> | |
| 16704 <param name="decoy_prefix" value="true"/> | |
| 16705 <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 16706 <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 16707 <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 16708 <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> | |
| 16709 <section name="precursor"> | |
| 16710 <param name="mass_tolerance" value="10.0"/> | |
| 16711 <param name="mass_tolerance_unit" value="ppm"/> | |
| 16712 <param name="min_charge" value="3"/> | |
| 16713 <param name="max_charge" value="7"/> | |
| 16714 <param name="corrections" value="2 1 0"/> | |
| 16715 </section> | |
| 16716 <section name="fragment"> | |
| 16717 <param name="mass_tolerance" value="20.0"/> | |
| 16718 <param name="mass_tolerance_xlinks" value="20.0"/> | |
| 16719 <param name="mass_tolerance_unit" value="ppm"/> | |
| 16720 </section> | |
| 16721 <section name="modifications"> | |
| 16722 <param name="fixed" value=""/> | |
| 16723 <param name="variable" value=""/> | |
| 16724 <param name="variable_max_per_peptide" value="2"/> | |
| 16725 </section> | |
| 16726 <section name="peptide"> | |
| 16727 <param name="min_size" value="5"/> | |
| 16728 <param name="missed_cleavages" value="2"/> | |
| 16729 <param name="enzyme" value="Trypsin"/> | |
| 16730 </section> | |
| 16731 <section name="cross_linker"> | |
| 16732 <param name="residue1" value=""K" "N-term""/> | |
| 16733 <param name="residue2" value=""K" "N-term""/> | |
| 16734 <param name="mass" value="138.0680796"/> | |
| 16735 <param name="mass_mono_link" value="156.07864431 155.094628715"/> | |
| 16736 <param name="name" value="DSS"/> | |
| 16737 </section> | |
| 16738 <section name="algorithm"> | |
| 16739 <param name="number_top_hits" value="5"/> | |
| 16740 <param name="deisotope" value="auto"/> | |
| 16741 <param name="use_sequence_tags" value="false"/> | |
| 16742 <param name="sequence_tag_min_length" value="2"/> | |
| 16743 </section> | |
| 16744 <section name="ions"> | |
| 16745 <param name="b_ions" value="true"/> | |
| 16746 <param name="y_ions" value="true"/> | |
| 16747 <param name="a_ions" value="false"/> | |
| 16748 <param name="x_ions" value="false"/> | |
| 16749 <param name="c_ions" value="false"/> | |
| 16750 <param name="z_ions" value="false"/> | |
| 16751 <param name="neutral_losses" value="true"/> | |
| 16752 </section> | |
| 16753 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> | |
| 16754 <output name="ctd_out" ftype="xml"> | |
| 16755 <assert_contents> | |
| 16756 <is_valid_xml/> | |
| 16757 </assert_contents> | |
| 16758 </output> | |
| 16759 </test> | |
| 16760 <test expect_num_outputs="2"> | |
| 16761 <conditional name="adv_opts_cond"> | |
| 16762 <param name="adv_opts_selector" value="advanced"/> | |
| 16763 <param name="force" value="false"/> | |
| 16764 <param name="test" value="true"/> | |
| 16765 </conditional> | |
| 16766 <param name="in" value="OpenPepXLLF_input2.mzML"/> | |
| 16767 <param name="database" value="OpenPepXLLF_input2.fasta"/> | |
| 16768 <param name="decoy_string" value="decoy_"/> | |
| 16769 <param name="decoy_prefix" value="true"/> | |
| 16770 <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 16771 <section name="precursor"> | |
| 16772 <param name="mass_tolerance" value="10.0"/> | |
| 16773 <param name="mass_tolerance_unit" value="ppm"/> | |
| 16774 <param name="min_charge" value="3"/> | |
| 16775 <param name="max_charge" value="7"/> | |
| 16776 <param name="corrections" value="1 0"/> | |
| 16777 </section> | |
| 16778 <section name="fragment"> | |
| 16779 <param name="mass_tolerance" value="0.2"/> | |
| 16780 <param name="mass_tolerance_xlinks" value="0.3"/> | |
| 16781 <param name="mass_tolerance_unit" value="Da"/> | |
| 16782 </section> | |
| 16783 <section name="modifications"> | |
| 16784 <param name="fixed" value="Carbamidomethyl (C)"/> | |
| 16785 <param name="variable" value="Oxidation (M)"/> | |
| 16786 <param name="variable_max_per_peptide" value="1"/> | |
| 16787 </section> | |
| 16788 <section name="peptide"> | |
| 16789 <param name="min_size" value="5"/> | |
| 16790 <param name="missed_cleavages" value="1"/> | |
| 16791 <param name="enzyme" value="Trypsin"/> | |
| 16792 </section> | |
| 16793 <section name="cross_linker"> | |
| 16794 <param name="residue1" value=""D" "E" "C-term""/> | |
| 16795 <param name="residue2" value=""K" "S" "T" "Y" "N-term""/> | |
| 16796 <param name="mass" value="-18.010595"/> | |
| 16797 <param name="mass_mono_link" value=""/> | |
| 16798 <param name="name" value="DMTMM"/> | |
| 16799 </section> | |
| 16800 <section name="algorithm"> | |
| 16801 <param name="number_top_hits" value="1"/> | |
| 16802 <param name="deisotope" value="auto"/> | |
| 16803 <param name="use_sequence_tags" value="false"/> | |
| 16804 <param name="sequence_tag_min_length" value="2"/> | |
| 16805 </section> | |
| 16806 <section name="ions"> | |
| 16807 <param name="b_ions" value="true"/> | |
| 16808 <param name="y_ions" value="true"/> | |
| 16809 <param name="a_ions" value="false"/> | |
| 16810 <param name="x_ions" value="false"/> | |
| 16811 <param name="c_ions" value="false"/> | |
| 16812 <param name="z_ions" value="false"/> | |
| 16813 <param name="neutral_losses" value="true"/> | |
| 16814 </section> | |
| 16815 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> | |
| 16816 <output name="ctd_out" ftype="xml"> | |
| 16817 <assert_contents> | |
| 16818 <is_valid_xml/> | |
| 16819 </assert_contents> | |
| 16820 </output> | |
| 16821 </test> | |
| 16822 </xml> | |
| 16823 <xml name="autotest_OpenPepXL"> | |
| 16824 <test expect_num_outputs="5"> | |
| 16825 <conditional name="adv_opts_cond"> | |
| 16826 <param name="adv_opts_selector" value="advanced"/> | |
| 16827 <param name="force" value="false"/> | |
| 16828 <param name="test" value="true"/> | |
| 16829 </conditional> | |
| 16830 <param name="in" value="OpenPepXL_input.mzML"/> | |
| 16831 <param name="consensus" value="OpenPepXL_input.consensusXML"/> | |
| 16832 <param name="database" value="OpenPepXL_input.fasta"/> | |
| 16833 <param name="decoy_string" value="decoy"/> | |
| 16834 <param name="decoy_prefix" value="true"/> | |
| 16835 <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 16836 <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 16837 <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 16838 <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> | |
| 16839 <section name="precursor"> | |
| 16840 <param name="mass_tolerance" value="10.0"/> | |
| 16841 <param name="mass_tolerance_unit" value="ppm"/> | |
| 16842 <param name="min_charge" value="3"/> | |
| 16843 <param name="max_charge" value="7"/> | |
| 16844 <param name="corrections" value="2 1 0"/> | |
| 16845 </section> | |
| 16846 <section name="fragment"> | |
| 16847 <param name="mass_tolerance" value="0.2"/> | |
| 16848 <param name="mass_tolerance_xlinks" value="0.3"/> | |
| 16849 <param name="mass_tolerance_unit" value="Da"/> | |
| 16850 </section> | |
| 16851 <section name="modifications"> | |
| 16852 <param name="fixed" value=""/> | |
| 16853 <param name="variable" value=""/> | |
| 16854 <param name="variable_max_per_peptide" value="2"/> | |
| 16855 </section> | |
| 16856 <section name="peptide"> | |
| 16857 <param name="min_size" value="5"/> | |
| 16858 <param name="missed_cleavages" value="2"/> | |
| 16859 <param name="enzyme" value="Trypsin"/> | |
| 16860 </section> | |
| 16861 <section name="cross_linker"> | |
| 16862 <param name="residue1" value=""K" "N-term""/> | |
| 16863 <param name="residue2" value=""K" "N-term""/> | |
| 16864 <param name="mass_light" value="138.0680796"/> | |
| 16865 <param name="mass_iso_shift" value="12.075321"/> | |
| 16866 <param name="mass_mono_link" value="156.07864431 155.094628715"/> | |
| 16867 <param name="name" value="DSS"/> | |
| 16868 </section> | |
| 16869 <section name="algorithm"> | |
| 16870 <param name="number_top_hits" value="5"/> | |
| 16871 <param name="deisotope" value="auto"/> | |
| 16872 </section> | |
| 16873 <section name="ions"> | |
| 16874 <param name="b_ions" value="true"/> | |
| 16875 <param name="y_ions" value="true"/> | |
| 16876 <param name="a_ions" value="false"/> | |
| 16877 <param name="x_ions" value="false"/> | |
| 16878 <param name="c_ions" value="false"/> | |
| 16879 <param name="z_ions" value="false"/> | |
| 16880 <param name="neutral_losses" value="true"/> | |
| 16881 </section> | |
| 16882 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> | |
| 16883 <output name="ctd_out" ftype="xml"> | |
| 16884 <assert_contents> | |
| 16885 <is_valid_xml/> | |
| 16886 </assert_contents> | |
| 16887 </output> | |
| 16888 </test> | |
| 16889 </xml> | |
| 16890 <xml name="autotest_OpenSwathAnalyzer"> | |
| 16891 <test expect_num_outputs="2"> | |
| 16892 <conditional name="adv_opts_cond"> | |
| 16893 <param name="adv_opts_selector" value="advanced"/> | |
| 16894 <param name="force" value="false"/> | |
| 16895 <param name="test" value="true"/> | |
| 16896 </conditional> | |
| 16897 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 16898 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 16899 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> | |
| 16900 <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 16901 <param name="no_strict" value="false"/> | |
| 16902 <param name="min_upper_edge_dist" value="0.0"/> | |
| 16903 <section name="model"> | |
| 16904 <param name="type" value="linear"/> | |
| 16905 <param name="symmetric_regression" value="false"/> | |
| 16906 </section> | |
| 16907 <section name="algorithm"> | |
| 16908 <param name="stop_report_after_feature" value="-1"/> | |
| 16909 <param name="rt_extraction_window" value="-1.0"/> | |
| 16910 <param name="rt_normalization_factor" value="1.0"/> | |
| 16911 <param name="quantification_cutoff" value="0.0"/> | |
| 16912 <param name="write_convex_hull" value="false"/> | |
| 16913 <param name="spectrum_addition_method" value="simple"/> | |
| 16914 <param name="add_up_spectra" value="1"/> | |
| 16915 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 16916 <param name="uis_threshold_sn" value="-1"/> | |
| 16917 <param name="uis_threshold_peak_area" value="0"/> | |
| 16918 <param name="scoring_model" value="default"/> | |
| 16919 <param name="im_extra_drift" value="0.0"/> | |
| 16920 <section name="TransitionGroupPicker"> | |
| 16921 <param name="stop_after_feature" value="-1"/> | |
| 16922 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 16923 <param name="min_peak_width" value="-1.0"/> | |
| 16924 <param name="peak_integration" value="original"/> | |
| 16925 <param name="background_subtraction" value="none"/> | |
| 16926 <param name="recalculate_peaks" value="false"/> | |
| 16927 <param name="use_precursors" value="false"/> | |
| 16928 <param name="use_consensus" value="true"/> | |
| 16929 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 16930 <param name="minimal_quality" value="-10000.0"/> | |
| 16931 <param name="resample_boundary" value="15.0"/> | |
| 16932 <param name="compute_peak_quality" value="false"/> | |
| 16933 <param name="compute_peak_shape_metrics" value="false"/> | |
| 16934 <param name="compute_total_mi" value="false"/> | |
| 16935 <param name="boundary_selection_method" value="largest"/> | |
| 16936 <section name="PeakPickerMRM"> | |
| 16937 <param name="sgolay_frame_length" value="15"/> | |
| 16938 <param name="sgolay_polynomial_order" value="3"/> | |
| 16939 <param name="gauss_width" value="50.0"/> | |
| 16940 <param name="use_gauss" value="true"/> | |
| 16941 <param name="peak_width" value="40.0"/> | |
| 16942 <param name="signal_to_noise" value="1.0"/> | |
| 16943 <param name="sn_win_len" value="1000.0"/> | |
| 16944 <param name="sn_bin_count" value="30"/> | |
| 16945 <param name="write_sn_log_messages" value="false"/> | |
| 16946 <param name="remove_overlapping_peaks" value="false"/> | |
| 16947 <param name="method" value="legacy"/> | |
| 16948 </section> | |
| 16949 <section name="PeakIntegrator"> | |
| 16950 <param name="integration_type" value="intensity_sum"/> | |
| 16951 <param name="baseline_type" value="base_to_base"/> | |
| 16952 <param name="fit_EMG" value="false"/> | |
| 16953 </section> | |
| 16954 </section> | |
| 16955 <section name="DIAScoring"> | |
| 16956 <param name="dia_extraction_window" value="0.05"/> | |
| 16957 <param name="dia_extraction_unit" value="Th"/> | |
| 16958 <param name="dia_centroided" value="false"/> | |
| 16959 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 16960 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 16961 <param name="dia_nr_isotopes" value="4"/> | |
| 16962 <param name="dia_nr_charges" value="4"/> | |
| 16963 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 16964 </section> | |
| 16965 <section name="EMGScoring"> | |
| 16966 <param name="interpolation_step" value="0.2"/> | |
| 16967 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 16968 <param name="max_iteration" value="500"/> | |
| 16969 <section name="statistics"> | |
| 16970 <param name="mean" value="1.0"/> | |
| 16971 <param name="variance" value="1.0"/> | |
| 16972 </section> | |
| 16973 </section> | |
| 16974 <section name="Scores"> | |
| 16975 <param name="use_shape_score" value="true"/> | |
| 16976 <param name="use_coelution_score" value="true"/> | |
| 16977 <param name="use_rt_score" value="true"/> | |
| 16978 <param name="use_library_score" value="true"/> | |
| 16979 <param name="use_elution_model_score" value="true"/> | |
| 16980 <param name="use_intensity_score" value="true"/> | |
| 16981 <param name="use_nr_peaks_score" value="true"/> | |
| 16982 <param name="use_total_xic_score" value="true"/> | |
| 16983 <param name="use_total_mi_score" value="false"/> | |
| 16984 <param name="use_sn_score" value="true"/> | |
| 16985 <param name="use_mi_score" value="false"/> | |
| 16986 <param name="use_dia_scores" value="true"/> | |
| 16987 <param name="use_ms1_correlation" value="false"/> | |
| 16988 <param name="use_sonar_scores" value="false"/> | |
| 16989 <param name="use_ion_mobility_scores" value="false"/> | |
| 16990 <param name="use_ms1_fullscan" value="false"/> | |
| 16991 <param name="use_ms1_mi" value="false"/> | |
| 16992 <param name="use_uis_scores" value="false"/> | |
| 16993 </section> | |
| 16994 </section> | |
| 16995 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 16996 <output name="ctd_out" ftype="xml"> | |
| 16997 <assert_contents> | |
| 16998 <is_valid_xml/> | |
| 16999 </assert_contents> | |
| 17000 </output> | |
| 17001 </test> | |
| 17002 <test expect_num_outputs="2"> | |
| 17003 <conditional name="adv_opts_cond"> | |
| 17004 <param name="adv_opts_selector" value="advanced"/> | |
| 17005 <param name="force" value="false"/> | |
| 17006 <param name="test" value="true"/> | |
| 17007 </conditional> | |
| 17008 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17009 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 17010 <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17011 <param name="no_strict" value="false"/> | |
| 17012 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> | |
| 17013 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17014 <section name="model"> | |
| 17015 <param name="type" value="linear"/> | |
| 17016 <param name="symmetric_regression" value="false"/> | |
| 17017 </section> | |
| 17018 <section name="algorithm"> | |
| 17019 <param name="stop_report_after_feature" value="-1"/> | |
| 17020 <param name="rt_extraction_window" value="-1.0"/> | |
| 17021 <param name="rt_normalization_factor" value="1.0"/> | |
| 17022 <param name="quantification_cutoff" value="0.0"/> | |
| 17023 <param name="write_convex_hull" value="false"/> | |
| 17024 <param name="spectrum_addition_method" value="simple"/> | |
| 17025 <param name="add_up_spectra" value="1"/> | |
| 17026 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17027 <param name="uis_threshold_sn" value="-1"/> | |
| 17028 <param name="uis_threshold_peak_area" value="0"/> | |
| 17029 <param name="scoring_model" value="default"/> | |
| 17030 <param name="im_extra_drift" value="0.0"/> | |
| 17031 <section name="TransitionGroupPicker"> | |
| 17032 <param name="stop_after_feature" value="-1"/> | |
| 17033 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17034 <param name="min_peak_width" value="-1.0"/> | |
| 17035 <param name="peak_integration" value="original"/> | |
| 17036 <param name="background_subtraction" value="none"/> | |
| 17037 <param name="recalculate_peaks" value="false"/> | |
| 17038 <param name="use_precursors" value="false"/> | |
| 17039 <param name="use_consensus" value="true"/> | |
| 17040 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17041 <param name="minimal_quality" value="-10000.0"/> | |
| 17042 <param name="resample_boundary" value="15.0"/> | |
| 17043 <param name="compute_peak_quality" value="false"/> | |
| 17044 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17045 <param name="compute_total_mi" value="false"/> | |
| 17046 <param name="boundary_selection_method" value="largest"/> | |
| 17047 <section name="PeakPickerMRM"> | |
| 17048 <param name="sgolay_frame_length" value="15"/> | |
| 17049 <param name="sgolay_polynomial_order" value="3"/> | |
| 17050 <param name="gauss_width" value="50.0"/> | |
| 17051 <param name="use_gauss" value="true"/> | |
| 17052 <param name="peak_width" value="40.0"/> | |
| 17053 <param name="signal_to_noise" value="1.0"/> | |
| 17054 <param name="sn_win_len" value="1000.0"/> | |
| 17055 <param name="sn_bin_count" value="30"/> | |
| 17056 <param name="write_sn_log_messages" value="false"/> | |
| 17057 <param name="remove_overlapping_peaks" value="false"/> | |
| 17058 <param name="method" value="legacy"/> | |
| 17059 </section> | |
| 17060 <section name="PeakIntegrator"> | |
| 17061 <param name="integration_type" value="intensity_sum"/> | |
| 17062 <param name="baseline_type" value="base_to_base"/> | |
| 17063 <param name="fit_EMG" value="false"/> | |
| 17064 </section> | |
| 17065 </section> | |
| 17066 <section name="DIAScoring"> | |
| 17067 <param name="dia_extraction_window" value="0.05"/> | |
| 17068 <param name="dia_extraction_unit" value="Th"/> | |
| 17069 <param name="dia_centroided" value="false"/> | |
| 17070 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 17071 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 17072 <param name="dia_nr_isotopes" value="4"/> | |
| 17073 <param name="dia_nr_charges" value="4"/> | |
| 17074 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17075 </section> | |
| 17076 <section name="EMGScoring"> | |
| 17077 <param name="interpolation_step" value="0.2"/> | |
| 17078 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17079 <param name="max_iteration" value="500"/> | |
| 17080 <section name="statistics"> | |
| 17081 <param name="mean" value="1.0"/> | |
| 17082 <param name="variance" value="1.0"/> | |
| 17083 </section> | |
| 17084 </section> | |
| 17085 <section name="Scores"> | |
| 17086 <param name="use_shape_score" value="true"/> | |
| 17087 <param name="use_coelution_score" value="true"/> | |
| 17088 <param name="use_rt_score" value="true"/> | |
| 17089 <param name="use_library_score" value="true"/> | |
| 17090 <param name="use_elution_model_score" value="true"/> | |
| 17091 <param name="use_intensity_score" value="true"/> | |
| 17092 <param name="use_nr_peaks_score" value="true"/> | |
| 17093 <param name="use_total_xic_score" value="true"/> | |
| 17094 <param name="use_total_mi_score" value="false"/> | |
| 17095 <param name="use_sn_score" value="true"/> | |
| 17096 <param name="use_mi_score" value="false"/> | |
| 17097 <param name="use_dia_scores" value="true"/> | |
| 17098 <param name="use_ms1_correlation" value="false"/> | |
| 17099 <param name="use_sonar_scores" value="false"/> | |
| 17100 <param name="use_ion_mobility_scores" value="false"/> | |
| 17101 <param name="use_ms1_fullscan" value="false"/> | |
| 17102 <param name="use_ms1_mi" value="false"/> | |
| 17103 <param name="use_uis_scores" value="false"/> | |
| 17104 </section> | |
| 17105 </section> | |
| 17106 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17107 <output name="ctd_out" ftype="xml"> | |
| 17108 <assert_contents> | |
| 17109 <is_valid_xml/> | |
| 17110 </assert_contents> | |
| 17111 </output> | |
| 17112 </test> | |
| 17113 <test expect_num_outputs="2"> | |
| 17114 <conditional name="adv_opts_cond"> | |
| 17115 <param name="adv_opts_selector" value="advanced"/> | |
| 17116 <param name="force" value="false"/> | |
| 17117 <param name="test" value="true"/> | |
| 17118 </conditional> | |
| 17119 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17120 <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/> | |
| 17121 <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17122 <param name="no_strict" value="false"/> | |
| 17123 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> | |
| 17124 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17125 <section name="model"> | |
| 17126 <param name="type" value="linear"/> | |
| 17127 <param name="symmetric_regression" value="false"/> | |
| 17128 </section> | |
| 17129 <section name="algorithm"> | |
| 17130 <param name="stop_report_after_feature" value="-1"/> | |
| 17131 <param name="rt_extraction_window" value="-1.0"/> | |
| 17132 <param name="rt_normalization_factor" value="1.0"/> | |
| 17133 <param name="quantification_cutoff" value="0.0"/> | |
| 17134 <param name="write_convex_hull" value="false"/> | |
| 17135 <param name="spectrum_addition_method" value="simple"/> | |
| 17136 <param name="add_up_spectra" value="1"/> | |
| 17137 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17138 <param name="uis_threshold_sn" value="-1"/> | |
| 17139 <param name="uis_threshold_peak_area" value="0"/> | |
| 17140 <param name="scoring_model" value="default"/> | |
| 17141 <param name="im_extra_drift" value="0.0"/> | |
| 17142 <section name="TransitionGroupPicker"> | |
| 17143 <param name="stop_after_feature" value="-1"/> | |
| 17144 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17145 <param name="min_peak_width" value="-1.0"/> | |
| 17146 <param name="peak_integration" value="original"/> | |
| 17147 <param name="background_subtraction" value="none"/> | |
| 17148 <param name="recalculate_peaks" value="false"/> | |
| 17149 <param name="use_precursors" value="false"/> | |
| 17150 <param name="use_consensus" value="true"/> | |
| 17151 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17152 <param name="minimal_quality" value="-10000.0"/> | |
| 17153 <param name="resample_boundary" value="15.0"/> | |
| 17154 <param name="compute_peak_quality" value="false"/> | |
| 17155 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17156 <param name="compute_total_mi" value="false"/> | |
| 17157 <param name="boundary_selection_method" value="largest"/> | |
| 17158 <section name="PeakPickerMRM"> | |
| 17159 <param name="sgolay_frame_length" value="15"/> | |
| 17160 <param name="sgolay_polynomial_order" value="3"/> | |
| 17161 <param name="gauss_width" value="50.0"/> | |
| 17162 <param name="use_gauss" value="true"/> | |
| 17163 <param name="peak_width" value="40.0"/> | |
| 17164 <param name="signal_to_noise" value="1.0"/> | |
| 17165 <param name="sn_win_len" value="1000.0"/> | |
| 17166 <param name="sn_bin_count" value="30"/> | |
| 17167 <param name="write_sn_log_messages" value="true"/> | |
| 17168 <param name="remove_overlapping_peaks" value="false"/> | |
| 17169 <param name="method" value="legacy"/> | |
| 17170 </section> | |
| 17171 <section name="PeakIntegrator"> | |
| 17172 <param name="integration_type" value="intensity_sum"/> | |
| 17173 <param name="baseline_type" value="base_to_base"/> | |
| 17174 <param name="fit_EMG" value="false"/> | |
| 17175 </section> | |
| 17176 </section> | |
| 17177 <section name="DIAScoring"> | |
| 17178 <param name="dia_extraction_window" value="0.05"/> | |
| 17179 <param name="dia_extraction_unit" value="Th"/> | |
| 17180 <param name="dia_centroided" value="false"/> | |
| 17181 <param name="dia_byseries_intensity_min" value="8.0"/> | |
| 17182 <param name="dia_byseries_ppm_diff" value="15.0"/> | |
| 17183 <param name="dia_nr_isotopes" value="4"/> | |
| 17184 <param name="dia_nr_charges" value="4"/> | |
| 17185 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17186 </section> | |
| 17187 <section name="EMGScoring"> | |
| 17188 <param name="interpolation_step" value="0.2"/> | |
| 17189 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17190 <param name="max_iteration" value="500"/> | |
| 17191 <section name="statistics"> | |
| 17192 <param name="mean" value="1.0"/> | |
| 17193 <param name="variance" value="1.0"/> | |
| 17194 </section> | |
| 17195 </section> | |
| 17196 <section name="Scores"> | |
| 17197 <param name="use_shape_score" value="true"/> | |
| 17198 <param name="use_coelution_score" value="true"/> | |
| 17199 <param name="use_rt_score" value="true"/> | |
| 17200 <param name="use_library_score" value="true"/> | |
| 17201 <param name="use_elution_model_score" value="true"/> | |
| 17202 <param name="use_intensity_score" value="true"/> | |
| 17203 <param name="use_nr_peaks_score" value="true"/> | |
| 17204 <param name="use_total_xic_score" value="true"/> | |
| 17205 <param name="use_total_mi_score" value="false"/> | |
| 17206 <param name="use_sn_score" value="true"/> | |
| 17207 <param name="use_mi_score" value="false"/> | |
| 17208 <param name="use_dia_scores" value="true"/> | |
| 17209 <param name="use_ms1_correlation" value="false"/> | |
| 17210 <param name="use_sonar_scores" value="false"/> | |
| 17211 <param name="use_ion_mobility_scores" value="false"/> | |
| 17212 <param name="use_ms1_fullscan" value="false"/> | |
| 17213 <param name="use_ms1_mi" value="false"/> | |
| 17214 <param name="use_uis_scores" value="false"/> | |
| 17215 </section> | |
| 17216 </section> | |
| 17217 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17218 <output name="ctd_out" ftype="xml"> | |
| 17219 <assert_contents> | |
| 17220 <is_valid_xml/> | |
| 17221 </assert_contents> | |
| 17222 </output> | |
| 17223 </test> | |
| 17224 <test expect_num_outputs="2"> | |
| 17225 <conditional name="adv_opts_cond"> | |
| 17226 <param name="adv_opts_selector" value="advanced"/> | |
| 17227 <param name="force" value="false"/> | |
| 17228 <param name="test" value="true"/> | |
| 17229 </conditional> | |
| 17230 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17231 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 17232 <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17233 <param name="no_strict" value="false"/> | |
| 17234 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> | |
| 17235 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17236 <section name="model"> | |
| 17237 <param name="type" value="linear"/> | |
| 17238 <param name="symmetric_regression" value="false"/> | |
| 17239 </section> | |
| 17240 <section name="algorithm"> | |
| 17241 <param name="stop_report_after_feature" value="-1"/> | |
| 17242 <param name="rt_extraction_window" value="-1.0"/> | |
| 17243 <param name="rt_normalization_factor" value="1.0"/> | |
| 17244 <param name="quantification_cutoff" value="0.0"/> | |
| 17245 <param name="write_convex_hull" value="false"/> | |
| 17246 <param name="spectrum_addition_method" value="simple"/> | |
| 17247 <param name="add_up_spectra" value="1"/> | |
| 17248 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17249 <param name="uis_threshold_sn" value="-1"/> | |
| 17250 <param name="uis_threshold_peak_area" value="0"/> | |
| 17251 <param name="scoring_model" value="default"/> | |
| 17252 <param name="im_extra_drift" value="0.0"/> | |
| 17253 <section name="TransitionGroupPicker"> | |
| 17254 <param name="stop_after_feature" value="-1"/> | |
| 17255 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17256 <param name="min_peak_width" value="-1.0"/> | |
| 17257 <param name="peak_integration" value="original"/> | |
| 17258 <param name="background_subtraction" value="none"/> | |
| 17259 <param name="recalculate_peaks" value="false"/> | |
| 17260 <param name="use_precursors" value="false"/> | |
| 17261 <param name="use_consensus" value="true"/> | |
| 17262 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17263 <param name="minimal_quality" value="-10000.0"/> | |
| 17264 <param name="resample_boundary" value="15.0"/> | |
| 17265 <param name="compute_peak_quality" value="false"/> | |
| 17266 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17267 <param name="compute_total_mi" value="false"/> | |
| 17268 <param name="boundary_selection_method" value="largest"/> | |
| 17269 <section name="PeakPickerMRM"> | |
| 17270 <param name="sgolay_frame_length" value="15"/> | |
| 17271 <param name="sgolay_polynomial_order" value="3"/> | |
| 17272 <param name="gauss_width" value="50.0"/> | |
| 17273 <param name="use_gauss" value="true"/> | |
| 17274 <param name="peak_width" value="40.0"/> | |
| 17275 <param name="signal_to_noise" value="1.0"/> | |
| 17276 <param name="sn_win_len" value="1000.0"/> | |
| 17277 <param name="sn_bin_count" value="30"/> | |
| 17278 <param name="write_sn_log_messages" value="true"/> | |
| 17279 <param name="remove_overlapping_peaks" value="false"/> | |
| 17280 <param name="method" value="legacy"/> | |
| 17281 </section> | |
| 17282 <section name="PeakIntegrator"> | |
| 17283 <param name="integration_type" value="intensity_sum"/> | |
| 17284 <param name="baseline_type" value="base_to_base"/> | |
| 17285 <param name="fit_EMG" value="false"/> | |
| 17286 </section> | |
| 17287 </section> | |
| 17288 <section name="DIAScoring"> | |
| 17289 <param name="dia_extraction_window" value="0.05"/> | |
| 17290 <param name="dia_extraction_unit" value="Th"/> | |
| 17291 <param name="dia_centroided" value="false"/> | |
| 17292 <param name="dia_byseries_intensity_min" value="8.0"/> | |
| 17293 <param name="dia_byseries_ppm_diff" value="15.0"/> | |
| 17294 <param name="dia_nr_isotopes" value="4"/> | |
| 17295 <param name="dia_nr_charges" value="4"/> | |
| 17296 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17297 </section> | |
| 17298 <section name="EMGScoring"> | |
| 17299 <param name="interpolation_step" value="0.2"/> | |
| 17300 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17301 <param name="max_iteration" value="500"/> | |
| 17302 <section name="statistics"> | |
| 17303 <param name="mean" value="1.0"/> | |
| 17304 <param name="variance" value="1.0"/> | |
| 17305 </section> | |
| 17306 </section> | |
| 17307 <section name="Scores"> | |
| 17308 <param name="use_shape_score" value="true"/> | |
| 17309 <param name="use_coelution_score" value="true"/> | |
| 17310 <param name="use_rt_score" value="true"/> | |
| 17311 <param name="use_library_score" value="true"/> | |
| 17312 <param name="use_elution_model_score" value="true"/> | |
| 17313 <param name="use_intensity_score" value="true"/> | |
| 17314 <param name="use_nr_peaks_score" value="true"/> | |
| 17315 <param name="use_total_xic_score" value="true"/> | |
| 17316 <param name="use_total_mi_score" value="false"/> | |
| 17317 <param name="use_sn_score" value="true"/> | |
| 17318 <param name="use_mi_score" value="false"/> | |
| 17319 <param name="use_dia_scores" value="true"/> | |
| 17320 <param name="use_ms1_correlation" value="false"/> | |
| 17321 <param name="use_sonar_scores" value="false"/> | |
| 17322 <param name="use_ion_mobility_scores" value="false"/> | |
| 17323 <param name="use_ms1_fullscan" value="false"/> | |
| 17324 <param name="use_ms1_mi" value="false"/> | |
| 17325 <param name="use_uis_scores" value="false"/> | |
| 17326 </section> | |
| 17327 </section> | |
| 17328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17329 <output name="ctd_out" ftype="xml"> | |
| 17330 <assert_contents> | |
| 17331 <is_valid_xml/> | |
| 17332 </assert_contents> | |
| 17333 </output> | |
| 17334 </test> | |
| 17335 <test expect_num_outputs="2"> | |
| 17336 <conditional name="adv_opts_cond"> | |
| 17337 <param name="adv_opts_selector" value="advanced"/> | |
| 17338 <param name="force" value="false"/> | |
| 17339 <param name="test" value="true"/> | |
| 17340 </conditional> | |
| 17341 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17342 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 17343 <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17344 <param name="no_strict" value="false"/> | |
| 17345 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17346 <section name="model"> | |
| 17347 <param name="type" value="linear"/> | |
| 17348 <param name="symmetric_regression" value="false"/> | |
| 17349 </section> | |
| 17350 <section name="algorithm"> | |
| 17351 <param name="stop_report_after_feature" value="-1"/> | |
| 17352 <param name="rt_extraction_window" value="-1.0"/> | |
| 17353 <param name="rt_normalization_factor" value="1.0"/> | |
| 17354 <param name="quantification_cutoff" value="0.0"/> | |
| 17355 <param name="write_convex_hull" value="false"/> | |
| 17356 <param name="spectrum_addition_method" value="simple"/> | |
| 17357 <param name="add_up_spectra" value="1"/> | |
| 17358 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17359 <param name="uis_threshold_sn" value="-1"/> | |
| 17360 <param name="uis_threshold_peak_area" value="0"/> | |
| 17361 <param name="scoring_model" value="default"/> | |
| 17362 <param name="im_extra_drift" value="0.0"/> | |
| 17363 <section name="TransitionGroupPicker"> | |
| 17364 <param name="stop_after_feature" value="-1"/> | |
| 17365 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17366 <param name="min_peak_width" value="-1.0"/> | |
| 17367 <param name="peak_integration" value="original"/> | |
| 17368 <param name="background_subtraction" value="original"/> | |
| 17369 <param name="recalculate_peaks" value="false"/> | |
| 17370 <param name="use_precursors" value="false"/> | |
| 17371 <param name="use_consensus" value="true"/> | |
| 17372 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17373 <param name="minimal_quality" value="-10000.0"/> | |
| 17374 <param name="resample_boundary" value="15.0"/> | |
| 17375 <param name="compute_peak_quality" value="false"/> | |
| 17376 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17377 <param name="compute_total_mi" value="false"/> | |
| 17378 <param name="boundary_selection_method" value="largest"/> | |
| 17379 <section name="PeakPickerMRM"> | |
| 17380 <param name="sgolay_frame_length" value="15"/> | |
| 17381 <param name="sgolay_polynomial_order" value="3"/> | |
| 17382 <param name="gauss_width" value="50.0"/> | |
| 17383 <param name="use_gauss" value="true"/> | |
| 17384 <param name="peak_width" value="40.0"/> | |
| 17385 <param name="signal_to_noise" value="1.0"/> | |
| 17386 <param name="sn_win_len" value="1000.0"/> | |
| 17387 <param name="sn_bin_count" value="30"/> | |
| 17388 <param name="write_sn_log_messages" value="true"/> | |
| 17389 <param name="remove_overlapping_peaks" value="false"/> | |
| 17390 <param name="method" value="legacy"/> | |
| 17391 </section> | |
| 17392 <section name="PeakIntegrator"> | |
| 17393 <param name="integration_type" value="intensity_sum"/> | |
| 17394 <param name="baseline_type" value="base_to_base"/> | |
| 17395 <param name="fit_EMG" value="false"/> | |
| 17396 </section> | |
| 17397 </section> | |
| 17398 <section name="DIAScoring"> | |
| 17399 <param name="dia_extraction_window" value="0.05"/> | |
| 17400 <param name="dia_extraction_unit" value="Th"/> | |
| 17401 <param name="dia_centroided" value="false"/> | |
| 17402 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 17403 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 17404 <param name="dia_nr_isotopes" value="4"/> | |
| 17405 <param name="dia_nr_charges" value="4"/> | |
| 17406 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17407 </section> | |
| 17408 <section name="EMGScoring"> | |
| 17409 <param name="interpolation_step" value="0.2"/> | |
| 17410 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17411 <param name="max_iteration" value="500"/> | |
| 17412 <section name="statistics"> | |
| 17413 <param name="mean" value="1.0"/> | |
| 17414 <param name="variance" value="1.0"/> | |
| 17415 </section> | |
| 17416 </section> | |
| 17417 <section name="Scores"> | |
| 17418 <param name="use_shape_score" value="true"/> | |
| 17419 <param name="use_coelution_score" value="true"/> | |
| 17420 <param name="use_rt_score" value="true"/> | |
| 17421 <param name="use_library_score" value="true"/> | |
| 17422 <param name="use_elution_model_score" value="true"/> | |
| 17423 <param name="use_intensity_score" value="true"/> | |
| 17424 <param name="use_nr_peaks_score" value="true"/> | |
| 17425 <param name="use_total_xic_score" value="true"/> | |
| 17426 <param name="use_total_mi_score" value="false"/> | |
| 17427 <param name="use_sn_score" value="true"/> | |
| 17428 <param name="use_mi_score" value="false"/> | |
| 17429 <param name="use_dia_scores" value="true"/> | |
| 17430 <param name="use_ms1_correlation" value="false"/> | |
| 17431 <param name="use_sonar_scores" value="false"/> | |
| 17432 <param name="use_ion_mobility_scores" value="false"/> | |
| 17433 <param name="use_ms1_fullscan" value="false"/> | |
| 17434 <param name="use_ms1_mi" value="false"/> | |
| 17435 <param name="use_uis_scores" value="false"/> | |
| 17436 </section> | |
| 17437 </section> | |
| 17438 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17439 <output name="ctd_out" ftype="xml"> | |
| 17440 <assert_contents> | |
| 17441 <is_valid_xml/> | |
| 17442 </assert_contents> | |
| 17443 </output> | |
| 17444 </test> | |
| 17445 <test expect_num_outputs="2"> | |
| 17446 <conditional name="adv_opts_cond"> | |
| 17447 <param name="adv_opts_selector" value="advanced"/> | |
| 17448 <param name="force" value="false"/> | |
| 17449 <param name="test" value="true"/> | |
| 17450 </conditional> | |
| 17451 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17452 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 17453 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> | |
| 17454 <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17455 <param name="no_strict" value="false"/> | |
| 17456 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17457 <section name="model"> | |
| 17458 <param name="type" value="linear"/> | |
| 17459 <param name="symmetric_regression" value="false"/> | |
| 17460 </section> | |
| 17461 <section name="algorithm"> | |
| 17462 <param name="stop_report_after_feature" value="-1"/> | |
| 17463 <param name="rt_extraction_window" value="-1.0"/> | |
| 17464 <param name="rt_normalization_factor" value="1.0"/> | |
| 17465 <param name="quantification_cutoff" value="0.0"/> | |
| 17466 <param name="write_convex_hull" value="false"/> | |
| 17467 <param name="spectrum_addition_method" value="simple"/> | |
| 17468 <param name="add_up_spectra" value="1"/> | |
| 17469 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17470 <param name="uis_threshold_sn" value="-1"/> | |
| 17471 <param name="uis_threshold_peak_area" value="0"/> | |
| 17472 <param name="scoring_model" value="default"/> | |
| 17473 <param name="im_extra_drift" value="0.0"/> | |
| 17474 <section name="TransitionGroupPicker"> | |
| 17475 <param name="stop_after_feature" value="-1"/> | |
| 17476 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17477 <param name="min_peak_width" value="-1.0"/> | |
| 17478 <param name="peak_integration" value="original"/> | |
| 17479 <param name="background_subtraction" value="none"/> | |
| 17480 <param name="recalculate_peaks" value="false"/> | |
| 17481 <param name="use_precursors" value="false"/> | |
| 17482 <param name="use_consensus" value="true"/> | |
| 17483 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17484 <param name="minimal_quality" value="-10000.0"/> | |
| 17485 <param name="resample_boundary" value="15.0"/> | |
| 17486 <param name="compute_peak_quality" value="false"/> | |
| 17487 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17488 <param name="compute_total_mi" value="false"/> | |
| 17489 <param name="boundary_selection_method" value="largest"/> | |
| 17490 <section name="PeakPickerMRM"> | |
| 17491 <param name="sgolay_frame_length" value="15"/> | |
| 17492 <param name="sgolay_polynomial_order" value="3"/> | |
| 17493 <param name="gauss_width" value="50.0"/> | |
| 17494 <param name="use_gauss" value="true"/> | |
| 17495 <param name="peak_width" value="40.0"/> | |
| 17496 <param name="signal_to_noise" value="1.0"/> | |
| 17497 <param name="sn_win_len" value="1000.0"/> | |
| 17498 <param name="sn_bin_count" value="30"/> | |
| 17499 <param name="write_sn_log_messages" value="false"/> | |
| 17500 <param name="remove_overlapping_peaks" value="false"/> | |
| 17501 <param name="method" value="legacy"/> | |
| 17502 </section> | |
| 17503 <section name="PeakIntegrator"> | |
| 17504 <param name="integration_type" value="intensity_sum"/> | |
| 17505 <param name="baseline_type" value="base_to_base"/> | |
| 17506 <param name="fit_EMG" value="false"/> | |
| 17507 </section> | |
| 17508 </section> | |
| 17509 <section name="DIAScoring"> | |
| 17510 <param name="dia_extraction_window" value="0.05"/> | |
| 17511 <param name="dia_extraction_unit" value="Th"/> | |
| 17512 <param name="dia_centroided" value="false"/> | |
| 17513 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 17514 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 17515 <param name="dia_nr_isotopes" value="4"/> | |
| 17516 <param name="dia_nr_charges" value="4"/> | |
| 17517 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17518 </section> | |
| 17519 <section name="EMGScoring"> | |
| 17520 <param name="interpolation_step" value="0.2"/> | |
| 17521 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17522 <param name="max_iteration" value="500"/> | |
| 17523 <section name="statistics"> | |
| 17524 <param name="mean" value="1.0"/> | |
| 17525 <param name="variance" value="1.0"/> | |
| 17526 </section> | |
| 17527 </section> | |
| 17528 <section name="Scores"> | |
| 17529 <param name="use_shape_score" value="true"/> | |
| 17530 <param name="use_coelution_score" value="true"/> | |
| 17531 <param name="use_rt_score" value="true"/> | |
| 17532 <param name="use_library_score" value="true"/> | |
| 17533 <param name="use_elution_model_score" value="true"/> | |
| 17534 <param name="use_intensity_score" value="true"/> | |
| 17535 <param name="use_nr_peaks_score" value="true"/> | |
| 17536 <param name="use_total_xic_score" value="true"/> | |
| 17537 <param name="use_total_mi_score" value="true"/> | |
| 17538 <param name="use_sn_score" value="true"/> | |
| 17539 <param name="use_mi_score" value="true"/> | |
| 17540 <param name="use_dia_scores" value="true"/> | |
| 17541 <param name="use_ms1_correlation" value="false"/> | |
| 17542 <param name="use_sonar_scores" value="false"/> | |
| 17543 <param name="use_ion_mobility_scores" value="false"/> | |
| 17544 <param name="use_ms1_fullscan" value="false"/> | |
| 17545 <param name="use_ms1_mi" value="true"/> | |
| 17546 <param name="use_uis_scores" value="false"/> | |
| 17547 </section> | |
| 17548 </section> | |
| 17549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17550 <output name="ctd_out" ftype="xml"> | |
| 17551 <assert_contents> | |
| 17552 <is_valid_xml/> | |
| 17553 </assert_contents> | |
| 17554 </output> | |
| 17555 </test> | |
| 17556 <test expect_num_outputs="2"> | |
| 17557 <conditional name="adv_opts_cond"> | |
| 17558 <param name="adv_opts_selector" value="advanced"/> | |
| 17559 <param name="force" value="false"/> | |
| 17560 <param name="test" value="true"/> | |
| 17561 </conditional> | |
| 17562 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17563 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 17564 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> | |
| 17565 <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17566 <param name="no_strict" value="false"/> | |
| 17567 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17568 <section name="model"> | |
| 17569 <param name="type" value="linear"/> | |
| 17570 <param name="symmetric_regression" value="false"/> | |
| 17571 </section> | |
| 17572 <section name="algorithm"> | |
| 17573 <param name="stop_report_after_feature" value="-1"/> | |
| 17574 <param name="rt_extraction_window" value="-1.0"/> | |
| 17575 <param name="rt_normalization_factor" value="1.0"/> | |
| 17576 <param name="quantification_cutoff" value="0.0"/> | |
| 17577 <param name="write_convex_hull" value="false"/> | |
| 17578 <param name="spectrum_addition_method" value="simple"/> | |
| 17579 <param name="add_up_spectra" value="1"/> | |
| 17580 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17581 <param name="uis_threshold_sn" value="-1"/> | |
| 17582 <param name="uis_threshold_peak_area" value="0"/> | |
| 17583 <param name="scoring_model" value="default"/> | |
| 17584 <param name="im_extra_drift" value="0.0"/> | |
| 17585 <section name="TransitionGroupPicker"> | |
| 17586 <param name="stop_after_feature" value="-1"/> | |
| 17587 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17588 <param name="min_peak_width" value="-1.0"/> | |
| 17589 <param name="peak_integration" value="original"/> | |
| 17590 <param name="background_subtraction" value="none"/> | |
| 17591 <param name="recalculate_peaks" value="false"/> | |
| 17592 <param name="use_precursors" value="false"/> | |
| 17593 <param name="use_consensus" value="true"/> | |
| 17594 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17595 <param name="minimal_quality" value="-10000.0"/> | |
| 17596 <param name="resample_boundary" value="15.0"/> | |
| 17597 <param name="compute_peak_quality" value="false"/> | |
| 17598 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17599 <param name="compute_total_mi" value="false"/> | |
| 17600 <param name="boundary_selection_method" value="largest"/> | |
| 17601 <section name="PeakPickerMRM"> | |
| 17602 <param name="sgolay_frame_length" value="15"/> | |
| 17603 <param name="sgolay_polynomial_order" value="3"/> | |
| 17604 <param name="gauss_width" value="50.0"/> | |
| 17605 <param name="use_gauss" value="true"/> | |
| 17606 <param name="peak_width" value="40.0"/> | |
| 17607 <param name="signal_to_noise" value="1.0"/> | |
| 17608 <param name="sn_win_len" value="1000.0"/> | |
| 17609 <param name="sn_bin_count" value="30"/> | |
| 17610 <param name="write_sn_log_messages" value="false"/> | |
| 17611 <param name="remove_overlapping_peaks" value="false"/> | |
| 17612 <param name="method" value="legacy"/> | |
| 17613 </section> | |
| 17614 <section name="PeakIntegrator"> | |
| 17615 <param name="integration_type" value="intensity_sum"/> | |
| 17616 <param name="baseline_type" value="base_to_base"/> | |
| 17617 <param name="fit_EMG" value="false"/> | |
| 17618 </section> | |
| 17619 </section> | |
| 17620 <section name="DIAScoring"> | |
| 17621 <param name="dia_extraction_window" value="0.05"/> | |
| 17622 <param name="dia_extraction_unit" value="Th"/> | |
| 17623 <param name="dia_centroided" value="false"/> | |
| 17624 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 17625 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 17626 <param name="dia_nr_isotopes" value="4"/> | |
| 17627 <param name="dia_nr_charges" value="4"/> | |
| 17628 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17629 </section> | |
| 17630 <section name="EMGScoring"> | |
| 17631 <param name="interpolation_step" value="0.2"/> | |
| 17632 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17633 <param name="max_iteration" value="500"/> | |
| 17634 <section name="statistics"> | |
| 17635 <param name="mean" value="1.0"/> | |
| 17636 <param name="variance" value="1.0"/> | |
| 17637 </section> | |
| 17638 </section> | |
| 17639 <section name="Scores"> | |
| 17640 <param name="use_shape_score" value="true"/> | |
| 17641 <param name="use_coelution_score" value="true"/> | |
| 17642 <param name="use_rt_score" value="true"/> | |
| 17643 <param name="use_library_score" value="true"/> | |
| 17644 <param name="use_elution_model_score" value="true"/> | |
| 17645 <param name="use_intensity_score" value="true"/> | |
| 17646 <param name="use_nr_peaks_score" value="true"/> | |
| 17647 <param name="use_total_xic_score" value="true"/> | |
| 17648 <param name="use_total_mi_score" value="false"/> | |
| 17649 <param name="use_sn_score" value="true"/> | |
| 17650 <param name="use_mi_score" value="true"/> | |
| 17651 <param name="use_dia_scores" value="true"/> | |
| 17652 <param name="use_ms1_correlation" value="false"/> | |
| 17653 <param name="use_sonar_scores" value="false"/> | |
| 17654 <param name="use_ion_mobility_scores" value="false"/> | |
| 17655 <param name="use_ms1_fullscan" value="false"/> | |
| 17656 <param name="use_ms1_mi" value="false"/> | |
| 17657 <param name="use_uis_scores" value="false"/> | |
| 17658 </section> | |
| 17659 </section> | |
| 17660 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17661 <output name="ctd_out" ftype="xml"> | |
| 17662 <assert_contents> | |
| 17663 <is_valid_xml/> | |
| 17664 </assert_contents> | |
| 17665 </output> | |
| 17666 </test> | |
| 17667 <test expect_num_outputs="2"> | |
| 17668 <conditional name="adv_opts_cond"> | |
| 17669 <param name="adv_opts_selector" value="advanced"/> | |
| 17670 <param name="force" value="false"/> | |
| 17671 <param name="test" value="true"/> | |
| 17672 </conditional> | |
| 17673 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17674 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 17675 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> | |
| 17676 <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17677 <param name="no_strict" value="false"/> | |
| 17678 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17679 <section name="model"> | |
| 17680 <param name="type" value="linear"/> | |
| 17681 <param name="symmetric_regression" value="false"/> | |
| 17682 </section> | |
| 17683 <section name="algorithm"> | |
| 17684 <param name="stop_report_after_feature" value="-1"/> | |
| 17685 <param name="rt_extraction_window" value="-1.0"/> | |
| 17686 <param name="rt_normalization_factor" value="1.0"/> | |
| 17687 <param name="quantification_cutoff" value="0.0"/> | |
| 17688 <param name="write_convex_hull" value="false"/> | |
| 17689 <param name="spectrum_addition_method" value="simple"/> | |
| 17690 <param name="add_up_spectra" value="1"/> | |
| 17691 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17692 <param name="uis_threshold_sn" value="-1"/> | |
| 17693 <param name="uis_threshold_peak_area" value="0"/> | |
| 17694 <param name="scoring_model" value="default"/> | |
| 17695 <param name="im_extra_drift" value="0.0"/> | |
| 17696 <section name="TransitionGroupPicker"> | |
| 17697 <param name="stop_after_feature" value="-1"/> | |
| 17698 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17699 <param name="min_peak_width" value="-1.0"/> | |
| 17700 <param name="peak_integration" value="original"/> | |
| 17701 <param name="background_subtraction" value="none"/> | |
| 17702 <param name="recalculate_peaks" value="false"/> | |
| 17703 <param name="use_precursors" value="false"/> | |
| 17704 <param name="use_consensus" value="true"/> | |
| 17705 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17706 <param name="minimal_quality" value="-10000.0"/> | |
| 17707 <param name="resample_boundary" value="15.0"/> | |
| 17708 <param name="compute_peak_quality" value="false"/> | |
| 17709 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17710 <param name="compute_total_mi" value="false"/> | |
| 17711 <param name="boundary_selection_method" value="largest"/> | |
| 17712 <section name="PeakPickerMRM"> | |
| 17713 <param name="sgolay_frame_length" value="15"/> | |
| 17714 <param name="sgolay_polynomial_order" value="3"/> | |
| 17715 <param name="gauss_width" value="50.0"/> | |
| 17716 <param name="use_gauss" value="true"/> | |
| 17717 <param name="peak_width" value="40.0"/> | |
| 17718 <param name="signal_to_noise" value="1.0"/> | |
| 17719 <param name="sn_win_len" value="1000.0"/> | |
| 17720 <param name="sn_bin_count" value="30"/> | |
| 17721 <param name="write_sn_log_messages" value="false"/> | |
| 17722 <param name="remove_overlapping_peaks" value="false"/> | |
| 17723 <param name="method" value="legacy"/> | |
| 17724 </section> | |
| 17725 <section name="PeakIntegrator"> | |
| 17726 <param name="integration_type" value="intensity_sum"/> | |
| 17727 <param name="baseline_type" value="base_to_base"/> | |
| 17728 <param name="fit_EMG" value="false"/> | |
| 17729 </section> | |
| 17730 </section> | |
| 17731 <section name="DIAScoring"> | |
| 17732 <param name="dia_extraction_window" value="0.05"/> | |
| 17733 <param name="dia_extraction_unit" value="Th"/> | |
| 17734 <param name="dia_centroided" value="false"/> | |
| 17735 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 17736 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 17737 <param name="dia_nr_isotopes" value="4"/> | |
| 17738 <param name="dia_nr_charges" value="4"/> | |
| 17739 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17740 </section> | |
| 17741 <section name="EMGScoring"> | |
| 17742 <param name="interpolation_step" value="0.2"/> | |
| 17743 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17744 <param name="max_iteration" value="500"/> | |
| 17745 <section name="statistics"> | |
| 17746 <param name="mean" value="1.0"/> | |
| 17747 <param name="variance" value="1.0"/> | |
| 17748 </section> | |
| 17749 </section> | |
| 17750 <section name="Scores"> | |
| 17751 <param name="use_shape_score" value="true"/> | |
| 17752 <param name="use_coelution_score" value="true"/> | |
| 17753 <param name="use_rt_score" value="true"/> | |
| 17754 <param name="use_library_score" value="true"/> | |
| 17755 <param name="use_elution_model_score" value="true"/> | |
| 17756 <param name="use_intensity_score" value="true"/> | |
| 17757 <param name="use_nr_peaks_score" value="true"/> | |
| 17758 <param name="use_total_xic_score" value="true"/> | |
| 17759 <param name="use_total_mi_score" value="true"/> | |
| 17760 <param name="use_sn_score" value="true"/> | |
| 17761 <param name="use_mi_score" value="true"/> | |
| 17762 <param name="use_dia_scores" value="true"/> | |
| 17763 <param name="use_ms1_correlation" value="false"/> | |
| 17764 <param name="use_sonar_scores" value="false"/> | |
| 17765 <param name="use_ion_mobility_scores" value="false"/> | |
| 17766 <param name="use_ms1_fullscan" value="false"/> | |
| 17767 <param name="use_ms1_mi" value="false"/> | |
| 17768 <param name="use_uis_scores" value="false"/> | |
| 17769 </section> | |
| 17770 </section> | |
| 17771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17772 <output name="ctd_out" ftype="xml"> | |
| 17773 <assert_contents> | |
| 17774 <is_valid_xml/> | |
| 17775 </assert_contents> | |
| 17776 </output> | |
| 17777 </test> | |
| 17778 <test expect_num_outputs="2"> | |
| 17779 <conditional name="adv_opts_cond"> | |
| 17780 <param name="adv_opts_selector" value="advanced"/> | |
| 17781 <param name="force" value="false"/> | |
| 17782 <param name="test" value="true"/> | |
| 17783 </conditional> | |
| 17784 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 17785 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> | |
| 17786 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> | |
| 17787 <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 17788 <param name="no_strict" value="false"/> | |
| 17789 <param name="min_upper_edge_dist" value="0.0"/> | |
| 17790 <section name="model"> | |
| 17791 <param name="type" value="linear"/> | |
| 17792 <param name="symmetric_regression" value="false"/> | |
| 17793 </section> | |
| 17794 <section name="algorithm"> | |
| 17795 <param name="stop_report_after_feature" value="-1"/> | |
| 17796 <param name="rt_extraction_window" value="-1.0"/> | |
| 17797 <param name="rt_normalization_factor" value="1.0"/> | |
| 17798 <param name="quantification_cutoff" value="0.0"/> | |
| 17799 <param name="write_convex_hull" value="false"/> | |
| 17800 <param name="spectrum_addition_method" value="simple"/> | |
| 17801 <param name="add_up_spectra" value="1"/> | |
| 17802 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 17803 <param name="uis_threshold_sn" value="-1"/> | |
| 17804 <param name="uis_threshold_peak_area" value="0"/> | |
| 17805 <param name="scoring_model" value="default"/> | |
| 17806 <param name="im_extra_drift" value="0.0"/> | |
| 17807 <section name="TransitionGroupPicker"> | |
| 17808 <param name="stop_after_feature" value="-1"/> | |
| 17809 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 17810 <param name="min_peak_width" value="-1.0"/> | |
| 17811 <param name="peak_integration" value="original"/> | |
| 17812 <param name="background_subtraction" value="none"/> | |
| 17813 <param name="recalculate_peaks" value="false"/> | |
| 17814 <param name="use_precursors" value="false"/> | |
| 17815 <param name="use_consensus" value="true"/> | |
| 17816 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 17817 <param name="minimal_quality" value="-10000.0"/> | |
| 17818 <param name="resample_boundary" value="15.0"/> | |
| 17819 <param name="compute_peak_quality" value="false"/> | |
| 17820 <param name="compute_peak_shape_metrics" value="false"/> | |
| 17821 <param name="compute_total_mi" value="false"/> | |
| 17822 <param name="boundary_selection_method" value="largest"/> | |
| 17823 <section name="PeakPickerMRM"> | |
| 17824 <param name="sgolay_frame_length" value="15"/> | |
| 17825 <param name="sgolay_polynomial_order" value="3"/> | |
| 17826 <param name="gauss_width" value="50.0"/> | |
| 17827 <param name="use_gauss" value="true"/> | |
| 17828 <param name="peak_width" value="40.0"/> | |
| 17829 <param name="signal_to_noise" value="1.0"/> | |
| 17830 <param name="sn_win_len" value="1000.0"/> | |
| 17831 <param name="sn_bin_count" value="30"/> | |
| 17832 <param name="write_sn_log_messages" value="false"/> | |
| 17833 <param name="remove_overlapping_peaks" value="false"/> | |
| 17834 <param name="method" value="legacy"/> | |
| 17835 </section> | |
| 17836 <section name="PeakIntegrator"> | |
| 17837 <param name="integration_type" value="intensity_sum"/> | |
| 17838 <param name="baseline_type" value="base_to_base"/> | |
| 17839 <param name="fit_EMG" value="false"/> | |
| 17840 </section> | |
| 17841 </section> | |
| 17842 <section name="DIAScoring"> | |
| 17843 <param name="dia_extraction_window" value="0.05"/> | |
| 17844 <param name="dia_extraction_unit" value="Th"/> | |
| 17845 <param name="dia_centroided" value="false"/> | |
| 17846 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 17847 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 17848 <param name="dia_nr_isotopes" value="4"/> | |
| 17849 <param name="dia_nr_charges" value="4"/> | |
| 17850 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 17851 </section> | |
| 17852 <section name="EMGScoring"> | |
| 17853 <param name="interpolation_step" value="0.2"/> | |
| 17854 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 17855 <param name="max_iteration" value="500"/> | |
| 17856 <section name="statistics"> | |
| 17857 <param name="mean" value="1.0"/> | |
| 17858 <param name="variance" value="1.0"/> | |
| 17859 </section> | |
| 17860 </section> | |
| 17861 <section name="Scores"> | |
| 17862 <param name="use_shape_score" value="true"/> | |
| 17863 <param name="use_coelution_score" value="true"/> | |
| 17864 <param name="use_rt_score" value="true"/> | |
| 17865 <param name="use_library_score" value="true"/> | |
| 17866 <param name="use_elution_model_score" value="true"/> | |
| 17867 <param name="use_intensity_score" value="true"/> | |
| 17868 <param name="use_nr_peaks_score" value="true"/> | |
| 17869 <param name="use_total_xic_score" value="true"/> | |
| 17870 <param name="use_total_mi_score" value="true"/> | |
| 17871 <param name="use_sn_score" value="true"/> | |
| 17872 <param name="use_mi_score" value="false"/> | |
| 17873 <param name="use_dia_scores" value="true"/> | |
| 17874 <param name="use_ms1_correlation" value="false"/> | |
| 17875 <param name="use_sonar_scores" value="false"/> | |
| 17876 <param name="use_ion_mobility_scores" value="false"/> | |
| 17877 <param name="use_ms1_fullscan" value="false"/> | |
| 17878 <param name="use_ms1_mi" value="false"/> | |
| 17879 <param name="use_uis_scores" value="false"/> | |
| 17880 </section> | |
| 17881 </section> | |
| 17882 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17883 <output name="ctd_out" ftype="xml"> | |
| 17884 <assert_contents> | |
| 17885 <is_valid_xml/> | |
| 17886 </assert_contents> | |
| 17887 </output> | |
| 17888 </test> | |
| 17889 </xml> | |
| 17890 <xml name="autotest_OpenSwathAssayGenerator"> | |
| 17891 <test expect_num_outputs="2"> | |
| 17892 <conditional name="adv_opts_cond"> | |
| 17893 <param name="adv_opts_selector" value="advanced"/> | |
| 17894 <param name="max_num_alternative_localizations" value="10000"/> | |
| 17895 <param name="disable_identification_ms2_precursors" value="false"/> | |
| 17896 <param name="disable_identification_specific_losses" value="false"/> | |
| 17897 <param name="enable_identification_unspecific_losses" value="false"/> | |
| 17898 <param name="enable_swath_specifity" value="false"/> | |
| 17899 <param name="force" value="false"/> | |
| 17900 <param name="test" value="true"/> | |
| 17901 </conditional> | |
| 17902 <param name="in" value="OpenSwathAssayGenerator_input.TraML"/> | |
| 17903 <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 17904 <param name="out_type" value="TraML"/> | |
| 17905 <param name="min_transitions" value="6"/> | |
| 17906 <param name="max_transitions" value="6"/> | |
| 17907 <param name="allowed_fragment_types" value="b,y"/> | |
| 17908 <param name="allowed_fragment_charges" value="2,3"/> | |
| 17909 <param name="enable_detection_specific_losses" value="true"/> | |
| 17910 <param name="enable_detection_unspecific_losses" value="false"/> | |
| 17911 <param name="precursor_mz_threshold" value="0.025"/> | |
| 17912 <param name="precursor_lower_mz_limit" value="400.0"/> | |
| 17913 <param name="precursor_upper_mz_limit" value="1200.0"/> | |
| 17914 <param name="product_mz_threshold" value="0.025"/> | |
| 17915 <param name="product_lower_mz_limit" value="350.0"/> | |
| 17916 <param name="product_upper_mz_limit" value="2000.0"/> | |
| 17917 <param name="enable_ipf" value="false"/> | |
| 17918 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17919 <output name="ctd_out" ftype="xml"> | |
| 17920 <assert_contents> | |
| 17921 <is_valid_xml/> | |
| 17922 </assert_contents> | |
| 17923 </output> | |
| 17924 </test> | |
| 17925 <test expect_num_outputs="2"> | |
| 17926 <conditional name="adv_opts_cond"> | |
| 17927 <param name="adv_opts_selector" value="advanced"/> | |
| 17928 <param name="max_num_alternative_localizations" value="10000"/> | |
| 17929 <param name="disable_identification_ms2_precursors" value="false"/> | |
| 17930 <param name="disable_identification_specific_losses" value="false"/> | |
| 17931 <param name="enable_identification_unspecific_losses" value="false"/> | |
| 17932 <param name="enable_swath_specifity" value="false"/> | |
| 17933 <param name="force" value="false"/> | |
| 17934 <param name="test" value="true"/> | |
| 17935 </conditional> | |
| 17936 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> | |
| 17937 <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 17938 <param name="out_type" value="TraML"/> | |
| 17939 <param name="min_transitions" value="6"/> | |
| 17940 <param name="max_transitions" value="6"/> | |
| 17941 <param name="allowed_fragment_types" value="b,y"/> | |
| 17942 <param name="allowed_fragment_charges" value="1,2,3,4"/> | |
| 17943 <param name="enable_detection_specific_losses" value="false"/> | |
| 17944 <param name="enable_detection_unspecific_losses" value="false"/> | |
| 17945 <param name="precursor_mz_threshold" value="0.025"/> | |
| 17946 <param name="precursor_lower_mz_limit" value="400.0"/> | |
| 17947 <param name="precursor_upper_mz_limit" value="1200.0"/> | |
| 17948 <param name="product_mz_threshold" value="0.025"/> | |
| 17949 <param name="product_lower_mz_limit" value="350.0"/> | |
| 17950 <param name="product_upper_mz_limit" value="2000.0"/> | |
| 17951 <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/> | |
| 17952 <param name="enable_ipf" value="true"/> | |
| 17953 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17954 <output name="ctd_out" ftype="xml"> | |
| 17955 <assert_contents> | |
| 17956 <is_valid_xml/> | |
| 17957 </assert_contents> | |
| 17958 </output> | |
| 17959 </test> | |
| 17960 <test expect_num_outputs="2"> | |
| 17961 <conditional name="adv_opts_cond"> | |
| 17962 <param name="adv_opts_selector" value="advanced"/> | |
| 17963 <param name="max_num_alternative_localizations" value="10000"/> | |
| 17964 <param name="disable_identification_ms2_precursors" value="false"/> | |
| 17965 <param name="disable_identification_specific_losses" value="false"/> | |
| 17966 <param name="enable_identification_unspecific_losses" value="false"/> | |
| 17967 <param name="enable_swath_specifity" value="false"/> | |
| 17968 <param name="force" value="false"/> | |
| 17969 <param name="test" value="true"/> | |
| 17970 </conditional> | |
| 17971 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> | |
| 17972 <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 17973 <param name="out_type" value="TraML"/> | |
| 17974 <param name="min_transitions" value="6"/> | |
| 17975 <param name="max_transitions" value="6"/> | |
| 17976 <param name="allowed_fragment_types" value="b,y"/> | |
| 17977 <param name="allowed_fragment_charges" value="1,2,3,4"/> | |
| 17978 <param name="enable_detection_specific_losses" value="false"/> | |
| 17979 <param name="enable_detection_unspecific_losses" value="false"/> | |
| 17980 <param name="precursor_mz_threshold" value="0.025"/> | |
| 17981 <param name="precursor_lower_mz_limit" value="400.0"/> | |
| 17982 <param name="precursor_upper_mz_limit" value="1200.0"/> | |
| 17983 <param name="product_mz_threshold" value="0.025"/> | |
| 17984 <param name="product_lower_mz_limit" value="350.0"/> | |
| 17985 <param name="product_upper_mz_limit" value="2000.0"/> | |
| 17986 <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/> | |
| 17987 <param name="enable_ipf" value="true"/> | |
| 17988 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 17989 <output name="ctd_out" ftype="xml"> | |
| 17990 <assert_contents> | |
| 17991 <is_valid_xml/> | |
| 17992 </assert_contents> | |
| 17993 </output> | |
| 17994 </test> | |
| 17995 </xml> | |
| 17996 <xml name="autotest_OpenSwathChromatogramExtractor"> | |
| 17997 <test expect_num_outputs="2"> | |
| 17998 <conditional name="adv_opts_cond"> | |
| 17999 <param name="adv_opts_selector" value="advanced"/> | |
| 18000 <param name="extraction_function" value="tophat"/> | |
| 18001 <param name="force" value="false"/> | |
| 18002 <param name="test" value="true"/> | |
| 18003 </conditional> | |
| 18004 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> | |
| 18005 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> | |
| 18006 <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18007 <param name="min_upper_edge_dist" value="0.0"/> | |
| 18008 <param name="rt_window" value="-1.0"/> | |
| 18009 <param name="ion_mobility_window" value="-1.0"/> | |
| 18010 <param name="mz_window" value="0.05"/> | |
| 18011 <param name="ppm" value="false"/> | |
| 18012 <param name="is_swath" value="false"/> | |
| 18013 <param name="extract_MS1" value="false"/> | |
| 18014 <section name="model"> | |
| 18015 <param name="type" value="linear"/> | |
| 18016 <param name="symmetric_regression" value="false"/> | |
| 18017 </section> | |
| 18018 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18019 <output name="ctd_out" ftype="xml"> | |
| 18020 <assert_contents> | |
| 18021 <is_valid_xml/> | |
| 18022 </assert_contents> | |
| 18023 </output> | |
| 18024 </test> | |
| 18025 <test expect_num_outputs="2"> | |
| 18026 <conditional name="adv_opts_cond"> | |
| 18027 <param name="adv_opts_selector" value="advanced"/> | |
| 18028 <param name="extraction_function" value="tophat"/> | |
| 18029 <param name="force" value="false"/> | |
| 18030 <param name="test" value="true"/> | |
| 18031 </conditional> | |
| 18032 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> | |
| 18033 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> | |
| 18034 <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/> | |
| 18035 <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18036 <param name="min_upper_edge_dist" value="0.0"/> | |
| 18037 <param name="rt_window" value="50.0"/> | |
| 18038 <param name="ion_mobility_window" value="-1.0"/> | |
| 18039 <param name="mz_window" value="0.05"/> | |
| 18040 <param name="ppm" value="false"/> | |
| 18041 <param name="is_swath" value="false"/> | |
| 18042 <param name="extract_MS1" value="false"/> | |
| 18043 <section name="model"> | |
| 18044 <param name="type" value="linear"/> | |
| 18045 <param name="symmetric_regression" value="false"/> | |
| 18046 </section> | |
| 18047 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18048 <output name="ctd_out" ftype="xml"> | |
| 18049 <assert_contents> | |
| 18050 <is_valid_xml/> | |
| 18051 </assert_contents> | |
| 18052 </output> | |
| 18053 </test> | |
| 18054 <test expect_num_outputs="2"> | |
| 18055 <conditional name="adv_opts_cond"> | |
| 18056 <param name="adv_opts_selector" value="advanced"/> | |
| 18057 <param name="extraction_function" value="tophat"/> | |
| 18058 <param name="force" value="false"/> | |
| 18059 <param name="test" value="true"/> | |
| 18060 </conditional> | |
| 18061 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> | |
| 18062 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> | |
| 18063 <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18064 <param name="min_upper_edge_dist" value="0.0"/> | |
| 18065 <param name="rt_window" value="-1.0"/> | |
| 18066 <param name="ion_mobility_window" value="-1.0"/> | |
| 18067 <param name="mz_window" value="0.05"/> | |
| 18068 <param name="ppm" value="false"/> | |
| 18069 <param name="is_swath" value="false"/> | |
| 18070 <param name="extract_MS1" value="true"/> | |
| 18071 <section name="model"> | |
| 18072 <param name="type" value="linear"/> | |
| 18073 <param name="symmetric_regression" value="false"/> | |
| 18074 </section> | |
| 18075 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18076 <output name="ctd_out" ftype="xml"> | |
| 18077 <assert_contents> | |
| 18078 <is_valid_xml/> | |
| 18079 </assert_contents> | |
| 18080 </output> | |
| 18081 </test> | |
| 18082 <test expect_num_outputs="2"> | |
| 18083 <conditional name="adv_opts_cond"> | |
| 18084 <param name="adv_opts_selector" value="advanced"/> | |
| 18085 <param name="extraction_function" value="tophat"/> | |
| 18086 <param name="force" value="false"/> | |
| 18087 <param name="test" value="true"/> | |
| 18088 </conditional> | |
| 18089 <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/> | |
| 18090 <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/> | |
| 18091 <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18092 <param name="min_upper_edge_dist" value="0.0"/> | |
| 18093 <param name="rt_window" value="-1.0"/> | |
| 18094 <param name="ion_mobility_window" value="0.05"/> | |
| 18095 <param name="mz_window" value="0.05"/> | |
| 18096 <param name="ppm" value="false"/> | |
| 18097 <param name="is_swath" value="true"/> | |
| 18098 <param name="extract_MS1" value="false"/> | |
| 18099 <section name="model"> | |
| 18100 <param name="type" value="linear"/> | |
| 18101 <param name="symmetric_regression" value="false"/> | |
| 18102 </section> | |
| 18103 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18104 <output name="ctd_out" ftype="xml"> | |
| 18105 <assert_contents> | |
| 18106 <is_valid_xml/> | |
| 18107 </assert_contents> | |
| 18108 </output> | |
| 18109 </test> | |
| 18110 <test expect_num_outputs="2"> | |
| 18111 <conditional name="adv_opts_cond"> | |
| 18112 <param name="adv_opts_selector" value="advanced"/> | |
| 18113 <param name="extraction_function" value="tophat"/> | |
| 18114 <param name="force" value="false"/> | |
| 18115 <param name="test" value="true"/> | |
| 18116 </conditional> | |
| 18117 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> | |
| 18118 <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/> | |
| 18119 <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18120 <param name="min_upper_edge_dist" value="0.0"/> | |
| 18121 <param name="rt_window" value="-1.0"/> | |
| 18122 <param name="ion_mobility_window" value="-1.0"/> | |
| 18123 <param name="mz_window" value="0.05"/> | |
| 18124 <param name="ppm" value="false"/> | |
| 18125 <param name="is_swath" value="false"/> | |
| 18126 <param name="extract_MS1" value="true"/> | |
| 18127 <section name="model"> | |
| 18128 <param name="type" value="linear"/> | |
| 18129 <param name="symmetric_regression" value="false"/> | |
| 18130 </section> | |
| 18131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18132 <output name="ctd_out" ftype="xml"> | |
| 18133 <assert_contents> | |
| 18134 <is_valid_xml/> | |
| 18135 </assert_contents> | |
| 18136 </output> | |
| 18137 </test> | |
| 18138 </xml> | |
| 18139 <xml name="autotest_OpenSwathConfidenceScoring"> | |
| 18140 <test expect_num_outputs="2"> | |
| 18141 <conditional name="adv_opts_cond"> | |
| 18142 <param name="adv_opts_selector" value="advanced"/> | |
| 18143 <param name="force" value="false"/> | |
| 18144 <param name="test" value="true"/> | |
| 18145 </conditional> | |
| 18146 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> | |
| 18147 <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/> | |
| 18148 <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 18149 <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/> | |
| 18150 <param name="decoys" value="1"/> | |
| 18151 <param name="transitions" value="2"/> | |
| 18152 <section name="GLM"> | |
| 18153 <param name="intercept" value="3.87333466"/> | |
| 18154 <param name="delta_rt" value="-0.02898629"/> | |
| 18155 <param name="dist_int" value="-7.75880768"/> | |
| 18156 </section> | |
| 18157 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18158 <output name="ctd_out" ftype="xml"> | |
| 18159 <assert_contents> | |
| 18160 <is_valid_xml/> | |
| 18161 </assert_contents> | |
| 18162 </output> | |
| 18163 </test> | |
| 18164 </xml> | |
| 18165 <xml name="autotest_OpenSwathDecoyGenerator"> | |
| 18166 <test expect_num_outputs="2"> | |
| 18167 <conditional name="adv_opts_cond"> | |
| 18168 <param name="adv_opts_selector" value="advanced"/> | |
| 18169 <param name="min_decoy_fraction" value="0.8"/> | |
| 18170 <param name="aim_decoy_fraction" value="1.0"/> | |
| 18171 <param name="shuffle_max_attempts" value="30"/> | |
| 18172 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 18173 <param name="shift_precursor_mz_shift" value="0.0"/> | |
| 18174 <param name="shift_product_mz_shift" value="20.0"/> | |
| 18175 <param name="product_mz_threshold" value="0.025"/> | |
| 18176 <param name="allowed_fragment_types" value="b,y"/> | |
| 18177 <param name="allowed_fragment_charges" value="1,2,3,4"/> | |
| 18178 <param name="enable_detection_specific_losses" value="false"/> | |
| 18179 <param name="enable_detection_unspecific_losses" value="false"/> | |
| 18180 <param name="separate" value="true"/> | |
| 18181 <param name="force" value="false"/> | |
| 18182 <param name="test" value="true"/> | |
| 18183 </conditional> | |
| 18184 <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> | |
| 18185 <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 18186 <param name="out_type" value="TraML"/> | |
| 18187 <param name="method" value="pseudo-reverse"/> | |
| 18188 <param name="decoy_tag" value="DECOY_"/> | |
| 18189 <param name="switchKR" value="false"/> | |
| 18190 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18191 <output name="ctd_out" ftype="xml"> | |
| 18192 <assert_contents> | |
| 18193 <is_valid_xml/> | |
| 18194 </assert_contents> | |
| 18195 </output> | |
| 18196 </test> | |
| 18197 <test expect_num_outputs="2"> | |
| 18198 <conditional name="adv_opts_cond"> | |
| 18199 <param name="adv_opts_selector" value="advanced"/> | |
| 18200 <param name="min_decoy_fraction" value="0.8"/> | |
| 18201 <param name="aim_decoy_fraction" value="1.0"/> | |
| 18202 <param name="shuffle_max_attempts" value="30"/> | |
| 18203 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 18204 <param name="shift_precursor_mz_shift" value="0.0"/> | |
| 18205 <param name="shift_product_mz_shift" value="20.0"/> | |
| 18206 <param name="product_mz_threshold" value="0.8"/> | |
| 18207 <param name="allowed_fragment_types" value="b,y"/> | |
| 18208 <param name="allowed_fragment_charges" value="1,2,3,4"/> | |
| 18209 <param name="enable_detection_specific_losses" value="false"/> | |
| 18210 <param name="enable_detection_unspecific_losses" value="false"/> | |
| 18211 <param name="separate" value="false"/> | |
| 18212 <param name="force" value="false"/> | |
| 18213 <param name="test" value="true"/> | |
| 18214 </conditional> | |
| 18215 <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> | |
| 18216 <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 18217 <param name="out_type" value="TraML"/> | |
| 18218 <param name="method" value="pseudo-reverse"/> | |
| 18219 <param name="decoy_tag" value="DECOY_"/> | |
| 18220 <param name="switchKR" value="false"/> | |
| 18221 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18222 <output name="ctd_out" ftype="xml"> | |
| 18223 <assert_contents> | |
| 18224 <is_valid_xml/> | |
| 18225 </assert_contents> | |
| 18226 </output> | |
| 18227 </test> | |
| 18228 <test expect_num_outputs="2"> | |
| 18229 <conditional name="adv_opts_cond"> | |
| 18230 <param name="adv_opts_selector" value="advanced"/> | |
| 18231 <param name="min_decoy_fraction" value="0.8"/> | |
| 18232 <param name="aim_decoy_fraction" value="1.0"/> | |
| 18233 <param name="shuffle_max_attempts" value="30"/> | |
| 18234 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 18235 <param name="shift_precursor_mz_shift" value="0.0"/> | |
| 18236 <param name="shift_product_mz_shift" value="20.0"/> | |
| 18237 <param name="product_mz_threshold" value="0.025"/> | |
| 18238 <param name="allowed_fragment_types" value="b,y"/> | |
| 18239 <param name="allowed_fragment_charges" value="1,2,3,4"/> | |
| 18240 <param name="enable_detection_specific_losses" value="false"/> | |
| 18241 <param name="enable_detection_unspecific_losses" value="false"/> | |
| 18242 <param name="separate" value="true"/> | |
| 18243 <param name="force" value="false"/> | |
| 18244 <param name="test" value="true"/> | |
| 18245 </conditional> | |
| 18246 <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> | |
| 18247 <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 18248 <param name="out_type" value="TraML"/> | |
| 18249 <param name="method" value="pseudo-reverse"/> | |
| 18250 <param name="decoy_tag" value="DECOY_"/> | |
| 18251 <param name="switchKR" value="false"/> | |
| 18252 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18253 <output name="ctd_out" ftype="xml"> | |
| 18254 <assert_contents> | |
| 18255 <is_valid_xml/> | |
| 18256 </assert_contents> | |
| 18257 </output> | |
| 18258 </test> | |
| 18259 <test expect_num_outputs="2"> | |
| 18260 <conditional name="adv_opts_cond"> | |
| 18261 <param name="adv_opts_selector" value="advanced"/> | |
| 18262 <param name="min_decoy_fraction" value="0.4"/> | |
| 18263 <param name="aim_decoy_fraction" value="1.0"/> | |
| 18264 <param name="shuffle_max_attempts" value="30"/> | |
| 18265 <param name="shuffle_sequence_identity_threshold" value="0.5"/> | |
| 18266 <param name="shift_precursor_mz_shift" value="0.0"/> | |
| 18267 <param name="shift_product_mz_shift" value="20.0"/> | |
| 18268 <param name="product_mz_threshold" value="0.025"/> | |
| 18269 <param name="allowed_fragment_types" value="b,y"/> | |
| 18270 <param name="allowed_fragment_charges" value="1,2,3,4"/> | |
| 18271 <param name="enable_detection_specific_losses" value="true"/> | |
| 18272 <param name="enable_detection_unspecific_losses" value="true"/> | |
| 18273 <param name="separate" value="true"/> | |
| 18274 <param name="force" value="false"/> | |
| 18275 <param name="test" value="true"/> | |
| 18276 </conditional> | |
| 18277 <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> | |
| 18278 <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 18279 <param name="out_type" value="TraML"/> | |
| 18280 <param name="method" value="pseudo-reverse"/> | |
| 18281 <param name="decoy_tag" value="DECOY_"/> | |
| 18282 <param name="switchKR" value="true"/> | |
| 18283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18284 <output name="ctd_out" ftype="xml"> | |
| 18285 <assert_contents> | |
| 18286 <is_valid_xml/> | |
| 18287 </assert_contents> | |
| 18288 </output> | |
| 18289 </test> | |
| 18290 </xml> | |
| 18291 <xml name="autotest_OpenSwathFeatureXMLToTSV"> | |
| 18292 <test expect_num_outputs="2"> | |
| 18293 <conditional name="adv_opts_cond"> | |
| 18294 <param name="adv_opts_selector" value="advanced"/> | |
| 18295 <param name="force" value="false"/> | |
| 18296 <param name="test" value="true"/> | |
| 18297 </conditional> | |
| 18298 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> | |
| 18299 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> | |
| 18300 <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 18301 <param name="short_format" value="true"/> | |
| 18302 <param name="best_scoring_peptide" value=""/> | |
| 18303 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18304 <output name="ctd_out" ftype="xml"> | |
| 18305 <assert_contents> | |
| 18306 <is_valid_xml/> | |
| 18307 </assert_contents> | |
| 18308 </output> | |
| 18309 </test> | |
| 18310 <test expect_num_outputs="2"> | |
| 18311 <conditional name="adv_opts_cond"> | |
| 18312 <param name="adv_opts_selector" value="advanced"/> | |
| 18313 <param name="force" value="false"/> | |
| 18314 <param name="test" value="true"/> | |
| 18315 </conditional> | |
| 18316 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> | |
| 18317 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> | |
| 18318 <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 18319 <param name="short_format" value="false"/> | |
| 18320 <param name="best_scoring_peptide" value=""/> | |
| 18321 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18322 <output name="ctd_out" ftype="xml"> | |
| 18323 <assert_contents> | |
| 18324 <is_valid_xml/> | |
| 18325 </assert_contents> | |
| 18326 </output> | |
| 18327 </test> | |
| 18328 <test expect_num_outputs="2"> | |
| 18329 <conditional name="adv_opts_cond"> | |
| 18330 <param name="adv_opts_selector" value="advanced"/> | |
| 18331 <param name="force" value="false"/> | |
| 18332 <param name="test" value="true"/> | |
| 18333 </conditional> | |
| 18334 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> | |
| 18335 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> | |
| 18336 <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> | |
| 18337 <param name="short_format" value="true"/> | |
| 18338 <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/> | |
| 18339 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18340 <output name="ctd_out" ftype="xml"> | |
| 18341 <assert_contents> | |
| 18342 <is_valid_xml/> | |
| 18343 </assert_contents> | |
| 18344 </output> | |
| 18345 </test> | |
| 18346 </xml> | |
| 18347 <xml name="autotest_OpenSwathFileSplitter"/> | |
| 18348 <xml name="autotest_OpenSwathMzMLFileCacher"> | |
| 18349 <test expect_num_outputs="2"> | |
| 18350 <conditional name="adv_opts_cond"> | |
| 18351 <param name="adv_opts_selector" value="advanced"/> | |
| 18352 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18353 <param name="process_lowmemory" value="false"/> | |
| 18354 <param name="lowmem_batchsize" value="500"/> | |
| 18355 <param name="force" value="false"/> | |
| 18356 <param name="test" value="true"/> | |
| 18357 </conditional> | |
| 18358 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> | |
| 18359 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18360 <param name="out_type" value="mzml"/> | |
| 18361 <param name="lossy_compression" value="true"/> | |
| 18362 <param name="full_meta" value="true"/> | |
| 18363 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18364 <output name="ctd_out" ftype="xml"> | |
| 18365 <assert_contents> | |
| 18366 <is_valid_xml/> | |
| 18367 </assert_contents> | |
| 18368 </output> | |
| 18369 </test> | |
| 18370 <test expect_num_outputs="2"> | |
| 18371 <conditional name="adv_opts_cond"> | |
| 18372 <param name="adv_opts_selector" value="advanced"/> | |
| 18373 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18374 <param name="process_lowmemory" value="false"/> | |
| 18375 <param name="lowmem_batchsize" value="500"/> | |
| 18376 <param name="force" value="false"/> | |
| 18377 <param name="test" value="true"/> | |
| 18378 </conditional> | |
| 18379 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> | |
| 18380 <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18381 <param name="out_type" value="mzml"/> | |
| 18382 <param name="lossy_compression" value="true"/> | |
| 18383 <param name="full_meta" value="true"/> | |
| 18384 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18385 <output name="ctd_out" ftype="xml"> | |
| 18386 <assert_contents> | |
| 18387 <is_valid_xml/> | |
| 18388 </assert_contents> | |
| 18389 </output> | |
| 18390 </test> | |
| 18391 <test expect_num_outputs="2"> | |
| 18392 <conditional name="adv_opts_cond"> | |
| 18393 <param name="adv_opts_selector" value="advanced"/> | |
| 18394 <param name="lossy_mass_accuracy" value="0.0001"/> | |
| 18395 <param name="process_lowmemory" value="false"/> | |
| 18396 <param name="lowmem_batchsize" value="500"/> | |
| 18397 <param name="force" value="false"/> | |
| 18398 <param name="test" value="true"/> | |
| 18399 </conditional> | |
| 18400 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> | |
| 18401 <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> | |
| 18402 <param name="out_type" value="sqmass"/> | |
| 18403 <param name="lossy_compression" value="true"/> | |
| 18404 <param name="full_meta" value="true"/> | |
| 18405 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18406 <output name="ctd_out" ftype="xml"> | |
| 18407 <assert_contents> | |
| 18408 <is_valid_xml/> | |
| 18409 </assert_contents> | |
| 18410 </output> | |
| 18411 </test> | |
| 18412 <test expect_num_outputs="2"> | |
| 18413 <conditional name="adv_opts_cond"> | |
| 18414 <param name="adv_opts_selector" value="advanced"/> | |
| 18415 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18416 <param name="process_lowmemory" value="false"/> | |
| 18417 <param name="lowmem_batchsize" value="500"/> | |
| 18418 <param name="force" value="false"/> | |
| 18419 <param name="test" value="true"/> | |
| 18420 </conditional> | |
| 18421 <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> | |
| 18422 <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18423 <param name="out_type" value="mzml"/> | |
| 18424 <param name="lossy_compression" value="true"/> | |
| 18425 <param name="full_meta" value="true"/> | |
| 18426 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18427 <output name="ctd_out" ftype="xml"> | |
| 18428 <assert_contents> | |
| 18429 <is_valid_xml/> | |
| 18430 </assert_contents> | |
| 18431 </output> | |
| 18432 </test> | |
| 18433 <test expect_num_outputs="2"> | |
| 18434 <conditional name="adv_opts_cond"> | |
| 18435 <param name="adv_opts_selector" value="advanced"/> | |
| 18436 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18437 <param name="process_lowmemory" value="false"/> | |
| 18438 <param name="lowmem_batchsize" value="500"/> | |
| 18439 <param name="force" value="false"/> | |
| 18440 <param name="test" value="true"/> | |
| 18441 </conditional> | |
| 18442 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> | |
| 18443 <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> | |
| 18444 <param name="out_type" value="sqmass"/> | |
| 18445 <param name="lossy_compression" value="true"/> | |
| 18446 <param name="full_meta" value="true"/> | |
| 18447 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18448 <output name="ctd_out" ftype="xml"> | |
| 18449 <assert_contents> | |
| 18450 <is_valid_xml/> | |
| 18451 </assert_contents> | |
| 18452 </output> | |
| 18453 </test> | |
| 18454 <test expect_num_outputs="2"> | |
| 18455 <conditional name="adv_opts_cond"> | |
| 18456 <param name="adv_opts_selector" value="advanced"/> | |
| 18457 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18458 <param name="process_lowmemory" value="false"/> | |
| 18459 <param name="lowmem_batchsize" value="500"/> | |
| 18460 <param name="force" value="false"/> | |
| 18461 <param name="test" value="true"/> | |
| 18462 </conditional> | |
| 18463 <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> | |
| 18464 <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18465 <param name="out_type" value="mzml"/> | |
| 18466 <param name="lossy_compression" value="true"/> | |
| 18467 <param name="full_meta" value="true"/> | |
| 18468 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18469 <output name="ctd_out" ftype="xml"> | |
| 18470 <assert_contents> | |
| 18471 <is_valid_xml/> | |
| 18472 </assert_contents> | |
| 18473 </output> | |
| 18474 </test> | |
| 18475 <test expect_num_outputs="2"> | |
| 18476 <conditional name="adv_opts_cond"> | |
| 18477 <param name="adv_opts_selector" value="advanced"/> | |
| 18478 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18479 <param name="process_lowmemory" value="true"/> | |
| 18480 <param name="lowmem_batchsize" value="500"/> | |
| 18481 <param name="force" value="false"/> | |
| 18482 <param name="test" value="true"/> | |
| 18483 </conditional> | |
| 18484 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> | |
| 18485 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18486 <param name="out_type" value="mzml"/> | |
| 18487 <param name="lossy_compression" value="true"/> | |
| 18488 <param name="full_meta" value="true"/> | |
| 18489 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18490 <output name="ctd_out" ftype="xml"> | |
| 18491 <assert_contents> | |
| 18492 <is_valid_xml/> | |
| 18493 </assert_contents> | |
| 18494 </output> | |
| 18495 </test> | |
| 18496 <test expect_num_outputs="2"> | |
| 18497 <conditional name="adv_opts_cond"> | |
| 18498 <param name="adv_opts_selector" value="advanced"/> | |
| 18499 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18500 <param name="process_lowmemory" value="false"/> | |
| 18501 <param name="lowmem_batchsize" value="500"/> | |
| 18502 <param name="force" value="false"/> | |
| 18503 <param name="test" value="true"/> | |
| 18504 </conditional> | |
| 18505 <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> | |
| 18506 <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/> | |
| 18507 <param name="out_type" value="mzML"/> | |
| 18508 <param name="lossy_compression" value="true"/> | |
| 18509 <param name="full_meta" value="true"/> | |
| 18510 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18511 <output name="ctd_out" ftype="xml"> | |
| 18512 <assert_contents> | |
| 18513 <is_valid_xml/> | |
| 18514 </assert_contents> | |
| 18515 </output> | |
| 18516 </test> | |
| 18517 <test expect_num_outputs="2"> | |
| 18518 <conditional name="adv_opts_cond"> | |
| 18519 <param name="adv_opts_selector" value="advanced"/> | |
| 18520 <param name="lossy_mass_accuracy" value="-1.0"/> | |
| 18521 <param name="process_lowmemory" value="false"/> | |
| 18522 <param name="lowmem_batchsize" value="500"/> | |
| 18523 <param name="force" value="false"/> | |
| 18524 <param name="test" value="true"/> | |
| 18525 </conditional> | |
| 18526 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> | |
| 18527 <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/> | |
| 18528 <param name="out_type" value="mzML"/> | |
| 18529 <param name="lossy_compression" value="true"/> | |
| 18530 <param name="full_meta" value="true"/> | |
| 18531 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18532 <output name="ctd_out" ftype="xml"> | |
| 18533 <assert_contents> | |
| 18534 <is_valid_xml/> | |
| 18535 </assert_contents> | |
| 18536 </output> | |
| 18537 </test> | |
| 18538 <test expect_num_outputs="2"> | |
| 18539 <conditional name="adv_opts_cond"> | |
| 18540 <param name="adv_opts_selector" value="advanced"/> | |
| 18541 <param name="lossy_mass_accuracy" value="0.0001"/> | |
| 18542 <param name="process_lowmemory" value="false"/> | |
| 18543 <param name="lowmem_batchsize" value="500"/> | |
| 18544 <param name="force" value="false"/> | |
| 18545 <param name="test" value="true"/> | |
| 18546 </conditional> | |
| 18547 <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> | |
| 18548 <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18549 <param name="out_type" value="mzml"/> | |
| 18550 <param name="lossy_compression" value="false"/> | |
| 18551 <param name="full_meta" value="false"/> | |
| 18552 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18553 <output name="ctd_out" ftype="xml"> | |
| 18554 <assert_contents> | |
| 18555 <is_valid_xml/> | |
| 18556 </assert_contents> | |
| 18557 </output> | |
| 18558 </test> | |
| 18559 </xml> | |
| 18560 <xml name="autotest_OpenSwathRewriteToFeatureXML"> | |
| 18561 </xml> | |
| 18562 <xml name="autotest_OpenSwathRTNormalizer"> | |
| 18563 <test expect_num_outputs="2"> | |
| 18564 <conditional name="adv_opts_cond"> | |
| 18565 <param name="adv_opts_selector" value="advanced"/> | |
| 18566 <param name="force" value="false"/> | |
| 18567 <param name="test" value="true"/> | |
| 18568 </conditional> | |
| 18569 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> | |
| 18570 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> | |
| 18571 <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> | |
| 18572 <param name="min_rsq" value="0.95"/> | |
| 18573 <param name="min_coverage" value="0.6"/> | |
| 18574 <param name="estimateBestPeptides" value="false"/> | |
| 18575 <section name="RTNormalization"> | |
| 18576 <param name="outlierMethod" value="iter_residual"/> | |
| 18577 <param name="useIterativeChauvenet" value="false"/> | |
| 18578 <param name="RANSACMaxIterations" value="1000"/> | |
| 18579 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 18580 <param name="RANSACSamplingSize" value="10"/> | |
| 18581 </section> | |
| 18582 <section name="algorithm"> | |
| 18583 <param name="stop_report_after_feature" value="-1"/> | |
| 18584 <param name="rt_extraction_window" value="-1.0"/> | |
| 18585 <param name="rt_normalization_factor" value="1.0"/> | |
| 18586 <param name="quantification_cutoff" value="0.0"/> | |
| 18587 <param name="write_convex_hull" value="false"/> | |
| 18588 <param name="spectrum_addition_method" value="simple"/> | |
| 18589 <param name="add_up_spectra" value="1"/> | |
| 18590 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 18591 <param name="uis_threshold_sn" value="-1"/> | |
| 18592 <param name="uis_threshold_peak_area" value="0"/> | |
| 18593 <param name="scoring_model" value="default"/> | |
| 18594 <param name="im_extra_drift" value="0.0"/> | |
| 18595 <section name="TransitionGroupPicker"> | |
| 18596 <param name="stop_after_feature" value="-1"/> | |
| 18597 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 18598 <param name="min_peak_width" value="-1.0"/> | |
| 18599 <param name="peak_integration" value="original"/> | |
| 18600 <param name="background_subtraction" value="none"/> | |
| 18601 <param name="recalculate_peaks" value="false"/> | |
| 18602 <param name="use_precursors" value="false"/> | |
| 18603 <param name="use_consensus" value="true"/> | |
| 18604 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 18605 <param name="minimal_quality" value="-10000.0"/> | |
| 18606 <param name="resample_boundary" value="15.0"/> | |
| 18607 <param name="compute_peak_quality" value="false"/> | |
| 18608 <param name="compute_peak_shape_metrics" value="false"/> | |
| 18609 <param name="compute_total_mi" value="false"/> | |
| 18610 <param name="boundary_selection_method" value="largest"/> | |
| 18611 <section name="PeakPickerMRM"> | |
| 18612 <param name="sgolay_frame_length" value="15"/> | |
| 18613 <param name="sgolay_polynomial_order" value="3"/> | |
| 18614 <param name="gauss_width" value="50.0"/> | |
| 18615 <param name="use_gauss" value="true"/> | |
| 18616 <param name="peak_width" value="-1.0"/> | |
| 18617 <param name="signal_to_noise" value="1.0"/> | |
| 18618 <param name="sn_win_len" value="1000.0"/> | |
| 18619 <param name="sn_bin_count" value="30"/> | |
| 18620 <param name="write_sn_log_messages" value="false"/> | |
| 18621 <param name="remove_overlapping_peaks" value="false"/> | |
| 18622 <param name="method" value="corrected"/> | |
| 18623 </section> | |
| 18624 <section name="PeakIntegrator"> | |
| 18625 <param name="integration_type" value="intensity_sum"/> | |
| 18626 <param name="baseline_type" value="base_to_base"/> | |
| 18627 <param name="fit_EMG" value="false"/> | |
| 18628 </section> | |
| 18629 </section> | |
| 18630 <section name="DIAScoring"> | |
| 18631 <param name="dia_extraction_window" value="0.05"/> | |
| 18632 <param name="dia_extraction_unit" value="Th"/> | |
| 18633 <param name="dia_centroided" value="false"/> | |
| 18634 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 18635 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 18636 <param name="dia_nr_isotopes" value="4"/> | |
| 18637 <param name="dia_nr_charges" value="4"/> | |
| 18638 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 18639 </section> | |
| 18640 <section name="EMGScoring"> | |
| 18641 <param name="interpolation_step" value="0.2"/> | |
| 18642 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 18643 <param name="max_iteration" value="500"/> | |
| 18644 <section name="statistics"> | |
| 18645 <param name="mean" value="1.0"/> | |
| 18646 <param name="variance" value="1.0"/> | |
| 18647 </section> | |
| 18648 </section> | |
| 18649 <section name="Scores"> | |
| 18650 <param name="use_shape_score" value="true"/> | |
| 18651 <param name="use_coelution_score" value="true"/> | |
| 18652 <param name="use_rt_score" value="true"/> | |
| 18653 <param name="use_library_score" value="true"/> | |
| 18654 <param name="use_elution_model_score" value="true"/> | |
| 18655 <param name="use_intensity_score" value="true"/> | |
| 18656 <param name="use_nr_peaks_score" value="true"/> | |
| 18657 <param name="use_total_xic_score" value="true"/> | |
| 18658 <param name="use_total_mi_score" value="false"/> | |
| 18659 <param name="use_sn_score" value="true"/> | |
| 18660 <param name="use_mi_score" value="false"/> | |
| 18661 <param name="use_dia_scores" value="true"/> | |
| 18662 <param name="use_ms1_correlation" value="false"/> | |
| 18663 <param name="use_sonar_scores" value="false"/> | |
| 18664 <param name="use_ion_mobility_scores" value="false"/> | |
| 18665 <param name="use_ms1_fullscan" value="false"/> | |
| 18666 <param name="use_ms1_mi" value="false"/> | |
| 18667 <param name="use_uis_scores" value="false"/> | |
| 18668 </section> | |
| 18669 </section> | |
| 18670 <section name="peptideEstimation"> | |
| 18671 <param name="InitialQualityCutoff" value="0.5"/> | |
| 18672 <param name="OverallQualityCutoff" value="5.5"/> | |
| 18673 <param name="NrRTBins" value="10"/> | |
| 18674 <param name="MinPeptidesPerBin" value="1"/> | |
| 18675 <param name="MinBinsFilled" value="8"/> | |
| 18676 </section> | |
| 18677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18678 <output name="ctd_out" ftype="xml"> | |
| 18679 <assert_contents> | |
| 18680 <is_valid_xml/> | |
| 18681 </assert_contents> | |
| 18682 </output> | |
| 18683 </test> | |
| 18684 <test expect_num_outputs="2"> | |
| 18685 <conditional name="adv_opts_cond"> | |
| 18686 <param name="adv_opts_selector" value="advanced"/> | |
| 18687 <param name="force" value="false"/> | |
| 18688 <param name="test" value="true"/> | |
| 18689 </conditional> | |
| 18690 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> | |
| 18691 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> | |
| 18692 <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> | |
| 18693 <param name="min_rsq" value="0.95"/> | |
| 18694 <param name="min_coverage" value="0.6"/> | |
| 18695 <param name="estimateBestPeptides" value="true"/> | |
| 18696 <section name="RTNormalization"> | |
| 18697 <param name="outlierMethod" value="iter_residual"/> | |
| 18698 <param name="useIterativeChauvenet" value="false"/> | |
| 18699 <param name="RANSACMaxIterations" value="1000"/> | |
| 18700 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 18701 <param name="RANSACSamplingSize" value="10"/> | |
| 18702 </section> | |
| 18703 <section name="algorithm"> | |
| 18704 <param name="stop_report_after_feature" value="-1"/> | |
| 18705 <param name="rt_extraction_window" value="-1.0"/> | |
| 18706 <param name="rt_normalization_factor" value="1.0"/> | |
| 18707 <param name="quantification_cutoff" value="0.0"/> | |
| 18708 <param name="write_convex_hull" value="false"/> | |
| 18709 <param name="spectrum_addition_method" value="simple"/> | |
| 18710 <param name="add_up_spectra" value="1"/> | |
| 18711 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 18712 <param name="uis_threshold_sn" value="-1"/> | |
| 18713 <param name="uis_threshold_peak_area" value="0"/> | |
| 18714 <param name="scoring_model" value="default"/> | |
| 18715 <param name="im_extra_drift" value="0.0"/> | |
| 18716 <section name="TransitionGroupPicker"> | |
| 18717 <param name="stop_after_feature" value="-1"/> | |
| 18718 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 18719 <param name="min_peak_width" value="-1.0"/> | |
| 18720 <param name="peak_integration" value="original"/> | |
| 18721 <param name="background_subtraction" value="none"/> | |
| 18722 <param name="recalculate_peaks" value="false"/> | |
| 18723 <param name="use_precursors" value="false"/> | |
| 18724 <param name="use_consensus" value="true"/> | |
| 18725 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 18726 <param name="minimal_quality" value="-10000.0"/> | |
| 18727 <param name="resample_boundary" value="15.0"/> | |
| 18728 <param name="compute_peak_quality" value="false"/> | |
| 18729 <param name="compute_peak_shape_metrics" value="false"/> | |
| 18730 <param name="compute_total_mi" value="false"/> | |
| 18731 <param name="boundary_selection_method" value="largest"/> | |
| 18732 <section name="PeakPickerMRM"> | |
| 18733 <param name="sgolay_frame_length" value="15"/> | |
| 18734 <param name="sgolay_polynomial_order" value="3"/> | |
| 18735 <param name="gauss_width" value="50.0"/> | |
| 18736 <param name="use_gauss" value="true"/> | |
| 18737 <param name="peak_width" value="-1.0"/> | |
| 18738 <param name="signal_to_noise" value="1.0"/> | |
| 18739 <param name="sn_win_len" value="1000.0"/> | |
| 18740 <param name="sn_bin_count" value="30"/> | |
| 18741 <param name="write_sn_log_messages" value="false"/> | |
| 18742 <param name="remove_overlapping_peaks" value="false"/> | |
| 18743 <param name="method" value="corrected"/> | |
| 18744 </section> | |
| 18745 <section name="PeakIntegrator"> | |
| 18746 <param name="integration_type" value="intensity_sum"/> | |
| 18747 <param name="baseline_type" value="base_to_base"/> | |
| 18748 <param name="fit_EMG" value="false"/> | |
| 18749 </section> | |
| 18750 </section> | |
| 18751 <section name="DIAScoring"> | |
| 18752 <param name="dia_extraction_window" value="0.05"/> | |
| 18753 <param name="dia_extraction_unit" value="Th"/> | |
| 18754 <param name="dia_centroided" value="false"/> | |
| 18755 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 18756 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 18757 <param name="dia_nr_isotopes" value="4"/> | |
| 18758 <param name="dia_nr_charges" value="4"/> | |
| 18759 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 18760 </section> | |
| 18761 <section name="EMGScoring"> | |
| 18762 <param name="interpolation_step" value="0.2"/> | |
| 18763 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 18764 <param name="max_iteration" value="500"/> | |
| 18765 <section name="statistics"> | |
| 18766 <param name="mean" value="1.0"/> | |
| 18767 <param name="variance" value="1.0"/> | |
| 18768 </section> | |
| 18769 </section> | |
| 18770 <section name="Scores"> | |
| 18771 <param name="use_shape_score" value="true"/> | |
| 18772 <param name="use_coelution_score" value="true"/> | |
| 18773 <param name="use_rt_score" value="true"/> | |
| 18774 <param name="use_library_score" value="true"/> | |
| 18775 <param name="use_elution_model_score" value="true"/> | |
| 18776 <param name="use_intensity_score" value="true"/> | |
| 18777 <param name="use_nr_peaks_score" value="true"/> | |
| 18778 <param name="use_total_xic_score" value="true"/> | |
| 18779 <param name="use_total_mi_score" value="false"/> | |
| 18780 <param name="use_sn_score" value="true"/> | |
| 18781 <param name="use_mi_score" value="false"/> | |
| 18782 <param name="use_dia_scores" value="true"/> | |
| 18783 <param name="use_ms1_correlation" value="false"/> | |
| 18784 <param name="use_sonar_scores" value="false"/> | |
| 18785 <param name="use_ion_mobility_scores" value="false"/> | |
| 18786 <param name="use_ms1_fullscan" value="false"/> | |
| 18787 <param name="use_ms1_mi" value="false"/> | |
| 18788 <param name="use_uis_scores" value="false"/> | |
| 18789 </section> | |
| 18790 </section> | |
| 18791 <section name="peptideEstimation"> | |
| 18792 <param name="InitialQualityCutoff" value="0.5"/> | |
| 18793 <param name="OverallQualityCutoff" value="5.5"/> | |
| 18794 <param name="NrRTBins" value="3"/> | |
| 18795 <param name="MinPeptidesPerBin" value="1"/> | |
| 18796 <param name="MinBinsFilled" value="3"/> | |
| 18797 </section> | |
| 18798 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18799 <output name="ctd_out" ftype="xml"> | |
| 18800 <assert_contents> | |
| 18801 <is_valid_xml/> | |
| 18802 </assert_contents> | |
| 18803 </output> | |
| 18804 </test> | |
| 18805 <test expect_num_outputs="2"> | |
| 18806 <conditional name="adv_opts_cond"> | |
| 18807 <param name="adv_opts_selector" value="advanced"/> | |
| 18808 <param name="force" value="false"/> | |
| 18809 <param name="test" value="true"/> | |
| 18810 </conditional> | |
| 18811 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> | |
| 18812 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> | |
| 18813 <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> | |
| 18814 <param name="min_rsq" value="0.95"/> | |
| 18815 <param name="min_coverage" value="0.6"/> | |
| 18816 <param name="estimateBestPeptides" value="false"/> | |
| 18817 <section name="RTNormalization"> | |
| 18818 <param name="outlierMethod" value="iter_residual"/> | |
| 18819 <param name="useIterativeChauvenet" value="false"/> | |
| 18820 <param name="RANSACMaxIterations" value="1000"/> | |
| 18821 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 18822 <param name="RANSACSamplingSize" value="10"/> | |
| 18823 </section> | |
| 18824 <section name="algorithm"> | |
| 18825 <param name="stop_report_after_feature" value="-1"/> | |
| 18826 <param name="rt_extraction_window" value="-1.0"/> | |
| 18827 <param name="rt_normalization_factor" value="1.0"/> | |
| 18828 <param name="quantification_cutoff" value="0.0"/> | |
| 18829 <param name="write_convex_hull" value="false"/> | |
| 18830 <param name="spectrum_addition_method" value="simple"/> | |
| 18831 <param name="add_up_spectra" value="1"/> | |
| 18832 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 18833 <param name="uis_threshold_sn" value="-1"/> | |
| 18834 <param name="uis_threshold_peak_area" value="0"/> | |
| 18835 <param name="scoring_model" value="default"/> | |
| 18836 <param name="im_extra_drift" value="0.0"/> | |
| 18837 <section name="TransitionGroupPicker"> | |
| 18838 <param name="stop_after_feature" value="-1"/> | |
| 18839 <param name="stop_after_intensity_ratio" value="0.0001"/> | |
| 18840 <param name="min_peak_width" value="-1.0"/> | |
| 18841 <param name="peak_integration" value="original"/> | |
| 18842 <param name="background_subtraction" value="none"/> | |
| 18843 <param name="recalculate_peaks" value="false"/> | |
| 18844 <param name="use_precursors" value="false"/> | |
| 18845 <param name="use_consensus" value="true"/> | |
| 18846 <param name="recalculate_peaks_max_z" value="1.0"/> | |
| 18847 <param name="minimal_quality" value="-10000.0"/> | |
| 18848 <param name="resample_boundary" value="15.0"/> | |
| 18849 <param name="compute_peak_quality" value="false"/> | |
| 18850 <param name="compute_peak_shape_metrics" value="false"/> | |
| 18851 <param name="compute_total_mi" value="false"/> | |
| 18852 <param name="boundary_selection_method" value="largest"/> | |
| 18853 <section name="PeakPickerMRM"> | |
| 18854 <param name="sgolay_frame_length" value="15"/> | |
| 18855 <param name="sgolay_polynomial_order" value="3"/> | |
| 18856 <param name="gauss_width" value="50.0"/> | |
| 18857 <param name="use_gauss" value="true"/> | |
| 18858 <param name="peak_width" value="-1.0"/> | |
| 18859 <param name="signal_to_noise" value="1.0"/> | |
| 18860 <param name="sn_win_len" value="1000.0"/> | |
| 18861 <param name="sn_bin_count" value="30"/> | |
| 18862 <param name="write_sn_log_messages" value="false"/> | |
| 18863 <param name="remove_overlapping_peaks" value="false"/> | |
| 18864 <param name="method" value="corrected"/> | |
| 18865 </section> | |
| 18866 <section name="PeakIntegrator"> | |
| 18867 <param name="integration_type" value="intensity_sum"/> | |
| 18868 <param name="baseline_type" value="base_to_base"/> | |
| 18869 <param name="fit_EMG" value="false"/> | |
| 18870 </section> | |
| 18871 </section> | |
| 18872 <section name="DIAScoring"> | |
| 18873 <param name="dia_extraction_window" value="0.05"/> | |
| 18874 <param name="dia_extraction_unit" value="Th"/> | |
| 18875 <param name="dia_centroided" value="false"/> | |
| 18876 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 18877 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 18878 <param name="dia_nr_isotopes" value="4"/> | |
| 18879 <param name="dia_nr_charges" value="4"/> | |
| 18880 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 18881 </section> | |
| 18882 <section name="EMGScoring"> | |
| 18883 <param name="interpolation_step" value="0.2"/> | |
| 18884 <param name="tolerance_stdev_bounding_box" value="3.0"/> | |
| 18885 <param name="max_iteration" value="500"/> | |
| 18886 <section name="statistics"> | |
| 18887 <param name="mean" value="1.0"/> | |
| 18888 <param name="variance" value="1.0"/> | |
| 18889 </section> | |
| 18890 </section> | |
| 18891 <section name="Scores"> | |
| 18892 <param name="use_shape_score" value="true"/> | |
| 18893 <param name="use_coelution_score" value="true"/> | |
| 18894 <param name="use_rt_score" value="true"/> | |
| 18895 <param name="use_library_score" value="true"/> | |
| 18896 <param name="use_elution_model_score" value="true"/> | |
| 18897 <param name="use_intensity_score" value="true"/> | |
| 18898 <param name="use_nr_peaks_score" value="true"/> | |
| 18899 <param name="use_total_xic_score" value="true"/> | |
| 18900 <param name="use_total_mi_score" value="false"/> | |
| 18901 <param name="use_sn_score" value="true"/> | |
| 18902 <param name="use_mi_score" value="false"/> | |
| 18903 <param name="use_dia_scores" value="true"/> | |
| 18904 <param name="use_ms1_correlation" value="false"/> | |
| 18905 <param name="use_sonar_scores" value="false"/> | |
| 18906 <param name="use_ion_mobility_scores" value="false"/> | |
| 18907 <param name="use_ms1_fullscan" value="false"/> | |
| 18908 <param name="use_ms1_mi" value="false"/> | |
| 18909 <param name="use_uis_scores" value="false"/> | |
| 18910 </section> | |
| 18911 </section> | |
| 18912 <section name="peptideEstimation"> | |
| 18913 <param name="InitialQualityCutoff" value="0.5"/> | |
| 18914 <param name="OverallQualityCutoff" value="5.5"/> | |
| 18915 <param name="NrRTBins" value="10"/> | |
| 18916 <param name="MinPeptidesPerBin" value="1"/> | |
| 18917 <param name="MinBinsFilled" value="8"/> | |
| 18918 </section> | |
| 18919 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 18920 <output name="ctd_out" ftype="xml"> | |
| 18921 <assert_contents> | |
| 18922 <is_valid_xml/> | |
| 18923 </assert_contents> | |
| 18924 </output> | |
| 18925 </test> | |
| 18926 </xml> | |
| 18927 <xml name="autotest_OpenSwathWorkflow"> | |
| 18928 <test expect_num_outputs="4"> | |
| 18929 <conditional name="adv_opts_cond"> | |
| 18930 <param name="adv_opts_selector" value="advanced"/> | |
| 18931 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 18932 <param name="sort_swath_maps" value="false"/> | |
| 18933 <param name="use_ms1_traces" value="false"/> | |
| 18934 <param name="enable_uis_scoring" value="false"/> | |
| 18935 <param name="out_chrom_type" value="mzML"/> | |
| 18936 <param name="min_upper_edge_dist" value="0.0"/> | |
| 18937 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 18938 <param name="mz_extraction_window_unit" value="Th"/> | |
| 18939 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 18940 <param name="use_ms1_ion_mobility" value="true"/> | |
| 18941 <param name="matching_window_only" value="false"/> | |
| 18942 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 18943 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 18944 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 18945 <param name="min_rsq" value="0.95"/> | |
| 18946 <param name="min_coverage" value="0.6"/> | |
| 18947 <param name="split_file_input" value="false"/> | |
| 18948 <param name="use_elution_model_score" value="false"/> | |
| 18949 <param name="readOptions" value="normal"/> | |
| 18950 <param name="mz_correction_function" value="none"/> | |
| 18951 <param name="extraction_function" value="tophat"/> | |
| 18952 <param name="batchSize" value="250"/> | |
| 18953 <param name="ms1_isotopes" value="0"/> | |
| 18954 <param name="force" value="false"/> | |
| 18955 <param name="test" value="true"/> | |
| 18956 </conditional> | |
| 18957 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 18958 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 18959 <param name="tr_type" value=""/> | |
| 18960 <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 18961 <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 18962 <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/> | |
| 18963 <param name="sonar" value="false"/> | |
| 18964 <param name="rt_extraction_window" value="600.0"/> | |
| 18965 <param name="ion_mobility_window" value="-1.0"/> | |
| 18966 <param name="mz_extraction_window" value="0.05"/> | |
| 18967 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 18968 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 18969 <section name="Debugging"/> | |
| 18970 <section name="Calibration"> | |
| 18971 <param name="ms1_im_calibration" value="false"/> | |
| 18972 <param name="im_correction_function" value="linear"/> | |
| 18973 <param name="debug_im_file" value=""/> | |
| 18974 <param name="debug_mz_file" value=""/> | |
| 18975 </section> | |
| 18976 <section name="Library"> | |
| 18977 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 18978 <param name="override_group_label_check" value="false"/> | |
| 18979 <param name="force_invalid_mods" value="false"/> | |
| 18980 </section> | |
| 18981 <section name="RTNormalization"> | |
| 18982 <param name="alignmentMethod" value="linear"/> | |
| 18983 <param name="outlierMethod" value="iter_residual"/> | |
| 18984 <param name="useIterativeChauvenet" value="false"/> | |
| 18985 <param name="RANSACMaxIterations" value="1000"/> | |
| 18986 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 18987 <param name="RANSACSamplingSize" value="10"/> | |
| 18988 <param name="estimateBestPeptides" value="false"/> | |
| 18989 <param name="InitialQualityCutoff" value="0.5"/> | |
| 18990 <param name="OverallQualityCutoff" value="5.5"/> | |
| 18991 <param name="NrRTBins" value="10"/> | |
| 18992 <param name="MinPeptidesPerBin" value="1"/> | |
| 18993 <param name="MinBinsFilled" value="8"/> | |
| 18994 <section name="lowess"> | |
| 18995 <param name="span" value="0.666666666666667"/> | |
| 18996 </section> | |
| 18997 <section name="b_spline"> | |
| 18998 <param name="num_nodes" value="5"/> | |
| 18999 </section> | |
| 19000 </section> | |
| 19001 <section name="Scoring"> | |
| 19002 <param name="stop_report_after_feature" value="5"/> | |
| 19003 <param name="rt_normalization_factor" value="100.0"/> | |
| 19004 <param name="quantification_cutoff" value="0.0"/> | |
| 19005 <param name="write_convex_hull" value="false"/> | |
| 19006 <param name="spectrum_addition_method" value="simple"/> | |
| 19007 <param name="add_up_spectra" value="1"/> | |
| 19008 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 19009 <param name="uis_threshold_sn" value="0"/> | |
| 19010 <param name="uis_threshold_peak_area" value="0"/> | |
| 19011 <param name="scoring_model" value="default"/> | |
| 19012 <param name="im_extra_drift" value="0.0"/> | |
| 19013 <section name="TransitionGroupPicker"> | |
| 19014 <param name="stop_after_feature" value="-1"/> | |
| 19015 <param name="min_peak_width" value="-1.0"/> | |
| 19016 <param name="peak_integration" value="original"/> | |
| 19017 <param name="background_subtraction" value="none"/> | |
| 19018 <param name="recalculate_peaks" value="true"/> | |
| 19019 <param name="use_precursors" value="false"/> | |
| 19020 <param name="use_consensus" value="true"/> | |
| 19021 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 19022 <param name="minimal_quality" value="-1.5"/> | |
| 19023 <param name="resample_boundary" value="15.0"/> | |
| 19024 <param name="compute_peak_quality" value="true"/> | |
| 19025 <param name="compute_peak_shape_metrics" value="false"/> | |
| 19026 <param name="compute_total_mi" value="false"/> | |
| 19027 <param name="boundary_selection_method" value="largest"/> | |
| 19028 <section name="PeakPickerMRM"> | |
| 19029 <param name="sgolay_frame_length" value="11"/> | |
| 19030 <param name="sgolay_polynomial_order" value="3"/> | |
| 19031 <param name="gauss_width" value="30.0"/> | |
| 19032 <param name="use_gauss" value="false"/> | |
| 19033 <param name="peak_width" value="-1.0"/> | |
| 19034 <param name="signal_to_noise" value="0.1"/> | |
| 19035 <param name="write_sn_log_messages" value="false"/> | |
| 19036 <param name="remove_overlapping_peaks" value="true"/> | |
| 19037 <param name="method" value="corrected"/> | |
| 19038 </section> | |
| 19039 <section name="PeakIntegrator"> | |
| 19040 <param name="integration_type" value="intensity_sum"/> | |
| 19041 <param name="baseline_type" value="base_to_base"/> | |
| 19042 <param name="fit_EMG" value="false"/> | |
| 19043 </section> | |
| 19044 </section> | |
| 19045 <section name="DIAScoring"> | |
| 19046 <param name="dia_extraction_window" value="0.05"/> | |
| 19047 <param name="dia_extraction_unit" value="Th"/> | |
| 19048 <param name="dia_centroided" value="false"/> | |
| 19049 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 19050 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 19051 <param name="dia_nr_isotopes" value="4"/> | |
| 19052 <param name="dia_nr_charges" value="4"/> | |
| 19053 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 19054 </section> | |
| 19055 <section name="EMGScoring"> | |
| 19056 <param name="max_iteration" value="10"/> | |
| 19057 </section> | |
| 19058 <section name="Scores"> | |
| 19059 <param name="use_shape_score" value="true"/> | |
| 19060 <param name="use_coelution_score" value="true"/> | |
| 19061 <param name="use_rt_score" value="true"/> | |
| 19062 <param name="use_library_score" value="true"/> | |
| 19063 <param name="use_intensity_score" value="true"/> | |
| 19064 <param name="use_nr_peaks_score" value="true"/> | |
| 19065 <param name="use_total_xic_score" value="true"/> | |
| 19066 <param name="use_total_mi_score" value="false"/> | |
| 19067 <param name="use_sn_score" value="true"/> | |
| 19068 <param name="use_mi_score" value="false"/> | |
| 19069 <param name="use_dia_scores" value="true"/> | |
| 19070 <param name="use_ms1_correlation" value="false"/> | |
| 19071 <param name="use_sonar_scores" value="false"/> | |
| 19072 <param name="use_ion_mobility_scores" value="false"/> | |
| 19073 <param name="use_ms1_fullscan" value="false"/> | |
| 19074 <param name="use_ms1_mi" value="false"/> | |
| 19075 <param name="use_uis_scores" value="false"/> | |
| 19076 </section> | |
| 19077 </section> | |
| 19078 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/> | |
| 19079 <output name="ctd_out" ftype="xml"> | |
| 19080 <assert_contents> | |
| 19081 <is_valid_xml/> | |
| 19082 </assert_contents> | |
| 19083 </output> | |
| 19084 </test> | |
| 19085 <test expect_num_outputs="3"> | |
| 19086 <conditional name="adv_opts_cond"> | |
| 19087 <param name="adv_opts_selector" value="advanced"/> | |
| 19088 <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/> | |
| 19089 <param name="sort_swath_maps" value="false"/> | |
| 19090 <param name="use_ms1_traces" value="false"/> | |
| 19091 <param name="enable_uis_scoring" value="false"/> | |
| 19092 <param name="out_chrom_type" value="mzML"/> | |
| 19093 <param name="min_upper_edge_dist" value="0.0"/> | |
| 19094 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 19095 <param name="mz_extraction_window_unit" value="Th"/> | |
| 19096 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 19097 <param name="use_ms1_ion_mobility" value="true"/> | |
| 19098 <param name="matching_window_only" value="false"/> | |
| 19099 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 19100 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 19101 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 19102 <param name="min_rsq" value="0.95"/> | |
| 19103 <param name="min_coverage" value="0.6"/> | |
| 19104 <param name="split_file_input" value="false"/> | |
| 19105 <param name="use_elution_model_score" value="false"/> | |
| 19106 <param name="readOptions" value="normal"/> | |
| 19107 <param name="mz_correction_function" value="none"/> | |
| 19108 <param name="extraction_function" value="tophat"/> | |
| 19109 <param name="batchSize" value="250"/> | |
| 19110 <param name="ms1_isotopes" value="0"/> | |
| 19111 <param name="force" value="false"/> | |
| 19112 <param name="test" value="true"/> | |
| 19113 </conditional> | |
| 19114 <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/> | |
| 19115 <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/> | |
| 19116 <param name="tr_type" value=""/> | |
| 19117 <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 19118 <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 19119 <param name="sonar" value="false"/> | |
| 19120 <param name="rt_extraction_window" value="600.0"/> | |
| 19121 <param name="ion_mobility_window" value="-1.0"/> | |
| 19122 <param name="mz_extraction_window" value="0.05"/> | |
| 19123 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 19124 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 19125 <section name="Debugging"/> | |
| 19126 <section name="Calibration"> | |
| 19127 <param name="ms1_im_calibration" value="false"/> | |
| 19128 <param name="im_correction_function" value="linear"/> | |
| 19129 <param name="debug_im_file" value=""/> | |
| 19130 <param name="debug_mz_file" value=""/> | |
| 19131 </section> | |
| 19132 <section name="Library"> | |
| 19133 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 19134 <param name="override_group_label_check" value="false"/> | |
| 19135 <param name="force_invalid_mods" value="false"/> | |
| 19136 </section> | |
| 19137 <section name="RTNormalization"> | |
| 19138 <param name="alignmentMethod" value="linear"/> | |
| 19139 <param name="outlierMethod" value="iter_residual"/> | |
| 19140 <param name="useIterativeChauvenet" value="false"/> | |
| 19141 <param name="RANSACMaxIterations" value="1000"/> | |
| 19142 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 19143 <param name="RANSACSamplingSize" value="10"/> | |
| 19144 <param name="estimateBestPeptides" value="false"/> | |
| 19145 <param name="InitialQualityCutoff" value="0.5"/> | |
| 19146 <param name="OverallQualityCutoff" value="5.5"/> | |
| 19147 <param name="NrRTBins" value="10"/> | |
| 19148 <param name="MinPeptidesPerBin" value="1"/> | |
| 19149 <param name="MinBinsFilled" value="8"/> | |
| 19150 <section name="lowess"> | |
| 19151 <param name="span" value="0.666666666666667"/> | |
| 19152 </section> | |
| 19153 <section name="b_spline"> | |
| 19154 <param name="num_nodes" value="5"/> | |
| 19155 </section> | |
| 19156 </section> | |
| 19157 <section name="Scoring"> | |
| 19158 <param name="stop_report_after_feature" value="5"/> | |
| 19159 <param name="rt_normalization_factor" value="100.0"/> | |
| 19160 <param name="quantification_cutoff" value="0.0"/> | |
| 19161 <param name="write_convex_hull" value="false"/> | |
| 19162 <param name="spectrum_addition_method" value="simple"/> | |
| 19163 <param name="add_up_spectra" value="1"/> | |
| 19164 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 19165 <param name="uis_threshold_sn" value="0"/> | |
| 19166 <param name="uis_threshold_peak_area" value="0"/> | |
| 19167 <param name="scoring_model" value="default"/> | |
| 19168 <param name="im_extra_drift" value="0.0"/> | |
| 19169 <section name="TransitionGroupPicker"> | |
| 19170 <param name="stop_after_feature" value="-1"/> | |
| 19171 <param name="min_peak_width" value="-1.0"/> | |
| 19172 <param name="peak_integration" value="original"/> | |
| 19173 <param name="background_subtraction" value="none"/> | |
| 19174 <param name="recalculate_peaks" value="true"/> | |
| 19175 <param name="use_precursors" value="false"/> | |
| 19176 <param name="use_consensus" value="true"/> | |
| 19177 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 19178 <param name="minimal_quality" value="-1.5"/> | |
| 19179 <param name="resample_boundary" value="15.0"/> | |
| 19180 <param name="compute_peak_quality" value="true"/> | |
| 19181 <param name="compute_peak_shape_metrics" value="false"/> | |
| 19182 <param name="compute_total_mi" value="false"/> | |
| 19183 <param name="boundary_selection_method" value="largest"/> | |
| 19184 <section name="PeakPickerMRM"> | |
| 19185 <param name="sgolay_frame_length" value="11"/> | |
| 19186 <param name="sgolay_polynomial_order" value="3"/> | |
| 19187 <param name="gauss_width" value="30.0"/> | |
| 19188 <param name="use_gauss" value="false"/> | |
| 19189 <param name="peak_width" value="-1.0"/> | |
| 19190 <param name="signal_to_noise" value="0.1"/> | |
| 19191 <param name="write_sn_log_messages" value="false"/> | |
| 19192 <param name="remove_overlapping_peaks" value="true"/> | |
| 19193 <param name="method" value="corrected"/> | |
| 19194 </section> | |
| 19195 <section name="PeakIntegrator"> | |
| 19196 <param name="integration_type" value="intensity_sum"/> | |
| 19197 <param name="baseline_type" value="base_to_base"/> | |
| 19198 <param name="fit_EMG" value="false"/> | |
| 19199 </section> | |
| 19200 </section> | |
| 19201 <section name="DIAScoring"> | |
| 19202 <param name="dia_extraction_window" value="0.05"/> | |
| 19203 <param name="dia_extraction_unit" value="Th"/> | |
| 19204 <param name="dia_centroided" value="false"/> | |
| 19205 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 19206 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 19207 <param name="dia_nr_isotopes" value="4"/> | |
| 19208 <param name="dia_nr_charges" value="4"/> | |
| 19209 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 19210 </section> | |
| 19211 <section name="EMGScoring"> | |
| 19212 <param name="max_iteration" value="10"/> | |
| 19213 </section> | |
| 19214 <section name="Scores"> | |
| 19215 <param name="use_shape_score" value="true"/> | |
| 19216 <param name="use_coelution_score" value="true"/> | |
| 19217 <param name="use_rt_score" value="true"/> | |
| 19218 <param name="use_library_score" value="true"/> | |
| 19219 <param name="use_intensity_score" value="true"/> | |
| 19220 <param name="use_nr_peaks_score" value="true"/> | |
| 19221 <param name="use_total_xic_score" value="true"/> | |
| 19222 <param name="use_total_mi_score" value="false"/> | |
| 19223 <param name="use_sn_score" value="true"/> | |
| 19224 <param name="use_mi_score" value="false"/> | |
| 19225 <param name="use_dia_scores" value="true"/> | |
| 19226 <param name="use_ms1_correlation" value="false"/> | |
| 19227 <param name="use_sonar_scores" value="false"/> | |
| 19228 <param name="use_ion_mobility_scores" value="false"/> | |
| 19229 <param name="use_ms1_fullscan" value="false"/> | |
| 19230 <param name="use_ms1_mi" value="false"/> | |
| 19231 <param name="use_uis_scores" value="false"/> | |
| 19232 </section> | |
| 19233 </section> | |
| 19234 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 19235 <output name="ctd_out" ftype="xml"> | |
| 19236 <assert_contents> | |
| 19237 <is_valid_xml/> | |
| 19238 </assert_contents> | |
| 19239 </output> | |
| 19240 </test> | |
| 19241 <test expect_num_outputs="3"> | |
| 19242 <conditional name="adv_opts_cond"> | |
| 19243 <param name="adv_opts_selector" value="advanced"/> | |
| 19244 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 19245 <param name="sort_swath_maps" value="false"/> | |
| 19246 <param name="use_ms1_traces" value="true"/> | |
| 19247 <param name="enable_uis_scoring" value="false"/> | |
| 19248 <param name="out_chrom_type" value="mzML"/> | |
| 19249 <param name="min_upper_edge_dist" value="0.0"/> | |
| 19250 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 19251 <param name="mz_extraction_window_unit" value="Th"/> | |
| 19252 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 19253 <param name="use_ms1_ion_mobility" value="true"/> | |
| 19254 <param name="matching_window_only" value="false"/> | |
| 19255 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 19256 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 19257 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 19258 <param name="min_rsq" value="0.95"/> | |
| 19259 <param name="min_coverage" value="0.6"/> | |
| 19260 <param name="split_file_input" value="false"/> | |
| 19261 <param name="use_elution_model_score" value="false"/> | |
| 19262 <param name="readOptions" value="normal"/> | |
| 19263 <param name="mz_correction_function" value="none"/> | |
| 19264 <param name="extraction_function" value="tophat"/> | |
| 19265 <param name="batchSize" value="250"/> | |
| 19266 <param name="ms1_isotopes" value="0"/> | |
| 19267 <param name="force" value="false"/> | |
| 19268 <param name="test" value="true"/> | |
| 19269 </conditional> | |
| 19270 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 19271 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 19272 <param name="tr_type" value=""/> | |
| 19273 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 19274 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 19275 <param name="sonar" value="false"/> | |
| 19276 <param name="rt_extraction_window" value="600.0"/> | |
| 19277 <param name="ion_mobility_window" value="-1.0"/> | |
| 19278 <param name="mz_extraction_window" value="0.05"/> | |
| 19279 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 19280 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 19281 <section name="Debugging"/> | |
| 19282 <section name="Calibration"> | |
| 19283 <param name="ms1_im_calibration" value="false"/> | |
| 19284 <param name="im_correction_function" value="linear"/> | |
| 19285 <param name="debug_im_file" value=""/> | |
| 19286 <param name="debug_mz_file" value=""/> | |
| 19287 </section> | |
| 19288 <section name="Library"> | |
| 19289 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 19290 <param name="override_group_label_check" value="false"/> | |
| 19291 <param name="force_invalid_mods" value="false"/> | |
| 19292 </section> | |
| 19293 <section name="RTNormalization"> | |
| 19294 <param name="alignmentMethod" value="linear"/> | |
| 19295 <param name="outlierMethod" value="iter_residual"/> | |
| 19296 <param name="useIterativeChauvenet" value="false"/> | |
| 19297 <param name="RANSACMaxIterations" value="1000"/> | |
| 19298 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 19299 <param name="RANSACSamplingSize" value="10"/> | |
| 19300 <param name="estimateBestPeptides" value="false"/> | |
| 19301 <param name="InitialQualityCutoff" value="0.5"/> | |
| 19302 <param name="OverallQualityCutoff" value="5.5"/> | |
| 19303 <param name="NrRTBins" value="10"/> | |
| 19304 <param name="MinPeptidesPerBin" value="1"/> | |
| 19305 <param name="MinBinsFilled" value="8"/> | |
| 19306 <section name="lowess"> | |
| 19307 <param name="span" value="0.666666666666667"/> | |
| 19308 </section> | |
| 19309 <section name="b_spline"> | |
| 19310 <param name="num_nodes" value="5"/> | |
| 19311 </section> | |
| 19312 </section> | |
| 19313 <section name="Scoring"> | |
| 19314 <param name="stop_report_after_feature" value="5"/> | |
| 19315 <param name="rt_normalization_factor" value="100.0"/> | |
| 19316 <param name="quantification_cutoff" value="0.0"/> | |
| 19317 <param name="write_convex_hull" value="false"/> | |
| 19318 <param name="spectrum_addition_method" value="simple"/> | |
| 19319 <param name="add_up_spectra" value="1"/> | |
| 19320 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 19321 <param name="uis_threshold_sn" value="0"/> | |
| 19322 <param name="uis_threshold_peak_area" value="0"/> | |
| 19323 <param name="scoring_model" value="default"/> | |
| 19324 <param name="im_extra_drift" value="0.0"/> | |
| 19325 <section name="TransitionGroupPicker"> | |
| 19326 <param name="stop_after_feature" value="-1"/> | |
| 19327 <param name="min_peak_width" value="-1.0"/> | |
| 19328 <param name="peak_integration" value="original"/> | |
| 19329 <param name="background_subtraction" value="none"/> | |
| 19330 <param name="recalculate_peaks" value="true"/> | |
| 19331 <param name="use_precursors" value="false"/> | |
| 19332 <param name="use_consensus" value="true"/> | |
| 19333 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 19334 <param name="minimal_quality" value="-1.5"/> | |
| 19335 <param name="resample_boundary" value="15.0"/> | |
| 19336 <param name="compute_peak_quality" value="true"/> | |
| 19337 <param name="compute_peak_shape_metrics" value="false"/> | |
| 19338 <param name="compute_total_mi" value="false"/> | |
| 19339 <param name="boundary_selection_method" value="largest"/> | |
| 19340 <section name="PeakPickerMRM"> | |
| 19341 <param name="sgolay_frame_length" value="11"/> | |
| 19342 <param name="sgolay_polynomial_order" value="3"/> | |
| 19343 <param name="gauss_width" value="30.0"/> | |
| 19344 <param name="use_gauss" value="false"/> | |
| 19345 <param name="peak_width" value="-1.0"/> | |
| 19346 <param name="signal_to_noise" value="0.1"/> | |
| 19347 <param name="write_sn_log_messages" value="false"/> | |
| 19348 <param name="remove_overlapping_peaks" value="true"/> | |
| 19349 <param name="method" value="corrected"/> | |
| 19350 </section> | |
| 19351 <section name="PeakIntegrator"> | |
| 19352 <param name="integration_type" value="intensity_sum"/> | |
| 19353 <param name="baseline_type" value="base_to_base"/> | |
| 19354 <param name="fit_EMG" value="false"/> | |
| 19355 </section> | |
| 19356 </section> | |
| 19357 <section name="DIAScoring"> | |
| 19358 <param name="dia_extraction_window" value="0.05"/> | |
| 19359 <param name="dia_extraction_unit" value="Th"/> | |
| 19360 <param name="dia_centroided" value="false"/> | |
| 19361 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 19362 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 19363 <param name="dia_nr_isotopes" value="4"/> | |
| 19364 <param name="dia_nr_charges" value="4"/> | |
| 19365 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 19366 </section> | |
| 19367 <section name="EMGScoring"> | |
| 19368 <param name="max_iteration" value="10"/> | |
| 19369 </section> | |
| 19370 <section name="Scores"> | |
| 19371 <param name="use_shape_score" value="true"/> | |
| 19372 <param name="use_coelution_score" value="true"/> | |
| 19373 <param name="use_rt_score" value="true"/> | |
| 19374 <param name="use_library_score" value="true"/> | |
| 19375 <param name="use_intensity_score" value="true"/> | |
| 19376 <param name="use_nr_peaks_score" value="true"/> | |
| 19377 <param name="use_total_xic_score" value="true"/> | |
| 19378 <param name="use_total_mi_score" value="false"/> | |
| 19379 <param name="use_sn_score" value="true"/> | |
| 19380 <param name="use_mi_score" value="false"/> | |
| 19381 <param name="use_dia_scores" value="true"/> | |
| 19382 <param name="use_ms1_correlation" value="false"/> | |
| 19383 <param name="use_sonar_scores" value="false"/> | |
| 19384 <param name="use_ion_mobility_scores" value="false"/> | |
| 19385 <param name="use_ms1_fullscan" value="false"/> | |
| 19386 <param name="use_ms1_mi" value="false"/> | |
| 19387 <param name="use_uis_scores" value="false"/> | |
| 19388 </section> | |
| 19389 </section> | |
| 19390 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 19391 <output name="ctd_out" ftype="xml"> | |
| 19392 <assert_contents> | |
| 19393 <is_valid_xml/> | |
| 19394 </assert_contents> | |
| 19395 </output> | |
| 19396 </test> | |
| 19397 <test expect_num_outputs="3"> | |
| 19398 <conditional name="adv_opts_cond"> | |
| 19399 <param name="adv_opts_selector" value="advanced"/> | |
| 19400 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 19401 <param name="sort_swath_maps" value="false"/> | |
| 19402 <param name="use_ms1_traces" value="true"/> | |
| 19403 <param name="enable_uis_scoring" value="false"/> | |
| 19404 <param name="out_chrom_type" value="mzML"/> | |
| 19405 <param name="min_upper_edge_dist" value="0.0"/> | |
| 19406 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 19407 <param name="mz_extraction_window_unit" value="Th"/> | |
| 19408 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 19409 <param name="use_ms1_ion_mobility" value="true"/> | |
| 19410 <param name="matching_window_only" value="false"/> | |
| 19411 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 19412 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 19413 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 19414 <param name="min_rsq" value="0.95"/> | |
| 19415 <param name="min_coverage" value="0.6"/> | |
| 19416 <param name="split_file_input" value="false"/> | |
| 19417 <param name="use_elution_model_score" value="false"/> | |
| 19418 <param name="readOptions" value="normal"/> | |
| 19419 <param name="mz_correction_function" value="none"/> | |
| 19420 <param name="extraction_function" value="tophat"/> | |
| 19421 <param name="batchSize" value="250"/> | |
| 19422 <param name="ms1_isotopes" value="0"/> | |
| 19423 <param name="force" value="false"/> | |
| 19424 <param name="test" value="true"/> | |
| 19425 </conditional> | |
| 19426 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 19427 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 19428 <param name="tr_type" value=""/> | |
| 19429 <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 19430 <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 19431 <param name="sonar" value="false"/> | |
| 19432 <param name="rt_extraction_window" value="600.0"/> | |
| 19433 <param name="ion_mobility_window" value="-1.0"/> | |
| 19434 <param name="mz_extraction_window" value="0.05"/> | |
| 19435 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 19436 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 19437 <section name="Debugging"/> | |
| 19438 <section name="Calibration"> | |
| 19439 <param name="ms1_im_calibration" value="false"/> | |
| 19440 <param name="im_correction_function" value="linear"/> | |
| 19441 <param name="debug_im_file" value=""/> | |
| 19442 <param name="debug_mz_file" value=""/> | |
| 19443 </section> | |
| 19444 <section name="Library"> | |
| 19445 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 19446 <param name="override_group_label_check" value="false"/> | |
| 19447 <param name="force_invalid_mods" value="false"/> | |
| 19448 </section> | |
| 19449 <section name="RTNormalization"> | |
| 19450 <param name="alignmentMethod" value="linear"/> | |
| 19451 <param name="outlierMethod" value="iter_residual"/> | |
| 19452 <param name="useIterativeChauvenet" value="false"/> | |
| 19453 <param name="RANSACMaxIterations" value="1000"/> | |
| 19454 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 19455 <param name="RANSACSamplingSize" value="10"/> | |
| 19456 <param name="estimateBestPeptides" value="false"/> | |
| 19457 <param name="InitialQualityCutoff" value="0.5"/> | |
| 19458 <param name="OverallQualityCutoff" value="5.5"/> | |
| 19459 <param name="NrRTBins" value="10"/> | |
| 19460 <param name="MinPeptidesPerBin" value="1"/> | |
| 19461 <param name="MinBinsFilled" value="8"/> | |
| 19462 <section name="lowess"> | |
| 19463 <param name="span" value="0.666666666666667"/> | |
| 19464 </section> | |
| 19465 <section name="b_spline"> | |
| 19466 <param name="num_nodes" value="5"/> | |
| 19467 </section> | |
| 19468 </section> | |
| 19469 <section name="Scoring"> | |
| 19470 <param name="stop_report_after_feature" value="5"/> | |
| 19471 <param name="rt_normalization_factor" value="100.0"/> | |
| 19472 <param name="quantification_cutoff" value="0.0"/> | |
| 19473 <param name="write_convex_hull" value="false"/> | |
| 19474 <param name="spectrum_addition_method" value="simple"/> | |
| 19475 <param name="add_up_spectra" value="1"/> | |
| 19476 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 19477 <param name="uis_threshold_sn" value="0"/> | |
| 19478 <param name="uis_threshold_peak_area" value="0"/> | |
| 19479 <param name="scoring_model" value="default"/> | |
| 19480 <param name="im_extra_drift" value="0.0"/> | |
| 19481 <section name="TransitionGroupPicker"> | |
| 19482 <param name="stop_after_feature" value="-1"/> | |
| 19483 <param name="min_peak_width" value="-1.0"/> | |
| 19484 <param name="peak_integration" value="original"/> | |
| 19485 <param name="background_subtraction" value="none"/> | |
| 19486 <param name="recalculate_peaks" value="true"/> | |
| 19487 <param name="use_precursors" value="false"/> | |
| 19488 <param name="use_consensus" value="true"/> | |
| 19489 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 19490 <param name="minimal_quality" value="-1.5"/> | |
| 19491 <param name="resample_boundary" value="15.0"/> | |
| 19492 <param name="compute_peak_quality" value="true"/> | |
| 19493 <param name="compute_peak_shape_metrics" value="false"/> | |
| 19494 <param name="compute_total_mi" value="false"/> | |
| 19495 <param name="boundary_selection_method" value="largest"/> | |
| 19496 <section name="PeakPickerMRM"> | |
| 19497 <param name="sgolay_frame_length" value="11"/> | |
| 19498 <param name="sgolay_polynomial_order" value="3"/> | |
| 19499 <param name="gauss_width" value="30.0"/> | |
| 19500 <param name="use_gauss" value="false"/> | |
| 19501 <param name="peak_width" value="-1.0"/> | |
| 19502 <param name="signal_to_noise" value="0.1"/> | |
| 19503 <param name="write_sn_log_messages" value="false"/> | |
| 19504 <param name="remove_overlapping_peaks" value="true"/> | |
| 19505 <param name="method" value="corrected"/> | |
| 19506 </section> | |
| 19507 <section name="PeakIntegrator"> | |
| 19508 <param name="integration_type" value="intensity_sum"/> | |
| 19509 <param name="baseline_type" value="base_to_base"/> | |
| 19510 <param name="fit_EMG" value="false"/> | |
| 19511 </section> | |
| 19512 </section> | |
| 19513 <section name="DIAScoring"> | |
| 19514 <param name="dia_extraction_window" value="0.05"/> | |
| 19515 <param name="dia_extraction_unit" value="Th"/> | |
| 19516 <param name="dia_centroided" value="false"/> | |
| 19517 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 19518 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 19519 <param name="dia_nr_isotopes" value="4"/> | |
| 19520 <param name="dia_nr_charges" value="4"/> | |
| 19521 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 19522 </section> | |
| 19523 <section name="EMGScoring"> | |
| 19524 <param name="max_iteration" value="10"/> | |
| 19525 </section> | |
| 19526 <section name="Scores"> | |
| 19527 <param name="use_shape_score" value="true"/> | |
| 19528 <param name="use_coelution_score" value="true"/> | |
| 19529 <param name="use_rt_score" value="true"/> | |
| 19530 <param name="use_library_score" value="true"/> | |
| 19531 <param name="use_intensity_score" value="true"/> | |
| 19532 <param name="use_nr_peaks_score" value="true"/> | |
| 19533 <param name="use_total_xic_score" value="true"/> | |
| 19534 <param name="use_total_mi_score" value="false"/> | |
| 19535 <param name="use_sn_score" value="true"/> | |
| 19536 <param name="use_mi_score" value="false"/> | |
| 19537 <param name="use_dia_scores" value="true"/> | |
| 19538 <param name="use_ms1_correlation" value="false"/> | |
| 19539 <param name="use_sonar_scores" value="false"/> | |
| 19540 <param name="use_ion_mobility_scores" value="false"/> | |
| 19541 <param name="use_ms1_fullscan" value="false"/> | |
| 19542 <param name="use_ms1_mi" value="false"/> | |
| 19543 <param name="use_uis_scores" value="false"/> | |
| 19544 </section> | |
| 19545 </section> | |
| 19546 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/> | |
| 19547 <output name="ctd_out" ftype="xml"> | |
| 19548 <assert_contents> | |
| 19549 <is_valid_xml/> | |
| 19550 </assert_contents> | |
| 19551 </output> | |
| 19552 </test> | |
| 19553 <test expect_num_outputs="3"> | |
| 19554 <conditional name="adv_opts_cond"> | |
| 19555 <param name="adv_opts_selector" value="advanced"/> | |
| 19556 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 19557 <param name="sort_swath_maps" value="false"/> | |
| 19558 <param name="use_ms1_traces" value="true"/> | |
| 19559 <param name="enable_uis_scoring" value="false"/> | |
| 19560 <param name="out_chrom_type" value="mzML"/> | |
| 19561 <param name="min_upper_edge_dist" value="0.0"/> | |
| 19562 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 19563 <param name="mz_extraction_window_unit" value="Th"/> | |
| 19564 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 19565 <param name="use_ms1_ion_mobility" value="true"/> | |
| 19566 <param name="matching_window_only" value="false"/> | |
| 19567 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 19568 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 19569 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 19570 <param name="min_rsq" value="0.95"/> | |
| 19571 <param name="min_coverage" value="0.6"/> | |
| 19572 <param name="split_file_input" value="false"/> | |
| 19573 <param name="use_elution_model_score" value="false"/> | |
| 19574 <param name="readOptions" value="cache"/> | |
| 19575 <param name="mz_correction_function" value="none"/> | |
| 19576 <param name="extraction_function" value="tophat"/> | |
| 19577 <param name="batchSize" value="250"/> | |
| 19578 <param name="ms1_isotopes" value="0"/> | |
| 19579 <param name="force" value="false"/> | |
| 19580 <param name="test" value="true"/> | |
| 19581 </conditional> | |
| 19582 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 19583 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 19584 <param name="tr_type" value=""/> | |
| 19585 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 19586 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 19587 <param name="sonar" value="false"/> | |
| 19588 <param name="rt_extraction_window" value="600.0"/> | |
| 19589 <param name="ion_mobility_window" value="-1.0"/> | |
| 19590 <param name="mz_extraction_window" value="0.05"/> | |
| 19591 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 19592 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 19593 <section name="Debugging"/> | |
| 19594 <section name="Calibration"> | |
| 19595 <param name="ms1_im_calibration" value="false"/> | |
| 19596 <param name="im_correction_function" value="linear"/> | |
| 19597 <param name="debug_im_file" value=""/> | |
| 19598 <param name="debug_mz_file" value=""/> | |
| 19599 </section> | |
| 19600 <section name="Library"> | |
| 19601 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 19602 <param name="override_group_label_check" value="false"/> | |
| 19603 <param name="force_invalid_mods" value="false"/> | |
| 19604 </section> | |
| 19605 <section name="RTNormalization"> | |
| 19606 <param name="alignmentMethod" value="linear"/> | |
| 19607 <param name="outlierMethod" value="iter_residual"/> | |
| 19608 <param name="useIterativeChauvenet" value="false"/> | |
| 19609 <param name="RANSACMaxIterations" value="1000"/> | |
| 19610 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 19611 <param name="RANSACSamplingSize" value="10"/> | |
| 19612 <param name="estimateBestPeptides" value="false"/> | |
| 19613 <param name="InitialQualityCutoff" value="0.5"/> | |
| 19614 <param name="OverallQualityCutoff" value="5.5"/> | |
| 19615 <param name="NrRTBins" value="10"/> | |
| 19616 <param name="MinPeptidesPerBin" value="1"/> | |
| 19617 <param name="MinBinsFilled" value="8"/> | |
| 19618 <section name="lowess"> | |
| 19619 <param name="span" value="0.666666666666667"/> | |
| 19620 </section> | |
| 19621 <section name="b_spline"> | |
| 19622 <param name="num_nodes" value="5"/> | |
| 19623 </section> | |
| 19624 </section> | |
| 19625 <section name="Scoring"> | |
| 19626 <param name="stop_report_after_feature" value="5"/> | |
| 19627 <param name="rt_normalization_factor" value="100.0"/> | |
| 19628 <param name="quantification_cutoff" value="0.0"/> | |
| 19629 <param name="write_convex_hull" value="false"/> | |
| 19630 <param name="spectrum_addition_method" value="simple"/> | |
| 19631 <param name="add_up_spectra" value="1"/> | |
| 19632 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 19633 <param name="uis_threshold_sn" value="0"/> | |
| 19634 <param name="uis_threshold_peak_area" value="0"/> | |
| 19635 <param name="scoring_model" value="default"/> | |
| 19636 <param name="im_extra_drift" value="0.0"/> | |
| 19637 <section name="TransitionGroupPicker"> | |
| 19638 <param name="stop_after_feature" value="-1"/> | |
| 19639 <param name="min_peak_width" value="-1.0"/> | |
| 19640 <param name="peak_integration" value="original"/> | |
| 19641 <param name="background_subtraction" value="none"/> | |
| 19642 <param name="recalculate_peaks" value="true"/> | |
| 19643 <param name="use_precursors" value="false"/> | |
| 19644 <param name="use_consensus" value="true"/> | |
| 19645 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 19646 <param name="minimal_quality" value="-1.5"/> | |
| 19647 <param name="resample_boundary" value="15.0"/> | |
| 19648 <param name="compute_peak_quality" value="true"/> | |
| 19649 <param name="compute_peak_shape_metrics" value="false"/> | |
| 19650 <param name="compute_total_mi" value="false"/> | |
| 19651 <param name="boundary_selection_method" value="largest"/> | |
| 19652 <section name="PeakPickerMRM"> | |
| 19653 <param name="sgolay_frame_length" value="11"/> | |
| 19654 <param name="sgolay_polynomial_order" value="3"/> | |
| 19655 <param name="gauss_width" value="30.0"/> | |
| 19656 <param name="use_gauss" value="false"/> | |
| 19657 <param name="peak_width" value="-1.0"/> | |
| 19658 <param name="signal_to_noise" value="0.1"/> | |
| 19659 <param name="write_sn_log_messages" value="false"/> | |
| 19660 <param name="remove_overlapping_peaks" value="true"/> | |
| 19661 <param name="method" value="corrected"/> | |
| 19662 </section> | |
| 19663 <section name="PeakIntegrator"> | |
| 19664 <param name="integration_type" value="intensity_sum"/> | |
| 19665 <param name="baseline_type" value="base_to_base"/> | |
| 19666 <param name="fit_EMG" value="false"/> | |
| 19667 </section> | |
| 19668 </section> | |
| 19669 <section name="DIAScoring"> | |
| 19670 <param name="dia_extraction_window" value="0.05"/> | |
| 19671 <param name="dia_extraction_unit" value="Th"/> | |
| 19672 <param name="dia_centroided" value="false"/> | |
| 19673 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 19674 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 19675 <param name="dia_nr_isotopes" value="4"/> | |
| 19676 <param name="dia_nr_charges" value="4"/> | |
| 19677 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 19678 </section> | |
| 19679 <section name="EMGScoring"> | |
| 19680 <param name="max_iteration" value="10"/> | |
| 19681 </section> | |
| 19682 <section name="Scores"> | |
| 19683 <param name="use_shape_score" value="true"/> | |
| 19684 <param name="use_coelution_score" value="true"/> | |
| 19685 <param name="use_rt_score" value="true"/> | |
| 19686 <param name="use_library_score" value="true"/> | |
| 19687 <param name="use_intensity_score" value="true"/> | |
| 19688 <param name="use_nr_peaks_score" value="true"/> | |
| 19689 <param name="use_total_xic_score" value="true"/> | |
| 19690 <param name="use_total_mi_score" value="false"/> | |
| 19691 <param name="use_sn_score" value="true"/> | |
| 19692 <param name="use_mi_score" value="false"/> | |
| 19693 <param name="use_dia_scores" value="true"/> | |
| 19694 <param name="use_ms1_correlation" value="false"/> | |
| 19695 <param name="use_sonar_scores" value="false"/> | |
| 19696 <param name="use_ion_mobility_scores" value="false"/> | |
| 19697 <param name="use_ms1_fullscan" value="false"/> | |
| 19698 <param name="use_ms1_mi" value="false"/> | |
| 19699 <param name="use_uis_scores" value="false"/> | |
| 19700 </section> | |
| 19701 </section> | |
| 19702 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 19703 <output name="ctd_out" ftype="xml"> | |
| 19704 <assert_contents> | |
| 19705 <is_valid_xml/> | |
| 19706 </assert_contents> | |
| 19707 </output> | |
| 19708 </test> | |
| 19709 <test expect_num_outputs="3"> | |
| 19710 <conditional name="adv_opts_cond"> | |
| 19711 <param name="adv_opts_selector" value="advanced"/> | |
| 19712 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 19713 <param name="sort_swath_maps" value="false"/> | |
| 19714 <param name="use_ms1_traces" value="true"/> | |
| 19715 <param name="enable_uis_scoring" value="false"/> | |
| 19716 <param name="out_chrom_type" value="mzML"/> | |
| 19717 <param name="min_upper_edge_dist" value="0.0"/> | |
| 19718 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 19719 <param name="mz_extraction_window_unit" value="Th"/> | |
| 19720 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 19721 <param name="use_ms1_ion_mobility" value="true"/> | |
| 19722 <param name="matching_window_only" value="false"/> | |
| 19723 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 19724 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 19725 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 19726 <param name="min_rsq" value="0.95"/> | |
| 19727 <param name="min_coverage" value="0.6"/> | |
| 19728 <param name="split_file_input" value="false"/> | |
| 19729 <param name="use_elution_model_score" value="false"/> | |
| 19730 <param name="readOptions" value="cacheWorkingInMemory"/> | |
| 19731 <param name="mz_correction_function" value="none"/> | |
| 19732 <param name="extraction_function" value="tophat"/> | |
| 19733 <param name="batchSize" value="250"/> | |
| 19734 <param name="ms1_isotopes" value="0"/> | |
| 19735 <param name="force" value="false"/> | |
| 19736 <param name="test" value="true"/> | |
| 19737 </conditional> | |
| 19738 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 19739 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 19740 <param name="tr_type" value=""/> | |
| 19741 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 19742 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 19743 <param name="sonar" value="false"/> | |
| 19744 <param name="rt_extraction_window" value="600.0"/> | |
| 19745 <param name="ion_mobility_window" value="-1.0"/> | |
| 19746 <param name="mz_extraction_window" value="0.05"/> | |
| 19747 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 19748 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 19749 <section name="Debugging"/> | |
| 19750 <section name="Calibration"> | |
| 19751 <param name="ms1_im_calibration" value="false"/> | |
| 19752 <param name="im_correction_function" value="linear"/> | |
| 19753 <param name="debug_im_file" value=""/> | |
| 19754 <param name="debug_mz_file" value=""/> | |
| 19755 </section> | |
| 19756 <section name="Library"> | |
| 19757 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 19758 <param name="override_group_label_check" value="false"/> | |
| 19759 <param name="force_invalid_mods" value="false"/> | |
| 19760 </section> | |
| 19761 <section name="RTNormalization"> | |
| 19762 <param name="alignmentMethod" value="linear"/> | |
| 19763 <param name="outlierMethod" value="iter_residual"/> | |
| 19764 <param name="useIterativeChauvenet" value="false"/> | |
| 19765 <param name="RANSACMaxIterations" value="1000"/> | |
| 19766 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 19767 <param name="RANSACSamplingSize" value="10"/> | |
| 19768 <param name="estimateBestPeptides" value="false"/> | |
| 19769 <param name="InitialQualityCutoff" value="0.5"/> | |
| 19770 <param name="OverallQualityCutoff" value="5.5"/> | |
| 19771 <param name="NrRTBins" value="10"/> | |
| 19772 <param name="MinPeptidesPerBin" value="1"/> | |
| 19773 <param name="MinBinsFilled" value="8"/> | |
| 19774 <section name="lowess"> | |
| 19775 <param name="span" value="0.666666666666667"/> | |
| 19776 </section> | |
| 19777 <section name="b_spline"> | |
| 19778 <param name="num_nodes" value="5"/> | |
| 19779 </section> | |
| 19780 </section> | |
| 19781 <section name="Scoring"> | |
| 19782 <param name="stop_report_after_feature" value="5"/> | |
| 19783 <param name="rt_normalization_factor" value="100.0"/> | |
| 19784 <param name="quantification_cutoff" value="0.0"/> | |
| 19785 <param name="write_convex_hull" value="false"/> | |
| 19786 <param name="spectrum_addition_method" value="simple"/> | |
| 19787 <param name="add_up_spectra" value="1"/> | |
| 19788 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 19789 <param name="uis_threshold_sn" value="0"/> | |
| 19790 <param name="uis_threshold_peak_area" value="0"/> | |
| 19791 <param name="scoring_model" value="default"/> | |
| 19792 <param name="im_extra_drift" value="0.0"/> | |
| 19793 <section name="TransitionGroupPicker"> | |
| 19794 <param name="stop_after_feature" value="-1"/> | |
| 19795 <param name="min_peak_width" value="-1.0"/> | |
| 19796 <param name="peak_integration" value="original"/> | |
| 19797 <param name="background_subtraction" value="none"/> | |
| 19798 <param name="recalculate_peaks" value="true"/> | |
| 19799 <param name="use_precursors" value="false"/> | |
| 19800 <param name="use_consensus" value="true"/> | |
| 19801 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 19802 <param name="minimal_quality" value="-1.5"/> | |
| 19803 <param name="resample_boundary" value="15.0"/> | |
| 19804 <param name="compute_peak_quality" value="true"/> | |
| 19805 <param name="compute_peak_shape_metrics" value="false"/> | |
| 19806 <param name="compute_total_mi" value="false"/> | |
| 19807 <param name="boundary_selection_method" value="largest"/> | |
| 19808 <section name="PeakPickerMRM"> | |
| 19809 <param name="sgolay_frame_length" value="11"/> | |
| 19810 <param name="sgolay_polynomial_order" value="3"/> | |
| 19811 <param name="gauss_width" value="30.0"/> | |
| 19812 <param name="use_gauss" value="false"/> | |
| 19813 <param name="peak_width" value="-1.0"/> | |
| 19814 <param name="signal_to_noise" value="0.1"/> | |
| 19815 <param name="write_sn_log_messages" value="false"/> | |
| 19816 <param name="remove_overlapping_peaks" value="true"/> | |
| 19817 <param name="method" value="corrected"/> | |
| 19818 </section> | |
| 19819 <section name="PeakIntegrator"> | |
| 19820 <param name="integration_type" value="intensity_sum"/> | |
| 19821 <param name="baseline_type" value="base_to_base"/> | |
| 19822 <param name="fit_EMG" value="false"/> | |
| 19823 </section> | |
| 19824 </section> | |
| 19825 <section name="DIAScoring"> | |
| 19826 <param name="dia_extraction_window" value="0.05"/> | |
| 19827 <param name="dia_extraction_unit" value="Th"/> | |
| 19828 <param name="dia_centroided" value="false"/> | |
| 19829 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 19830 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 19831 <param name="dia_nr_isotopes" value="4"/> | |
| 19832 <param name="dia_nr_charges" value="4"/> | |
| 19833 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 19834 </section> | |
| 19835 <section name="EMGScoring"> | |
| 19836 <param name="max_iteration" value="10"/> | |
| 19837 </section> | |
| 19838 <section name="Scores"> | |
| 19839 <param name="use_shape_score" value="true"/> | |
| 19840 <param name="use_coelution_score" value="true"/> | |
| 19841 <param name="use_rt_score" value="true"/> | |
| 19842 <param name="use_library_score" value="true"/> | |
| 19843 <param name="use_intensity_score" value="true"/> | |
| 19844 <param name="use_nr_peaks_score" value="true"/> | |
| 19845 <param name="use_total_xic_score" value="true"/> | |
| 19846 <param name="use_total_mi_score" value="false"/> | |
| 19847 <param name="use_sn_score" value="true"/> | |
| 19848 <param name="use_mi_score" value="false"/> | |
| 19849 <param name="use_dia_scores" value="true"/> | |
| 19850 <param name="use_ms1_correlation" value="false"/> | |
| 19851 <param name="use_sonar_scores" value="false"/> | |
| 19852 <param name="use_ion_mobility_scores" value="false"/> | |
| 19853 <param name="use_ms1_fullscan" value="false"/> | |
| 19854 <param name="use_ms1_mi" value="false"/> | |
| 19855 <param name="use_uis_scores" value="false"/> | |
| 19856 </section> | |
| 19857 </section> | |
| 19858 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 19859 <output name="ctd_out" ftype="xml"> | |
| 19860 <assert_contents> | |
| 19861 <is_valid_xml/> | |
| 19862 </assert_contents> | |
| 19863 </output> | |
| 19864 </test> | |
| 19865 <test expect_num_outputs="3"> | |
| 19866 <conditional name="adv_opts_cond"> | |
| 19867 <param name="adv_opts_selector" value="advanced"/> | |
| 19868 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 19869 <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/> | |
| 19870 <param name="sort_swath_maps" value="false"/> | |
| 19871 <param name="use_ms1_traces" value="true"/> | |
| 19872 <param name="enable_uis_scoring" value="false"/> | |
| 19873 <param name="out_chrom_type" value="mzML"/> | |
| 19874 <param name="min_upper_edge_dist" value="0.0"/> | |
| 19875 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 19876 <param name="mz_extraction_window_unit" value="Th"/> | |
| 19877 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 19878 <param name="use_ms1_ion_mobility" value="true"/> | |
| 19879 <param name="matching_window_only" value="false"/> | |
| 19880 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 19881 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 19882 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 19883 <param name="min_rsq" value="0.95"/> | |
| 19884 <param name="min_coverage" value="0.6"/> | |
| 19885 <param name="split_file_input" value="false"/> | |
| 19886 <param name="use_elution_model_score" value="false"/> | |
| 19887 <param name="readOptions" value="normal"/> | |
| 19888 <param name="mz_correction_function" value="none"/> | |
| 19889 <param name="extraction_function" value="tophat"/> | |
| 19890 <param name="batchSize" value="250"/> | |
| 19891 <param name="ms1_isotopes" value="0"/> | |
| 19892 <param name="force" value="false"/> | |
| 19893 <param name="test" value="true"/> | |
| 19894 </conditional> | |
| 19895 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 19896 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 19897 <param name="tr_type" value=""/> | |
| 19898 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 19899 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 19900 <param name="sonar" value="false"/> | |
| 19901 <param name="rt_extraction_window" value="600.0"/> | |
| 19902 <param name="ion_mobility_window" value="-1.0"/> | |
| 19903 <param name="mz_extraction_window" value="0.05"/> | |
| 19904 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 19905 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 19906 <section name="Debugging"/> | |
| 19907 <section name="Calibration"> | |
| 19908 <param name="ms1_im_calibration" value="false"/> | |
| 19909 <param name="im_correction_function" value="linear"/> | |
| 19910 <param name="debug_im_file" value=""/> | |
| 19911 <param name="debug_mz_file" value=""/> | |
| 19912 </section> | |
| 19913 <section name="Library"> | |
| 19914 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 19915 <param name="override_group_label_check" value="false"/> | |
| 19916 <param name="force_invalid_mods" value="false"/> | |
| 19917 </section> | |
| 19918 <section name="RTNormalization"> | |
| 19919 <param name="alignmentMethod" value="linear"/> | |
| 19920 <param name="outlierMethod" value="iter_residual"/> | |
| 19921 <param name="useIterativeChauvenet" value="false"/> | |
| 19922 <param name="RANSACMaxIterations" value="1000"/> | |
| 19923 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 19924 <param name="RANSACSamplingSize" value="10"/> | |
| 19925 <param name="estimateBestPeptides" value="false"/> | |
| 19926 <param name="InitialQualityCutoff" value="0.5"/> | |
| 19927 <param name="OverallQualityCutoff" value="5.5"/> | |
| 19928 <param name="NrRTBins" value="10"/> | |
| 19929 <param name="MinPeptidesPerBin" value="1"/> | |
| 19930 <param name="MinBinsFilled" value="8"/> | |
| 19931 <section name="lowess"> | |
| 19932 <param name="span" value="0.666666666666667"/> | |
| 19933 </section> | |
| 19934 <section name="b_spline"> | |
| 19935 <param name="num_nodes" value="5"/> | |
| 19936 </section> | |
| 19937 </section> | |
| 19938 <section name="Scoring"> | |
| 19939 <param name="stop_report_after_feature" value="5"/> | |
| 19940 <param name="rt_normalization_factor" value="100.0"/> | |
| 19941 <param name="quantification_cutoff" value="0.0"/> | |
| 19942 <param name="write_convex_hull" value="false"/> | |
| 19943 <param name="spectrum_addition_method" value="simple"/> | |
| 19944 <param name="add_up_spectra" value="1"/> | |
| 19945 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 19946 <param name="uis_threshold_sn" value="0"/> | |
| 19947 <param name="uis_threshold_peak_area" value="0"/> | |
| 19948 <param name="scoring_model" value="default"/> | |
| 19949 <param name="im_extra_drift" value="0.0"/> | |
| 19950 <section name="TransitionGroupPicker"> | |
| 19951 <param name="stop_after_feature" value="-1"/> | |
| 19952 <param name="min_peak_width" value="-1.0"/> | |
| 19953 <param name="peak_integration" value="original"/> | |
| 19954 <param name="background_subtraction" value="none"/> | |
| 19955 <param name="recalculate_peaks" value="true"/> | |
| 19956 <param name="use_precursors" value="false"/> | |
| 19957 <param name="use_consensus" value="true"/> | |
| 19958 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 19959 <param name="minimal_quality" value="-1.5"/> | |
| 19960 <param name="resample_boundary" value="15.0"/> | |
| 19961 <param name="compute_peak_quality" value="true"/> | |
| 19962 <param name="compute_peak_shape_metrics" value="false"/> | |
| 19963 <param name="compute_total_mi" value="false"/> | |
| 19964 <param name="boundary_selection_method" value="largest"/> | |
| 19965 <section name="PeakPickerMRM"> | |
| 19966 <param name="sgolay_frame_length" value="11"/> | |
| 19967 <param name="sgolay_polynomial_order" value="3"/> | |
| 19968 <param name="gauss_width" value="30.0"/> | |
| 19969 <param name="use_gauss" value="false"/> | |
| 19970 <param name="peak_width" value="-1.0"/> | |
| 19971 <param name="signal_to_noise" value="0.1"/> | |
| 19972 <param name="write_sn_log_messages" value="false"/> | |
| 19973 <param name="remove_overlapping_peaks" value="true"/> | |
| 19974 <param name="method" value="corrected"/> | |
| 19975 </section> | |
| 19976 <section name="PeakIntegrator"> | |
| 19977 <param name="integration_type" value="intensity_sum"/> | |
| 19978 <param name="baseline_type" value="base_to_base"/> | |
| 19979 <param name="fit_EMG" value="false"/> | |
| 19980 </section> | |
| 19981 </section> | |
| 19982 <section name="DIAScoring"> | |
| 19983 <param name="dia_extraction_window" value="0.05"/> | |
| 19984 <param name="dia_extraction_unit" value="Th"/> | |
| 19985 <param name="dia_centroided" value="false"/> | |
| 19986 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 19987 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 19988 <param name="dia_nr_isotopes" value="4"/> | |
| 19989 <param name="dia_nr_charges" value="4"/> | |
| 19990 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 19991 </section> | |
| 19992 <section name="EMGScoring"> | |
| 19993 <param name="max_iteration" value="10"/> | |
| 19994 </section> | |
| 19995 <section name="Scores"> | |
| 19996 <param name="use_shape_score" value="true"/> | |
| 19997 <param name="use_coelution_score" value="true"/> | |
| 19998 <param name="use_rt_score" value="true"/> | |
| 19999 <param name="use_library_score" value="true"/> | |
| 20000 <param name="use_intensity_score" value="true"/> | |
| 20001 <param name="use_nr_peaks_score" value="true"/> | |
| 20002 <param name="use_total_xic_score" value="true"/> | |
| 20003 <param name="use_total_mi_score" value="false"/> | |
| 20004 <param name="use_sn_score" value="true"/> | |
| 20005 <param name="use_mi_score" value="false"/> | |
| 20006 <param name="use_dia_scores" value="true"/> | |
| 20007 <param name="use_ms1_correlation" value="false"/> | |
| 20008 <param name="use_sonar_scores" value="false"/> | |
| 20009 <param name="use_ion_mobility_scores" value="false"/> | |
| 20010 <param name="use_ms1_fullscan" value="false"/> | |
| 20011 <param name="use_ms1_mi" value="false"/> | |
| 20012 <param name="use_uis_scores" value="false"/> | |
| 20013 </section> | |
| 20014 </section> | |
| 20015 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 20016 <output name="ctd_out" ftype="xml"> | |
| 20017 <assert_contents> | |
| 20018 <is_valid_xml/> | |
| 20019 </assert_contents> | |
| 20020 </output> | |
| 20021 </test> | |
| 20022 <test expect_num_outputs="3"> | |
| 20023 <conditional name="adv_opts_cond"> | |
| 20024 <param name="adv_opts_selector" value="advanced"/> | |
| 20025 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 20026 <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/> | |
| 20027 <param name="sort_swath_maps" value="false"/> | |
| 20028 <param name="use_ms1_traces" value="true"/> | |
| 20029 <param name="enable_uis_scoring" value="false"/> | |
| 20030 <param name="out_chrom_type" value="mzML"/> | |
| 20031 <param name="min_upper_edge_dist" value="0.0"/> | |
| 20032 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 20033 <param name="mz_extraction_window_unit" value="Th"/> | |
| 20034 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 20035 <param name="use_ms1_ion_mobility" value="true"/> | |
| 20036 <param name="matching_window_only" value="false"/> | |
| 20037 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 20038 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 20039 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 20040 <param name="min_rsq" value="0.95"/> | |
| 20041 <param name="min_coverage" value="0.6"/> | |
| 20042 <param name="split_file_input" value="false"/> | |
| 20043 <param name="use_elution_model_score" value="false"/> | |
| 20044 <param name="readOptions" value="normal"/> | |
| 20045 <param name="mz_correction_function" value="none"/> | |
| 20046 <param name="extraction_function" value="tophat"/> | |
| 20047 <param name="batchSize" value="250"/> | |
| 20048 <param name="ms1_isotopes" value="0"/> | |
| 20049 <param name="force" value="true"/> | |
| 20050 <param name="test" value="true"/> | |
| 20051 </conditional> | |
| 20052 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 20053 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 20054 <param name="tr_type" value=""/> | |
| 20055 <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 20056 <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 20057 <param name="sonar" value="false"/> | |
| 20058 <param name="rt_extraction_window" value="600.0"/> | |
| 20059 <param name="ion_mobility_window" value="-1.0"/> | |
| 20060 <param name="mz_extraction_window" value="0.05"/> | |
| 20061 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 20062 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 20063 <section name="Debugging"/> | |
| 20064 <section name="Calibration"> | |
| 20065 <param name="ms1_im_calibration" value="false"/> | |
| 20066 <param name="im_correction_function" value="linear"/> | |
| 20067 <param name="debug_im_file" value=""/> | |
| 20068 <param name="debug_mz_file" value=""/> | |
| 20069 </section> | |
| 20070 <section name="Library"> | |
| 20071 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 20072 <param name="override_group_label_check" value="false"/> | |
| 20073 <param name="force_invalid_mods" value="false"/> | |
| 20074 </section> | |
| 20075 <section name="RTNormalization"> | |
| 20076 <param name="alignmentMethod" value="linear"/> | |
| 20077 <param name="outlierMethod" value="iter_residual"/> | |
| 20078 <param name="useIterativeChauvenet" value="false"/> | |
| 20079 <param name="RANSACMaxIterations" value="1000"/> | |
| 20080 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 20081 <param name="RANSACSamplingSize" value="10"/> | |
| 20082 <param name="estimateBestPeptides" value="false"/> | |
| 20083 <param name="InitialQualityCutoff" value="0.5"/> | |
| 20084 <param name="OverallQualityCutoff" value="5.5"/> | |
| 20085 <param name="NrRTBins" value="10"/> | |
| 20086 <param name="MinPeptidesPerBin" value="1"/> | |
| 20087 <param name="MinBinsFilled" value="8"/> | |
| 20088 <section name="lowess"> | |
| 20089 <param name="span" value="0.666666666666667"/> | |
| 20090 </section> | |
| 20091 <section name="b_spline"> | |
| 20092 <param name="num_nodes" value="5"/> | |
| 20093 </section> | |
| 20094 </section> | |
| 20095 <section name="Scoring"> | |
| 20096 <param name="stop_report_after_feature" value="5"/> | |
| 20097 <param name="rt_normalization_factor" value="100.0"/> | |
| 20098 <param name="quantification_cutoff" value="0.0"/> | |
| 20099 <param name="write_convex_hull" value="false"/> | |
| 20100 <param name="spectrum_addition_method" value="simple"/> | |
| 20101 <param name="add_up_spectra" value="1"/> | |
| 20102 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 20103 <param name="uis_threshold_sn" value="0"/> | |
| 20104 <param name="uis_threshold_peak_area" value="0"/> | |
| 20105 <param name="scoring_model" value="default"/> | |
| 20106 <param name="im_extra_drift" value="0.0"/> | |
| 20107 <section name="TransitionGroupPicker"> | |
| 20108 <param name="stop_after_feature" value="-1"/> | |
| 20109 <param name="min_peak_width" value="-1.0"/> | |
| 20110 <param name="peak_integration" value="original"/> | |
| 20111 <param name="background_subtraction" value="none"/> | |
| 20112 <param name="recalculate_peaks" value="true"/> | |
| 20113 <param name="use_precursors" value="false"/> | |
| 20114 <param name="use_consensus" value="true"/> | |
| 20115 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 20116 <param name="minimal_quality" value="-1.5"/> | |
| 20117 <param name="resample_boundary" value="15.0"/> | |
| 20118 <param name="compute_peak_quality" value="true"/> | |
| 20119 <param name="compute_peak_shape_metrics" value="false"/> | |
| 20120 <param name="compute_total_mi" value="false"/> | |
| 20121 <param name="boundary_selection_method" value="largest"/> | |
| 20122 <section name="PeakPickerMRM"> | |
| 20123 <param name="sgolay_frame_length" value="11"/> | |
| 20124 <param name="sgolay_polynomial_order" value="3"/> | |
| 20125 <param name="gauss_width" value="30.0"/> | |
| 20126 <param name="use_gauss" value="false"/> | |
| 20127 <param name="peak_width" value="-1.0"/> | |
| 20128 <param name="signal_to_noise" value="0.1"/> | |
| 20129 <param name="write_sn_log_messages" value="false"/> | |
| 20130 <param name="remove_overlapping_peaks" value="true"/> | |
| 20131 <param name="method" value="corrected"/> | |
| 20132 </section> | |
| 20133 <section name="PeakIntegrator"> | |
| 20134 <param name="integration_type" value="intensity_sum"/> | |
| 20135 <param name="baseline_type" value="base_to_base"/> | |
| 20136 <param name="fit_EMG" value="false"/> | |
| 20137 </section> | |
| 20138 </section> | |
| 20139 <section name="DIAScoring"> | |
| 20140 <param name="dia_extraction_window" value="0.05"/> | |
| 20141 <param name="dia_extraction_unit" value="Th"/> | |
| 20142 <param name="dia_centroided" value="false"/> | |
| 20143 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 20144 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 20145 <param name="dia_nr_isotopes" value="4"/> | |
| 20146 <param name="dia_nr_charges" value="4"/> | |
| 20147 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 20148 </section> | |
| 20149 <section name="EMGScoring"> | |
| 20150 <param name="max_iteration" value="10"/> | |
| 20151 </section> | |
| 20152 <section name="Scores"> | |
| 20153 <param name="use_shape_score" value="true"/> | |
| 20154 <param name="use_coelution_score" value="true"/> | |
| 20155 <param name="use_rt_score" value="true"/> | |
| 20156 <param name="use_library_score" value="true"/> | |
| 20157 <param name="use_intensity_score" value="true"/> | |
| 20158 <param name="use_nr_peaks_score" value="true"/> | |
| 20159 <param name="use_total_xic_score" value="true"/> | |
| 20160 <param name="use_total_mi_score" value="false"/> | |
| 20161 <param name="use_sn_score" value="true"/> | |
| 20162 <param name="use_mi_score" value="false"/> | |
| 20163 <param name="use_dia_scores" value="true"/> | |
| 20164 <param name="use_ms1_correlation" value="false"/> | |
| 20165 <param name="use_sonar_scores" value="false"/> | |
| 20166 <param name="use_ion_mobility_scores" value="false"/> | |
| 20167 <param name="use_ms1_fullscan" value="false"/> | |
| 20168 <param name="use_ms1_mi" value="false"/> | |
| 20169 <param name="use_uis_scores" value="false"/> | |
| 20170 </section> | |
| 20171 </section> | |
| 20172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 20173 <output name="ctd_out" ftype="xml"> | |
| 20174 <assert_contents> | |
| 20175 <is_valid_xml/> | |
| 20176 </assert_contents> | |
| 20177 </output> | |
| 20178 </test> | |
| 20179 <test expect_num_outputs="3"> | |
| 20180 <conditional name="adv_opts_cond"> | |
| 20181 <param name="adv_opts_selector" value="advanced"/> | |
| 20182 <param name="sort_swath_maps" value="false"/> | |
| 20183 <param name="use_ms1_traces" value="false"/> | |
| 20184 <param name="enable_uis_scoring" value="false"/> | |
| 20185 <param name="out_chrom_type" value="mzML"/> | |
| 20186 <param name="min_upper_edge_dist" value="0.0"/> | |
| 20187 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 20188 <param name="mz_extraction_window_unit" value="Th"/> | |
| 20189 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 20190 <param name="use_ms1_ion_mobility" value="true"/> | |
| 20191 <param name="matching_window_only" value="false"/> | |
| 20192 <param name="irt_mz_extraction_window" value="550.0"/> | |
| 20193 <param name="irt_mz_extraction_window_unit" value="ppm"/> | |
| 20194 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 20195 <param name="min_rsq" value="0.95"/> | |
| 20196 <param name="min_coverage" value="0.6"/> | |
| 20197 <param name="split_file_input" value="false"/> | |
| 20198 <param name="use_elution_model_score" value="false"/> | |
| 20199 <param name="readOptions" value="normal"/> | |
| 20200 <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/> | |
| 20201 <param name="extraction_function" value="tophat"/> | |
| 20202 <param name="batchSize" value="250"/> | |
| 20203 <param name="ms1_isotopes" value="0"/> | |
| 20204 <param name="force" value="false"/> | |
| 20205 <param name="test" value="true"/> | |
| 20206 </conditional> | |
| 20207 <param name="in" value="OpenSwathWorkflow_11_input.mzML"/> | |
| 20208 <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/> | |
| 20209 <param name="tr_type" value=""/> | |
| 20210 <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/> | |
| 20211 <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 20212 <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 20213 <param name="sonar" value="true"/> | |
| 20214 <param name="rt_extraction_window" value="-1.0"/> | |
| 20215 <param name="ion_mobility_window" value="-1.0"/> | |
| 20216 <param name="mz_extraction_window" value="0.2"/> | |
| 20217 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 20218 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 20219 <section name="Debugging"/> | |
| 20220 <section name="Calibration"> | |
| 20221 <param name="ms1_im_calibration" value="false"/> | |
| 20222 <param name="im_correction_function" value="linear"/> | |
| 20223 <param name="debug_im_file" value=""/> | |
| 20224 <param name="debug_mz_file" value=""/> | |
| 20225 </section> | |
| 20226 <section name="Library"> | |
| 20227 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 20228 <param name="override_group_label_check" value="false"/> | |
| 20229 <param name="force_invalid_mods" value="false"/> | |
| 20230 </section> | |
| 20231 <section name="RTNormalization"> | |
| 20232 <param name="alignmentMethod" value="linear"/> | |
| 20233 <param name="outlierMethod" value="none"/> | |
| 20234 <param name="useIterativeChauvenet" value="false"/> | |
| 20235 <param name="RANSACMaxIterations" value="1000"/> | |
| 20236 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 20237 <param name="RANSACSamplingSize" value="10"/> | |
| 20238 <param name="estimateBestPeptides" value="false"/> | |
| 20239 <param name="InitialQualityCutoff" value="0.5"/> | |
| 20240 <param name="OverallQualityCutoff" value="5.5"/> | |
| 20241 <param name="NrRTBins" value="10"/> | |
| 20242 <param name="MinPeptidesPerBin" value="1"/> | |
| 20243 <param name="MinBinsFilled" value="8"/> | |
| 20244 <section name="lowess"> | |
| 20245 <param name="span" value="0.666666666666667"/> | |
| 20246 </section> | |
| 20247 <section name="b_spline"> | |
| 20248 <param name="num_nodes" value="5"/> | |
| 20249 </section> | |
| 20250 </section> | |
| 20251 <section name="Scoring"> | |
| 20252 <param name="stop_report_after_feature" value="5"/> | |
| 20253 <param name="rt_normalization_factor" value="100.0"/> | |
| 20254 <param name="quantification_cutoff" value="0.0"/> | |
| 20255 <param name="write_convex_hull" value="false"/> | |
| 20256 <param name="spectrum_addition_method" value="simple"/> | |
| 20257 <param name="add_up_spectra" value="1"/> | |
| 20258 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 20259 <param name="uis_threshold_sn" value="0"/> | |
| 20260 <param name="uis_threshold_peak_area" value="0"/> | |
| 20261 <param name="scoring_model" value="default"/> | |
| 20262 <param name="im_extra_drift" value="0.0"/> | |
| 20263 <section name="TransitionGroupPicker"> | |
| 20264 <param name="stop_after_feature" value="-1"/> | |
| 20265 <param name="min_peak_width" value="-1.0"/> | |
| 20266 <param name="peak_integration" value="original"/> | |
| 20267 <param name="background_subtraction" value="none"/> | |
| 20268 <param name="recalculate_peaks" value="true"/> | |
| 20269 <param name="use_precursors" value="false"/> | |
| 20270 <param name="use_consensus" value="true"/> | |
| 20271 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 20272 <param name="minimal_quality" value="-1.5"/> | |
| 20273 <param name="resample_boundary" value="15.0"/> | |
| 20274 <param name="compute_peak_quality" value="true"/> | |
| 20275 <param name="compute_peak_shape_metrics" value="false"/> | |
| 20276 <param name="compute_total_mi" value="false"/> | |
| 20277 <param name="boundary_selection_method" value="largest"/> | |
| 20278 <section name="PeakPickerMRM"> | |
| 20279 <param name="sgolay_frame_length" value="11"/> | |
| 20280 <param name="sgolay_polynomial_order" value="3"/> | |
| 20281 <param name="gauss_width" value="30.0"/> | |
| 20282 <param name="use_gauss" value="false"/> | |
| 20283 <param name="peak_width" value="-1.0"/> | |
| 20284 <param name="signal_to_noise" value="0.1"/> | |
| 20285 <param name="write_sn_log_messages" value="false"/> | |
| 20286 <param name="remove_overlapping_peaks" value="true"/> | |
| 20287 <param name="method" value="corrected"/> | |
| 20288 </section> | |
| 20289 <section name="PeakIntegrator"> | |
| 20290 <param name="integration_type" value="intensity_sum"/> | |
| 20291 <param name="baseline_type" value="base_to_base"/> | |
| 20292 <param name="fit_EMG" value="false"/> | |
| 20293 </section> | |
| 20294 </section> | |
| 20295 <section name="DIAScoring"> | |
| 20296 <param name="dia_extraction_window" value="0.05"/> | |
| 20297 <param name="dia_extraction_unit" value="Th"/> | |
| 20298 <param name="dia_centroided" value="false"/> | |
| 20299 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 20300 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 20301 <param name="dia_nr_isotopes" value="4"/> | |
| 20302 <param name="dia_nr_charges" value="4"/> | |
| 20303 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 20304 </section> | |
| 20305 <section name="EMGScoring"> | |
| 20306 <param name="max_iteration" value="10"/> | |
| 20307 </section> | |
| 20308 <section name="Scores"> | |
| 20309 <param name="use_shape_score" value="true"/> | |
| 20310 <param name="use_coelution_score" value="true"/> | |
| 20311 <param name="use_rt_score" value="true"/> | |
| 20312 <param name="use_library_score" value="true"/> | |
| 20313 <param name="use_intensity_score" value="true"/> | |
| 20314 <param name="use_nr_peaks_score" value="true"/> | |
| 20315 <param name="use_total_xic_score" value="true"/> | |
| 20316 <param name="use_total_mi_score" value="false"/> | |
| 20317 <param name="use_sn_score" value="true"/> | |
| 20318 <param name="use_mi_score" value="false"/> | |
| 20319 <param name="use_dia_scores" value="true"/> | |
| 20320 <param name="use_ms1_correlation" value="false"/> | |
| 20321 <param name="use_sonar_scores" value="true"/> | |
| 20322 <param name="use_ion_mobility_scores" value="false"/> | |
| 20323 <param name="use_ms1_fullscan" value="false"/> | |
| 20324 <param name="use_ms1_mi" value="false"/> | |
| 20325 <param name="use_uis_scores" value="false"/> | |
| 20326 </section> | |
| 20327 </section> | |
| 20328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 20329 <output name="ctd_out" ftype="xml"> | |
| 20330 <assert_contents> | |
| 20331 <is_valid_xml/> | |
| 20332 </assert_contents> | |
| 20333 </output> | |
| 20334 </test> | |
| 20335 <test expect_num_outputs="3"> | |
| 20336 <conditional name="adv_opts_cond"> | |
| 20337 <param name="adv_opts_selector" value="advanced"/> | |
| 20338 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 20339 <param name="sort_swath_maps" value="false"/> | |
| 20340 <param name="use_ms1_traces" value="true"/> | |
| 20341 <param name="enable_uis_scoring" value="false"/> | |
| 20342 <param name="out_chrom_type" value="mzML"/> | |
| 20343 <param name="min_upper_edge_dist" value="0.0"/> | |
| 20344 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 20345 <param name="mz_extraction_window_unit" value="Th"/> | |
| 20346 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 20347 <param name="use_ms1_ion_mobility" value="true"/> | |
| 20348 <param name="matching_window_only" value="false"/> | |
| 20349 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 20350 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 20351 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 20352 <param name="min_rsq" value="0.95"/> | |
| 20353 <param name="min_coverage" value="0.6"/> | |
| 20354 <param name="split_file_input" value="false"/> | |
| 20355 <param name="use_elution_model_score" value="false"/> | |
| 20356 <param name="readOptions" value="normal"/> | |
| 20357 <param name="mz_correction_function" value="none"/> | |
| 20358 <param name="extraction_function" value="tophat"/> | |
| 20359 <param name="batchSize" value="250"/> | |
| 20360 <param name="ms1_isotopes" value="0"/> | |
| 20361 <param name="force" value="false"/> | |
| 20362 <param name="test" value="true"/> | |
| 20363 </conditional> | |
| 20364 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 20365 <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/> | |
| 20366 <param name="tr_type" value="pqp"/> | |
| 20367 <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/> | |
| 20368 <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 20369 <param name="sonar" value="false"/> | |
| 20370 <param name="rt_extraction_window" value="600.0"/> | |
| 20371 <param name="ion_mobility_window" value="-1.0"/> | |
| 20372 <param name="mz_extraction_window" value="0.05"/> | |
| 20373 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 20374 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 20375 <section name="Debugging"/> | |
| 20376 <section name="Calibration"> | |
| 20377 <param name="ms1_im_calibration" value="false"/> | |
| 20378 <param name="im_correction_function" value="linear"/> | |
| 20379 <param name="debug_im_file" value=""/> | |
| 20380 <param name="debug_mz_file" value=""/> | |
| 20381 </section> | |
| 20382 <section name="Library"> | |
| 20383 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 20384 <param name="override_group_label_check" value="false"/> | |
| 20385 <param name="force_invalid_mods" value="false"/> | |
| 20386 </section> | |
| 20387 <section name="RTNormalization"> | |
| 20388 <param name="alignmentMethod" value="linear"/> | |
| 20389 <param name="outlierMethod" value="iter_residual"/> | |
| 20390 <param name="useIterativeChauvenet" value="false"/> | |
| 20391 <param name="RANSACMaxIterations" value="1000"/> | |
| 20392 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 20393 <param name="RANSACSamplingSize" value="10"/> | |
| 20394 <param name="estimateBestPeptides" value="false"/> | |
| 20395 <param name="InitialQualityCutoff" value="0.5"/> | |
| 20396 <param name="OverallQualityCutoff" value="5.5"/> | |
| 20397 <param name="NrRTBins" value="10"/> | |
| 20398 <param name="MinPeptidesPerBin" value="1"/> | |
| 20399 <param name="MinBinsFilled" value="8"/> | |
| 20400 <section name="lowess"> | |
| 20401 <param name="span" value="0.666666666666667"/> | |
| 20402 </section> | |
| 20403 <section name="b_spline"> | |
| 20404 <param name="num_nodes" value="5"/> | |
| 20405 </section> | |
| 20406 </section> | |
| 20407 <section name="Scoring"> | |
| 20408 <param name="stop_report_after_feature" value="5"/> | |
| 20409 <param name="rt_normalization_factor" value="100.0"/> | |
| 20410 <param name="quantification_cutoff" value="0.0"/> | |
| 20411 <param name="write_convex_hull" value="false"/> | |
| 20412 <param name="spectrum_addition_method" value="simple"/> | |
| 20413 <param name="add_up_spectra" value="1"/> | |
| 20414 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 20415 <param name="uis_threshold_sn" value="0"/> | |
| 20416 <param name="uis_threshold_peak_area" value="0"/> | |
| 20417 <param name="scoring_model" value="default"/> | |
| 20418 <param name="im_extra_drift" value="0.0"/> | |
| 20419 <section name="TransitionGroupPicker"> | |
| 20420 <param name="stop_after_feature" value="-1"/> | |
| 20421 <param name="min_peak_width" value="-1.0"/> | |
| 20422 <param name="peak_integration" value="original"/> | |
| 20423 <param name="background_subtraction" value="none"/> | |
| 20424 <param name="recalculate_peaks" value="true"/> | |
| 20425 <param name="use_precursors" value="false"/> | |
| 20426 <param name="use_consensus" value="true"/> | |
| 20427 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 20428 <param name="minimal_quality" value="-1.5"/> | |
| 20429 <param name="resample_boundary" value="15.0"/> | |
| 20430 <param name="compute_peak_quality" value="true"/> | |
| 20431 <param name="compute_peak_shape_metrics" value="false"/> | |
| 20432 <param name="compute_total_mi" value="false"/> | |
| 20433 <param name="boundary_selection_method" value="largest"/> | |
| 20434 <section name="PeakPickerMRM"> | |
| 20435 <param name="sgolay_frame_length" value="11"/> | |
| 20436 <param name="sgolay_polynomial_order" value="3"/> | |
| 20437 <param name="gauss_width" value="30.0"/> | |
| 20438 <param name="use_gauss" value="false"/> | |
| 20439 <param name="peak_width" value="-1.0"/> | |
| 20440 <param name="signal_to_noise" value="0.1"/> | |
| 20441 <param name="write_sn_log_messages" value="false"/> | |
| 20442 <param name="remove_overlapping_peaks" value="true"/> | |
| 20443 <param name="method" value="corrected"/> | |
| 20444 </section> | |
| 20445 <section name="PeakIntegrator"> | |
| 20446 <param name="integration_type" value="intensity_sum"/> | |
| 20447 <param name="baseline_type" value="base_to_base"/> | |
| 20448 <param name="fit_EMG" value="false"/> | |
| 20449 </section> | |
| 20450 </section> | |
| 20451 <section name="DIAScoring"> | |
| 20452 <param name="dia_extraction_window" value="0.05"/> | |
| 20453 <param name="dia_extraction_unit" value="Th"/> | |
| 20454 <param name="dia_centroided" value="false"/> | |
| 20455 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 20456 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 20457 <param name="dia_nr_isotopes" value="4"/> | |
| 20458 <param name="dia_nr_charges" value="4"/> | |
| 20459 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 20460 </section> | |
| 20461 <section name="EMGScoring"> | |
| 20462 <param name="max_iteration" value="10"/> | |
| 20463 </section> | |
| 20464 <section name="Scores"> | |
| 20465 <param name="use_shape_score" value="true"/> | |
| 20466 <param name="use_coelution_score" value="true"/> | |
| 20467 <param name="use_rt_score" value="true"/> | |
| 20468 <param name="use_library_score" value="true"/> | |
| 20469 <param name="use_intensity_score" value="true"/> | |
| 20470 <param name="use_nr_peaks_score" value="true"/> | |
| 20471 <param name="use_total_xic_score" value="true"/> | |
| 20472 <param name="use_total_mi_score" value="false"/> | |
| 20473 <param name="use_sn_score" value="true"/> | |
| 20474 <param name="use_mi_score" value="false"/> | |
| 20475 <param name="use_dia_scores" value="true"/> | |
| 20476 <param name="use_ms1_correlation" value="false"/> | |
| 20477 <param name="use_sonar_scores" value="false"/> | |
| 20478 <param name="use_ion_mobility_scores" value="false"/> | |
| 20479 <param name="use_ms1_fullscan" value="false"/> | |
| 20480 <param name="use_ms1_mi" value="false"/> | |
| 20481 <param name="use_uis_scores" value="false"/> | |
| 20482 </section> | |
| 20483 </section> | |
| 20484 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> | |
| 20485 <output name="ctd_out" ftype="xml"> | |
| 20486 <assert_contents> | |
| 20487 <is_valid_xml/> | |
| 20488 </assert_contents> | |
| 20489 </output> | |
| 20490 </test> | |
| 20491 <test expect_num_outputs="3"> | |
| 20492 <conditional name="adv_opts_cond"> | |
| 20493 <param name="adv_opts_selector" value="advanced"/> | |
| 20494 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 20495 <param name="sort_swath_maps" value="false"/> | |
| 20496 <param name="use_ms1_traces" value="true"/> | |
| 20497 <param name="enable_uis_scoring" value="false"/> | |
| 20498 <param name="out_chrom_type" value="sqMass"/> | |
| 20499 <param name="min_upper_edge_dist" value="0.0"/> | |
| 20500 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 20501 <param name="mz_extraction_window_unit" value="Th"/> | |
| 20502 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 20503 <param name="use_ms1_ion_mobility" value="true"/> | |
| 20504 <param name="matching_window_only" value="false"/> | |
| 20505 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 20506 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 20507 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 20508 <param name="min_rsq" value="0.95"/> | |
| 20509 <param name="min_coverage" value="0.6"/> | |
| 20510 <param name="split_file_input" value="false"/> | |
| 20511 <param name="use_elution_model_score" value="false"/> | |
| 20512 <param name="readOptions" value="normal"/> | |
| 20513 <param name="mz_correction_function" value="none"/> | |
| 20514 <param name="extraction_function" value="tophat"/> | |
| 20515 <param name="batchSize" value="250"/> | |
| 20516 <param name="ms1_isotopes" value="0"/> | |
| 20517 <param name="force" value="false"/> | |
| 20518 <param name="test" value="true"/> | |
| 20519 </conditional> | |
| 20520 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 20521 <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/> | |
| 20522 <param name="tr_type" value="pqp"/> | |
| 20523 <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/> | |
| 20524 <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> | |
| 20525 <param name="sonar" value="false"/> | |
| 20526 <param name="rt_extraction_window" value="600.0"/> | |
| 20527 <param name="ion_mobility_window" value="-1.0"/> | |
| 20528 <param name="mz_extraction_window" value="0.05"/> | |
| 20529 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 20530 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 20531 <section name="Debugging"/> | |
| 20532 <section name="Calibration"> | |
| 20533 <param name="ms1_im_calibration" value="false"/> | |
| 20534 <param name="im_correction_function" value="linear"/> | |
| 20535 <param name="debug_im_file" value=""/> | |
| 20536 <param name="debug_mz_file" value=""/> | |
| 20537 </section> | |
| 20538 <section name="Library"> | |
| 20539 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 20540 <param name="override_group_label_check" value="false"/> | |
| 20541 <param name="force_invalid_mods" value="false"/> | |
| 20542 </section> | |
| 20543 <section name="RTNormalization"> | |
| 20544 <param name="alignmentMethod" value="linear"/> | |
| 20545 <param name="outlierMethod" value="iter_residual"/> | |
| 20546 <param name="useIterativeChauvenet" value="false"/> | |
| 20547 <param name="RANSACMaxIterations" value="1000"/> | |
| 20548 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 20549 <param name="RANSACSamplingSize" value="10"/> | |
| 20550 <param name="estimateBestPeptides" value="false"/> | |
| 20551 <param name="InitialQualityCutoff" value="0.5"/> | |
| 20552 <param name="OverallQualityCutoff" value="5.5"/> | |
| 20553 <param name="NrRTBins" value="10"/> | |
| 20554 <param name="MinPeptidesPerBin" value="1"/> | |
| 20555 <param name="MinBinsFilled" value="8"/> | |
| 20556 <section name="lowess"> | |
| 20557 <param name="span" value="0.666666666666667"/> | |
| 20558 </section> | |
| 20559 <section name="b_spline"> | |
| 20560 <param name="num_nodes" value="5"/> | |
| 20561 </section> | |
| 20562 </section> | |
| 20563 <section name="Scoring"> | |
| 20564 <param name="stop_report_after_feature" value="5"/> | |
| 20565 <param name="rt_normalization_factor" value="100.0"/> | |
| 20566 <param name="quantification_cutoff" value="0.0"/> | |
| 20567 <param name="write_convex_hull" value="false"/> | |
| 20568 <param name="spectrum_addition_method" value="simple"/> | |
| 20569 <param name="add_up_spectra" value="1"/> | |
| 20570 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 20571 <param name="uis_threshold_sn" value="0"/> | |
| 20572 <param name="uis_threshold_peak_area" value="0"/> | |
| 20573 <param name="scoring_model" value="default"/> | |
| 20574 <param name="im_extra_drift" value="0.0"/> | |
| 20575 <section name="TransitionGroupPicker"> | |
| 20576 <param name="stop_after_feature" value="-1"/> | |
| 20577 <param name="min_peak_width" value="-1.0"/> | |
| 20578 <param name="peak_integration" value="original"/> | |
| 20579 <param name="background_subtraction" value="none"/> | |
| 20580 <param name="recalculate_peaks" value="true"/> | |
| 20581 <param name="use_precursors" value="false"/> | |
| 20582 <param name="use_consensus" value="true"/> | |
| 20583 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 20584 <param name="minimal_quality" value="-1.5"/> | |
| 20585 <param name="resample_boundary" value="15.0"/> | |
| 20586 <param name="compute_peak_quality" value="true"/> | |
| 20587 <param name="compute_peak_shape_metrics" value="false"/> | |
| 20588 <param name="compute_total_mi" value="false"/> | |
| 20589 <param name="boundary_selection_method" value="largest"/> | |
| 20590 <section name="PeakPickerMRM"> | |
| 20591 <param name="sgolay_frame_length" value="11"/> | |
| 20592 <param name="sgolay_polynomial_order" value="3"/> | |
| 20593 <param name="gauss_width" value="30.0"/> | |
| 20594 <param name="use_gauss" value="false"/> | |
| 20595 <param name="peak_width" value="-1.0"/> | |
| 20596 <param name="signal_to_noise" value="0.1"/> | |
| 20597 <param name="write_sn_log_messages" value="false"/> | |
| 20598 <param name="remove_overlapping_peaks" value="true"/> | |
| 20599 <param name="method" value="corrected"/> | |
| 20600 </section> | |
| 20601 <section name="PeakIntegrator"> | |
| 20602 <param name="integration_type" value="intensity_sum"/> | |
| 20603 <param name="baseline_type" value="base_to_base"/> | |
| 20604 <param name="fit_EMG" value="false"/> | |
| 20605 </section> | |
| 20606 </section> | |
| 20607 <section name="DIAScoring"> | |
| 20608 <param name="dia_extraction_window" value="0.05"/> | |
| 20609 <param name="dia_extraction_unit" value="Th"/> | |
| 20610 <param name="dia_centroided" value="false"/> | |
| 20611 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 20612 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 20613 <param name="dia_nr_isotopes" value="4"/> | |
| 20614 <param name="dia_nr_charges" value="4"/> | |
| 20615 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 20616 </section> | |
| 20617 <section name="EMGScoring"> | |
| 20618 <param name="max_iteration" value="10"/> | |
| 20619 </section> | |
| 20620 <section name="Scores"> | |
| 20621 <param name="use_shape_score" value="true"/> | |
| 20622 <param name="use_coelution_score" value="true"/> | |
| 20623 <param name="use_rt_score" value="true"/> | |
| 20624 <param name="use_library_score" value="true"/> | |
| 20625 <param name="use_intensity_score" value="true"/> | |
| 20626 <param name="use_nr_peaks_score" value="true"/> | |
| 20627 <param name="use_total_xic_score" value="true"/> | |
| 20628 <param name="use_total_mi_score" value="false"/> | |
| 20629 <param name="use_sn_score" value="true"/> | |
| 20630 <param name="use_mi_score" value="false"/> | |
| 20631 <param name="use_dia_scores" value="true"/> | |
| 20632 <param name="use_ms1_correlation" value="false"/> | |
| 20633 <param name="use_sonar_scores" value="false"/> | |
| 20634 <param name="use_ion_mobility_scores" value="false"/> | |
| 20635 <param name="use_ms1_fullscan" value="false"/> | |
| 20636 <param name="use_ms1_mi" value="false"/> | |
| 20637 <param name="use_uis_scores" value="false"/> | |
| 20638 </section> | |
| 20639 </section> | |
| 20640 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> | |
| 20641 <output name="ctd_out" ftype="xml"> | |
| 20642 <assert_contents> | |
| 20643 <is_valid_xml/> | |
| 20644 </assert_contents> | |
| 20645 </output> | |
| 20646 </test> | |
| 20647 <test expect_num_outputs="3"> | |
| 20648 <conditional name="adv_opts_cond"> | |
| 20649 <param name="adv_opts_selector" value="advanced"/> | |
| 20650 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 20651 <param name="sort_swath_maps" value="false"/> | |
| 20652 <param name="use_ms1_traces" value="true"/> | |
| 20653 <param name="enable_uis_scoring" value="false"/> | |
| 20654 <param name="out_chrom_type" value="mzML"/> | |
| 20655 <param name="min_upper_edge_dist" value="0.0"/> | |
| 20656 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 20657 <param name="mz_extraction_window_unit" value="Th"/> | |
| 20658 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 20659 <param name="use_ms1_ion_mobility" value="true"/> | |
| 20660 <param name="matching_window_only" value="false"/> | |
| 20661 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 20662 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 20663 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 20664 <param name="min_rsq" value="0.95"/> | |
| 20665 <param name="min_coverage" value="0.6"/> | |
| 20666 <param name="split_file_input" value="false"/> | |
| 20667 <param name="use_elution_model_score" value="false"/> | |
| 20668 <param name="readOptions" value="normal"/> | |
| 20669 <param name="mz_correction_function" value="none"/> | |
| 20670 <param name="extraction_function" value="tophat"/> | |
| 20671 <param name="batchSize" value="250"/> | |
| 20672 <param name="ms1_isotopes" value="2"/> | |
| 20673 <param name="force" value="false"/> | |
| 20674 <param name="test" value="true"/> | |
| 20675 </conditional> | |
| 20676 <param name="in" value="OpenSwathWorkflow_15_input.mzML"/> | |
| 20677 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 20678 <param name="tr_type" value=""/> | |
| 20679 <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 20680 <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 20681 <param name="sonar" value="false"/> | |
| 20682 <param name="rt_extraction_window" value="600.0"/> | |
| 20683 <param name="ion_mobility_window" value="-1.0"/> | |
| 20684 <param name="mz_extraction_window" value="0.05"/> | |
| 20685 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 20686 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 20687 <section name="Debugging"/> | |
| 20688 <section name="Calibration"> | |
| 20689 <param name="ms1_im_calibration" value="false"/> | |
| 20690 <param name="im_correction_function" value="linear"/> | |
| 20691 <param name="debug_im_file" value=""/> | |
| 20692 <param name="debug_mz_file" value=""/> | |
| 20693 </section> | |
| 20694 <section name="Library"> | |
| 20695 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 20696 <param name="override_group_label_check" value="false"/> | |
| 20697 <param name="force_invalid_mods" value="false"/> | |
| 20698 </section> | |
| 20699 <section name="RTNormalization"> | |
| 20700 <param name="alignmentMethod" value="linear"/> | |
| 20701 <param name="outlierMethod" value="iter_residual"/> | |
| 20702 <param name="useIterativeChauvenet" value="false"/> | |
| 20703 <param name="RANSACMaxIterations" value="1000"/> | |
| 20704 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 20705 <param name="RANSACSamplingSize" value="10"/> | |
| 20706 <param name="estimateBestPeptides" value="false"/> | |
| 20707 <param name="InitialQualityCutoff" value="0.5"/> | |
| 20708 <param name="OverallQualityCutoff" value="5.5"/> | |
| 20709 <param name="NrRTBins" value="10"/> | |
| 20710 <param name="MinPeptidesPerBin" value="1"/> | |
| 20711 <param name="MinBinsFilled" value="8"/> | |
| 20712 <section name="lowess"> | |
| 20713 <param name="span" value="0.666666666666667"/> | |
| 20714 </section> | |
| 20715 <section name="b_spline"> | |
| 20716 <param name="num_nodes" value="5"/> | |
| 20717 </section> | |
| 20718 </section> | |
| 20719 <section name="Scoring"> | |
| 20720 <param name="stop_report_after_feature" value="5"/> | |
| 20721 <param name="rt_normalization_factor" value="100.0"/> | |
| 20722 <param name="quantification_cutoff" value="0.0"/> | |
| 20723 <param name="write_convex_hull" value="false"/> | |
| 20724 <param name="spectrum_addition_method" value="simple"/> | |
| 20725 <param name="add_up_spectra" value="1"/> | |
| 20726 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 20727 <param name="uis_threshold_sn" value="0"/> | |
| 20728 <param name="uis_threshold_peak_area" value="0"/> | |
| 20729 <param name="scoring_model" value="default"/> | |
| 20730 <param name="im_extra_drift" value="0.0"/> | |
| 20731 <section name="TransitionGroupPicker"> | |
| 20732 <param name="stop_after_feature" value="-1"/> | |
| 20733 <param name="min_peak_width" value="-1.0"/> | |
| 20734 <param name="peak_integration" value="original"/> | |
| 20735 <param name="background_subtraction" value="none"/> | |
| 20736 <param name="recalculate_peaks" value="true"/> | |
| 20737 <param name="use_precursors" value="true"/> | |
| 20738 <param name="use_consensus" value="true"/> | |
| 20739 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 20740 <param name="minimal_quality" value="-1.5"/> | |
| 20741 <param name="resample_boundary" value="15.0"/> | |
| 20742 <param name="compute_peak_quality" value="false"/> | |
| 20743 <param name="compute_peak_shape_metrics" value="false"/> | |
| 20744 <param name="compute_total_mi" value="false"/> | |
| 20745 <param name="boundary_selection_method" value="largest"/> | |
| 20746 <section name="PeakPickerMRM"> | |
| 20747 <param name="sgolay_frame_length" value="11"/> | |
| 20748 <param name="sgolay_polynomial_order" value="3"/> | |
| 20749 <param name="gauss_width" value="30.0"/> | |
| 20750 <param name="use_gauss" value="false"/> | |
| 20751 <param name="peak_width" value="-1.0"/> | |
| 20752 <param name="signal_to_noise" value="0.1"/> | |
| 20753 <param name="write_sn_log_messages" value="false"/> | |
| 20754 <param name="remove_overlapping_peaks" value="true"/> | |
| 20755 <param name="method" value="corrected"/> | |
| 20756 </section> | |
| 20757 <section name="PeakIntegrator"> | |
| 20758 <param name="integration_type" value="intensity_sum"/> | |
| 20759 <param name="baseline_type" value="base_to_base"/> | |
| 20760 <param name="fit_EMG" value="false"/> | |
| 20761 </section> | |
| 20762 </section> | |
| 20763 <section name="DIAScoring"> | |
| 20764 <param name="dia_extraction_window" value="0.05"/> | |
| 20765 <param name="dia_extraction_unit" value="Th"/> | |
| 20766 <param name="dia_centroided" value="false"/> | |
| 20767 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 20768 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 20769 <param name="dia_nr_isotopes" value="4"/> | |
| 20770 <param name="dia_nr_charges" value="4"/> | |
| 20771 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 20772 </section> | |
| 20773 <section name="EMGScoring"> | |
| 20774 <param name="max_iteration" value="10"/> | |
| 20775 </section> | |
| 20776 <section name="Scores"> | |
| 20777 <param name="use_shape_score" value="true"/> | |
| 20778 <param name="use_coelution_score" value="true"/> | |
| 20779 <param name="use_rt_score" value="true"/> | |
| 20780 <param name="use_library_score" value="true"/> | |
| 20781 <param name="use_intensity_score" value="true"/> | |
| 20782 <param name="use_nr_peaks_score" value="true"/> | |
| 20783 <param name="use_total_xic_score" value="true"/> | |
| 20784 <param name="use_total_mi_score" value="false"/> | |
| 20785 <param name="use_sn_score" value="true"/> | |
| 20786 <param name="use_mi_score" value="false"/> | |
| 20787 <param name="use_dia_scores" value="true"/> | |
| 20788 <param name="use_ms1_correlation" value="false"/> | |
| 20789 <param name="use_sonar_scores" value="false"/> | |
| 20790 <param name="use_ion_mobility_scores" value="false"/> | |
| 20791 <param name="use_ms1_fullscan" value="false"/> | |
| 20792 <param name="use_ms1_mi" value="false"/> | |
| 20793 <param name="use_uis_scores" value="false"/> | |
| 20794 </section> | |
| 20795 </section> | |
| 20796 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 20797 <output name="ctd_out" ftype="xml"> | |
| 20798 <assert_contents> | |
| 20799 <is_valid_xml/> | |
| 20800 </assert_contents> | |
| 20801 </output> | |
| 20802 </test> | |
| 20803 <test expect_num_outputs="3"> | |
| 20804 <conditional name="adv_opts_cond"> | |
| 20805 <param name="adv_opts_selector" value="advanced"/> | |
| 20806 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 20807 <param name="sort_swath_maps" value="false"/> | |
| 20808 <param name="use_ms1_traces" value="true"/> | |
| 20809 <param name="enable_uis_scoring" value="false"/> | |
| 20810 <param name="out_chrom_type" value="mzML"/> | |
| 20811 <param name="min_upper_edge_dist" value="0.0"/> | |
| 20812 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 20813 <param name="mz_extraction_window_unit" value="Th"/> | |
| 20814 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 20815 <param name="use_ms1_ion_mobility" value="true"/> | |
| 20816 <param name="matching_window_only" value="false"/> | |
| 20817 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 20818 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 20819 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 20820 <param name="min_rsq" value="0.95"/> | |
| 20821 <param name="min_coverage" value="0.6"/> | |
| 20822 <param name="split_file_input" value="false"/> | |
| 20823 <param name="use_elution_model_score" value="false"/> | |
| 20824 <param name="readOptions" value="workingInMemory"/> | |
| 20825 <param name="mz_correction_function" value="none"/> | |
| 20826 <param name="extraction_function" value="tophat"/> | |
| 20827 <param name="batchSize" value="250"/> | |
| 20828 <param name="ms1_isotopes" value="2"/> | |
| 20829 <param name="force" value="false"/> | |
| 20830 <param name="test" value="true"/> | |
| 20831 </conditional> | |
| 20832 <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/> | |
| 20833 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 20834 <param name="tr_type" value=""/> | |
| 20835 <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 20836 <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 20837 <param name="sonar" value="false"/> | |
| 20838 <param name="rt_extraction_window" value="600.0"/> | |
| 20839 <param name="ion_mobility_window" value="-1.0"/> | |
| 20840 <param name="mz_extraction_window" value="0.05"/> | |
| 20841 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 20842 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 20843 <section name="Debugging"/> | |
| 20844 <section name="Calibration"> | |
| 20845 <param name="ms1_im_calibration" value="false"/> | |
| 20846 <param name="im_correction_function" value="linear"/> | |
| 20847 <param name="debug_im_file" value=""/> | |
| 20848 <param name="debug_mz_file" value=""/> | |
| 20849 </section> | |
| 20850 <section name="Library"> | |
| 20851 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 20852 <param name="override_group_label_check" value="false"/> | |
| 20853 <param name="force_invalid_mods" value="false"/> | |
| 20854 </section> | |
| 20855 <section name="RTNormalization"> | |
| 20856 <param name="alignmentMethod" value="linear"/> | |
| 20857 <param name="outlierMethod" value="iter_residual"/> | |
| 20858 <param name="useIterativeChauvenet" value="false"/> | |
| 20859 <param name="RANSACMaxIterations" value="1000"/> | |
| 20860 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 20861 <param name="RANSACSamplingSize" value="10"/> | |
| 20862 <param name="estimateBestPeptides" value="false"/> | |
| 20863 <param name="InitialQualityCutoff" value="0.5"/> | |
| 20864 <param name="OverallQualityCutoff" value="5.5"/> | |
| 20865 <param name="NrRTBins" value="10"/> | |
| 20866 <param name="MinPeptidesPerBin" value="1"/> | |
| 20867 <param name="MinBinsFilled" value="8"/> | |
| 20868 <section name="lowess"> | |
| 20869 <param name="span" value="0.666666666666667"/> | |
| 20870 </section> | |
| 20871 <section name="b_spline"> | |
| 20872 <param name="num_nodes" value="5"/> | |
| 20873 </section> | |
| 20874 </section> | |
| 20875 <section name="Scoring"> | |
| 20876 <param name="stop_report_after_feature" value="5"/> | |
| 20877 <param name="rt_normalization_factor" value="100.0"/> | |
| 20878 <param name="quantification_cutoff" value="0.0"/> | |
| 20879 <param name="write_convex_hull" value="false"/> | |
| 20880 <param name="spectrum_addition_method" value="simple"/> | |
| 20881 <param name="add_up_spectra" value="1"/> | |
| 20882 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 20883 <param name="uis_threshold_sn" value="0"/> | |
| 20884 <param name="uis_threshold_peak_area" value="0"/> | |
| 20885 <param name="scoring_model" value="default"/> | |
| 20886 <param name="im_extra_drift" value="0.0"/> | |
| 20887 <section name="TransitionGroupPicker"> | |
| 20888 <param name="stop_after_feature" value="-1"/> | |
| 20889 <param name="min_peak_width" value="-1.0"/> | |
| 20890 <param name="peak_integration" value="original"/> | |
| 20891 <param name="background_subtraction" value="none"/> | |
| 20892 <param name="recalculate_peaks" value="true"/> | |
| 20893 <param name="use_precursors" value="false"/> | |
| 20894 <param name="use_consensus" value="true"/> | |
| 20895 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 20896 <param name="minimal_quality" value="-1.5"/> | |
| 20897 <param name="resample_boundary" value="15.0"/> | |
| 20898 <param name="compute_peak_quality" value="true"/> | |
| 20899 <param name="compute_peak_shape_metrics" value="false"/> | |
| 20900 <param name="compute_total_mi" value="false"/> | |
| 20901 <param name="boundary_selection_method" value="largest"/> | |
| 20902 <section name="PeakPickerMRM"> | |
| 20903 <param name="sgolay_frame_length" value="11"/> | |
| 20904 <param name="sgolay_polynomial_order" value="3"/> | |
| 20905 <param name="gauss_width" value="30.0"/> | |
| 20906 <param name="use_gauss" value="false"/> | |
| 20907 <param name="peak_width" value="-1.0"/> | |
| 20908 <param name="signal_to_noise" value="0.1"/> | |
| 20909 <param name="write_sn_log_messages" value="false"/> | |
| 20910 <param name="remove_overlapping_peaks" value="true"/> | |
| 20911 <param name="method" value="corrected"/> | |
| 20912 </section> | |
| 20913 <section name="PeakIntegrator"> | |
| 20914 <param name="integration_type" value="intensity_sum"/> | |
| 20915 <param name="baseline_type" value="base_to_base"/> | |
| 20916 <param name="fit_EMG" value="false"/> | |
| 20917 </section> | |
| 20918 </section> | |
| 20919 <section name="DIAScoring"> | |
| 20920 <param name="dia_extraction_window" value="0.05"/> | |
| 20921 <param name="dia_extraction_unit" value="Th"/> | |
| 20922 <param name="dia_centroided" value="false"/> | |
| 20923 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 20924 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 20925 <param name="dia_nr_isotopes" value="4"/> | |
| 20926 <param name="dia_nr_charges" value="4"/> | |
| 20927 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 20928 </section> | |
| 20929 <section name="EMGScoring"> | |
| 20930 <param name="max_iteration" value="10"/> | |
| 20931 </section> | |
| 20932 <section name="Scores"> | |
| 20933 <param name="use_shape_score" value="true"/> | |
| 20934 <param name="use_coelution_score" value="true"/> | |
| 20935 <param name="use_rt_score" value="true"/> | |
| 20936 <param name="use_library_score" value="true"/> | |
| 20937 <param name="use_intensity_score" value="true"/> | |
| 20938 <param name="use_nr_peaks_score" value="true"/> | |
| 20939 <param name="use_total_xic_score" value="true"/> | |
| 20940 <param name="use_total_mi_score" value="false"/> | |
| 20941 <param name="use_sn_score" value="true"/> | |
| 20942 <param name="use_mi_score" value="false"/> | |
| 20943 <param name="use_dia_scores" value="true"/> | |
| 20944 <param name="use_ms1_correlation" value="false"/> | |
| 20945 <param name="use_sonar_scores" value="false"/> | |
| 20946 <param name="use_ion_mobility_scores" value="false"/> | |
| 20947 <param name="use_ms1_fullscan" value="false"/> | |
| 20948 <param name="use_ms1_mi" value="false"/> | |
| 20949 <param name="use_uis_scores" value="false"/> | |
| 20950 </section> | |
| 20951 </section> | |
| 20952 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 20953 <output name="ctd_out" ftype="xml"> | |
| 20954 <assert_contents> | |
| 20955 <is_valid_xml/> | |
| 20956 </assert_contents> | |
| 20957 </output> | |
| 20958 </test> | |
| 20959 <test expect_num_outputs="3"> | |
| 20960 <conditional name="adv_opts_cond"> | |
| 20961 <param name="adv_opts_selector" value="advanced"/> | |
| 20962 <param name="sort_swath_maps" value="false"/> | |
| 20963 <param name="use_ms1_traces" value="true"/> | |
| 20964 <param name="enable_uis_scoring" value="false"/> | |
| 20965 <param name="out_chrom_type" value="mzML"/> | |
| 20966 <param name="min_upper_edge_dist" value="0.0"/> | |
| 20967 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 20968 <param name="mz_extraction_window_unit" value="Th"/> | |
| 20969 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 20970 <param name="use_ms1_ion_mobility" value="false"/> | |
| 20971 <param name="matching_window_only" value="false"/> | |
| 20972 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 20973 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 20974 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 20975 <param name="min_rsq" value="0.95"/> | |
| 20976 <param name="min_coverage" value="0.6"/> | |
| 20977 <param name="split_file_input" value="false"/> | |
| 20978 <param name="use_elution_model_score" value="false"/> | |
| 20979 <param name="readOptions" value="workingInMemory"/> | |
| 20980 <param name="mz_correction_function" value="none"/> | |
| 20981 <param name="extraction_function" value="tophat"/> | |
| 20982 <param name="batchSize" value="250"/> | |
| 20983 <param name="ms1_isotopes" value="0"/> | |
| 20984 <param name="force" value="false"/> | |
| 20985 <param name="test" value="true"/> | |
| 20986 </conditional> | |
| 20987 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> | |
| 20988 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> | |
| 20989 <param name="tr_type" value=""/> | |
| 20990 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 20991 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 20992 <param name="sonar" value="false"/> | |
| 20993 <param name="rt_extraction_window" value="600.0"/> | |
| 20994 <param name="ion_mobility_window" value="0.05"/> | |
| 20995 <param name="mz_extraction_window" value="0.05"/> | |
| 20996 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 20997 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 20998 <section name="Debugging"/> | |
| 20999 <section name="Calibration"> | |
| 21000 <param name="ms1_im_calibration" value="false"/> | |
| 21001 <param name="im_correction_function" value="linear"/> | |
| 21002 <param name="debug_im_file" value=""/> | |
| 21003 <param name="debug_mz_file" value=""/> | |
| 21004 </section> | |
| 21005 <section name="Library"> | |
| 21006 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 21007 <param name="override_group_label_check" value="false"/> | |
| 21008 <param name="force_invalid_mods" value="false"/> | |
| 21009 </section> | |
| 21010 <section name="RTNormalization"> | |
| 21011 <param name="alignmentMethod" value="linear"/> | |
| 21012 <param name="outlierMethod" value="iter_residual"/> | |
| 21013 <param name="useIterativeChauvenet" value="false"/> | |
| 21014 <param name="RANSACMaxIterations" value="1000"/> | |
| 21015 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 21016 <param name="RANSACSamplingSize" value="10"/> | |
| 21017 <param name="estimateBestPeptides" value="false"/> | |
| 21018 <param name="InitialQualityCutoff" value="0.5"/> | |
| 21019 <param name="OverallQualityCutoff" value="5.5"/> | |
| 21020 <param name="NrRTBins" value="10"/> | |
| 21021 <param name="MinPeptidesPerBin" value="1"/> | |
| 21022 <param name="MinBinsFilled" value="8"/> | |
| 21023 <section name="lowess"> | |
| 21024 <param name="span" value="0.666666666666667"/> | |
| 21025 </section> | |
| 21026 <section name="b_spline"> | |
| 21027 <param name="num_nodes" value="5"/> | |
| 21028 </section> | |
| 21029 </section> | |
| 21030 <section name="Scoring"> | |
| 21031 <param name="stop_report_after_feature" value="5"/> | |
| 21032 <param name="rt_normalization_factor" value="100.0"/> | |
| 21033 <param name="quantification_cutoff" value="0.0"/> | |
| 21034 <param name="write_convex_hull" value="false"/> | |
| 21035 <param name="spectrum_addition_method" value="simple"/> | |
| 21036 <param name="add_up_spectra" value="1"/> | |
| 21037 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 21038 <param name="uis_threshold_sn" value="0"/> | |
| 21039 <param name="uis_threshold_peak_area" value="0"/> | |
| 21040 <param name="scoring_model" value="default"/> | |
| 21041 <param name="im_extra_drift" value="0.0"/> | |
| 21042 <section name="TransitionGroupPicker"> | |
| 21043 <param name="stop_after_feature" value="-1"/> | |
| 21044 <param name="min_peak_width" value="-1.0"/> | |
| 21045 <param name="peak_integration" value="original"/> | |
| 21046 <param name="background_subtraction" value="none"/> | |
| 21047 <param name="recalculate_peaks" value="true"/> | |
| 21048 <param name="use_precursors" value="false"/> | |
| 21049 <param name="use_consensus" value="true"/> | |
| 21050 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 21051 <param name="minimal_quality" value="-1.5"/> | |
| 21052 <param name="resample_boundary" value="15.0"/> | |
| 21053 <param name="compute_peak_quality" value="true"/> | |
| 21054 <param name="compute_peak_shape_metrics" value="false"/> | |
| 21055 <param name="compute_total_mi" value="false"/> | |
| 21056 <param name="boundary_selection_method" value="largest"/> | |
| 21057 <section name="PeakPickerMRM"> | |
| 21058 <param name="sgolay_frame_length" value="11"/> | |
| 21059 <param name="sgolay_polynomial_order" value="3"/> | |
| 21060 <param name="gauss_width" value="30.0"/> | |
| 21061 <param name="use_gauss" value="false"/> | |
| 21062 <param name="peak_width" value="-1.0"/> | |
| 21063 <param name="signal_to_noise" value="0.1"/> | |
| 21064 <param name="write_sn_log_messages" value="false"/> | |
| 21065 <param name="remove_overlapping_peaks" value="true"/> | |
| 21066 <param name="method" value="corrected"/> | |
| 21067 </section> | |
| 21068 <section name="PeakIntegrator"> | |
| 21069 <param name="integration_type" value="intensity_sum"/> | |
| 21070 <param name="baseline_type" value="base_to_base"/> | |
| 21071 <param name="fit_EMG" value="false"/> | |
| 21072 </section> | |
| 21073 </section> | |
| 21074 <section name="DIAScoring"> | |
| 21075 <param name="dia_extraction_window" value="0.05"/> | |
| 21076 <param name="dia_extraction_unit" value="Th"/> | |
| 21077 <param name="dia_centroided" value="false"/> | |
| 21078 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 21079 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 21080 <param name="dia_nr_isotopes" value="4"/> | |
| 21081 <param name="dia_nr_charges" value="4"/> | |
| 21082 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 21083 </section> | |
| 21084 <section name="EMGScoring"> | |
| 21085 <param name="max_iteration" value="10"/> | |
| 21086 </section> | |
| 21087 <section name="Scores"> | |
| 21088 <param name="use_shape_score" value="true"/> | |
| 21089 <param name="use_coelution_score" value="true"/> | |
| 21090 <param name="use_rt_score" value="true"/> | |
| 21091 <param name="use_library_score" value="true"/> | |
| 21092 <param name="use_intensity_score" value="true"/> | |
| 21093 <param name="use_nr_peaks_score" value="true"/> | |
| 21094 <param name="use_total_xic_score" value="true"/> | |
| 21095 <param name="use_total_mi_score" value="false"/> | |
| 21096 <param name="use_sn_score" value="true"/> | |
| 21097 <param name="use_mi_score" value="false"/> | |
| 21098 <param name="use_dia_scores" value="true"/> | |
| 21099 <param name="use_ms1_correlation" value="false"/> | |
| 21100 <param name="use_sonar_scores" value="false"/> | |
| 21101 <param name="use_ion_mobility_scores" value="true"/> | |
| 21102 <param name="use_ms1_fullscan" value="false"/> | |
| 21103 <param name="use_ms1_mi" value="false"/> | |
| 21104 <param name="use_uis_scores" value="false"/> | |
| 21105 </section> | |
| 21106 </section> | |
| 21107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 21108 <output name="ctd_out" ftype="xml"> | |
| 21109 <assert_contents> | |
| 21110 <is_valid_xml/> | |
| 21111 </assert_contents> | |
| 21112 </output> | |
| 21113 </test> | |
| 21114 <test expect_num_outputs="3"> | |
| 21115 <conditional name="adv_opts_cond"> | |
| 21116 <param name="adv_opts_selector" value="advanced"/> | |
| 21117 <param name="sort_swath_maps" value="false"/> | |
| 21118 <param name="use_ms1_traces" value="true"/> | |
| 21119 <param name="enable_uis_scoring" value="false"/> | |
| 21120 <param name="out_chrom_type" value="mzML"/> | |
| 21121 <param name="min_upper_edge_dist" value="0.0"/> | |
| 21122 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 21123 <param name="mz_extraction_window_unit" value="Th"/> | |
| 21124 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 21125 <param name="use_ms1_ion_mobility" value="false"/> | |
| 21126 <param name="matching_window_only" value="false"/> | |
| 21127 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 21128 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 21129 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 21130 <param name="min_rsq" value="0.95"/> | |
| 21131 <param name="min_coverage" value="0.6"/> | |
| 21132 <param name="split_file_input" value="false"/> | |
| 21133 <param name="use_elution_model_score" value="false"/> | |
| 21134 <param name="readOptions" value="cache"/> | |
| 21135 <param name="mz_correction_function" value="none"/> | |
| 21136 <param name="extraction_function" value="tophat"/> | |
| 21137 <param name="batchSize" value="250"/> | |
| 21138 <param name="ms1_isotopes" value="0"/> | |
| 21139 <param name="force" value="false"/> | |
| 21140 <param name="test" value="true"/> | |
| 21141 </conditional> | |
| 21142 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> | |
| 21143 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> | |
| 21144 <param name="tr_type" value=""/> | |
| 21145 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 21146 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 21147 <param name="sonar" value="false"/> | |
| 21148 <param name="rt_extraction_window" value="600.0"/> | |
| 21149 <param name="ion_mobility_window" value="0.05"/> | |
| 21150 <param name="mz_extraction_window" value="0.05"/> | |
| 21151 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 21152 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 21153 <section name="Debugging"/> | |
| 21154 <section name="Calibration"> | |
| 21155 <param name="ms1_im_calibration" value="false"/> | |
| 21156 <param name="im_correction_function" value="linear"/> | |
| 21157 <param name="debug_im_file" value=""/> | |
| 21158 <param name="debug_mz_file" value=""/> | |
| 21159 </section> | |
| 21160 <section name="Library"> | |
| 21161 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 21162 <param name="override_group_label_check" value="false"/> | |
| 21163 <param name="force_invalid_mods" value="false"/> | |
| 21164 </section> | |
| 21165 <section name="RTNormalization"> | |
| 21166 <param name="alignmentMethod" value="linear"/> | |
| 21167 <param name="outlierMethod" value="iter_residual"/> | |
| 21168 <param name="useIterativeChauvenet" value="false"/> | |
| 21169 <param name="RANSACMaxIterations" value="1000"/> | |
| 21170 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 21171 <param name="RANSACSamplingSize" value="10"/> | |
| 21172 <param name="estimateBestPeptides" value="false"/> | |
| 21173 <param name="InitialQualityCutoff" value="0.5"/> | |
| 21174 <param name="OverallQualityCutoff" value="5.5"/> | |
| 21175 <param name="NrRTBins" value="10"/> | |
| 21176 <param name="MinPeptidesPerBin" value="1"/> | |
| 21177 <param name="MinBinsFilled" value="8"/> | |
| 21178 <section name="lowess"> | |
| 21179 <param name="span" value="0.666666666666667"/> | |
| 21180 </section> | |
| 21181 <section name="b_spline"> | |
| 21182 <param name="num_nodes" value="5"/> | |
| 21183 </section> | |
| 21184 </section> | |
| 21185 <section name="Scoring"> | |
| 21186 <param name="stop_report_after_feature" value="5"/> | |
| 21187 <param name="rt_normalization_factor" value="100.0"/> | |
| 21188 <param name="quantification_cutoff" value="0.0"/> | |
| 21189 <param name="write_convex_hull" value="false"/> | |
| 21190 <param name="spectrum_addition_method" value="simple"/> | |
| 21191 <param name="add_up_spectra" value="1"/> | |
| 21192 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 21193 <param name="uis_threshold_sn" value="0"/> | |
| 21194 <param name="uis_threshold_peak_area" value="0"/> | |
| 21195 <param name="scoring_model" value="default"/> | |
| 21196 <param name="im_extra_drift" value="0.0"/> | |
| 21197 <section name="TransitionGroupPicker"> | |
| 21198 <param name="stop_after_feature" value="-1"/> | |
| 21199 <param name="min_peak_width" value="-1.0"/> | |
| 21200 <param name="peak_integration" value="original"/> | |
| 21201 <param name="background_subtraction" value="none"/> | |
| 21202 <param name="recalculate_peaks" value="true"/> | |
| 21203 <param name="use_precursors" value="false"/> | |
| 21204 <param name="use_consensus" value="true"/> | |
| 21205 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 21206 <param name="minimal_quality" value="-1.5"/> | |
| 21207 <param name="resample_boundary" value="15.0"/> | |
| 21208 <param name="compute_peak_quality" value="true"/> | |
| 21209 <param name="compute_peak_shape_metrics" value="false"/> | |
| 21210 <param name="compute_total_mi" value="false"/> | |
| 21211 <param name="boundary_selection_method" value="largest"/> | |
| 21212 <section name="PeakPickerMRM"> | |
| 21213 <param name="sgolay_frame_length" value="11"/> | |
| 21214 <param name="sgolay_polynomial_order" value="3"/> | |
| 21215 <param name="gauss_width" value="30.0"/> | |
| 21216 <param name="use_gauss" value="false"/> | |
| 21217 <param name="peak_width" value="-1.0"/> | |
| 21218 <param name="signal_to_noise" value="0.1"/> | |
| 21219 <param name="write_sn_log_messages" value="false"/> | |
| 21220 <param name="remove_overlapping_peaks" value="true"/> | |
| 21221 <param name="method" value="corrected"/> | |
| 21222 </section> | |
| 21223 <section name="PeakIntegrator"> | |
| 21224 <param name="integration_type" value="intensity_sum"/> | |
| 21225 <param name="baseline_type" value="base_to_base"/> | |
| 21226 <param name="fit_EMG" value="false"/> | |
| 21227 </section> | |
| 21228 </section> | |
| 21229 <section name="DIAScoring"> | |
| 21230 <param name="dia_extraction_window" value="0.05"/> | |
| 21231 <param name="dia_extraction_unit" value="Th"/> | |
| 21232 <param name="dia_centroided" value="false"/> | |
| 21233 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 21234 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 21235 <param name="dia_nr_isotopes" value="4"/> | |
| 21236 <param name="dia_nr_charges" value="4"/> | |
| 21237 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 21238 </section> | |
| 21239 <section name="EMGScoring"> | |
| 21240 <param name="max_iteration" value="10"/> | |
| 21241 </section> | |
| 21242 <section name="Scores"> | |
| 21243 <param name="use_shape_score" value="true"/> | |
| 21244 <param name="use_coelution_score" value="true"/> | |
| 21245 <param name="use_rt_score" value="true"/> | |
| 21246 <param name="use_library_score" value="true"/> | |
| 21247 <param name="use_intensity_score" value="true"/> | |
| 21248 <param name="use_nr_peaks_score" value="true"/> | |
| 21249 <param name="use_total_xic_score" value="true"/> | |
| 21250 <param name="use_total_mi_score" value="false"/> | |
| 21251 <param name="use_sn_score" value="true"/> | |
| 21252 <param name="use_mi_score" value="false"/> | |
| 21253 <param name="use_dia_scores" value="true"/> | |
| 21254 <param name="use_ms1_correlation" value="false"/> | |
| 21255 <param name="use_sonar_scores" value="false"/> | |
| 21256 <param name="use_ion_mobility_scores" value="true"/> | |
| 21257 <param name="use_ms1_fullscan" value="false"/> | |
| 21258 <param name="use_ms1_mi" value="false"/> | |
| 21259 <param name="use_uis_scores" value="false"/> | |
| 21260 </section> | |
| 21261 </section> | |
| 21262 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 21263 <output name="ctd_out" ftype="xml"> | |
| 21264 <assert_contents> | |
| 21265 <is_valid_xml/> | |
| 21266 </assert_contents> | |
| 21267 </output> | |
| 21268 </test> | |
| 21269 <test expect_num_outputs="3"> | |
| 21270 <conditional name="adv_opts_cond"> | |
| 21271 <param name="adv_opts_selector" value="advanced"/> | |
| 21272 <param name="sort_swath_maps" value="false"/> | |
| 21273 <param name="use_ms1_traces" value="true"/> | |
| 21274 <param name="enable_uis_scoring" value="false"/> | |
| 21275 <param name="out_chrom_type" value="mzML"/> | |
| 21276 <param name="min_upper_edge_dist" value="0.0"/> | |
| 21277 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 21278 <param name="mz_extraction_window_unit" value="Th"/> | |
| 21279 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 21280 <param name="use_ms1_ion_mobility" value="false"/> | |
| 21281 <param name="matching_window_only" value="false"/> | |
| 21282 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 21283 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 21284 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 21285 <param name="min_rsq" value="0.95"/> | |
| 21286 <param name="min_coverage" value="0.6"/> | |
| 21287 <param name="split_file_input" value="false"/> | |
| 21288 <param name="use_elution_model_score" value="false"/> | |
| 21289 <param name="readOptions" value="workingInMemory"/> | |
| 21290 <param name="mz_correction_function" value="none"/> | |
| 21291 <param name="extraction_function" value="tophat"/> | |
| 21292 <param name="batchSize" value="250"/> | |
| 21293 <param name="ms1_isotopes" value="0"/> | |
| 21294 <param name="force" value="false"/> | |
| 21295 <param name="test" value="true"/> | |
| 21296 </conditional> | |
| 21297 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> | |
| 21298 <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/> | |
| 21299 <param name="tr_type" value="pqp"/> | |
| 21300 <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 21301 <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 21302 <param name="sonar" value="false"/> | |
| 21303 <param name="rt_extraction_window" value="600.0"/> | |
| 21304 <param name="ion_mobility_window" value="0.05"/> | |
| 21305 <param name="mz_extraction_window" value="0.05"/> | |
| 21306 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 21307 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 21308 <section name="Debugging"/> | |
| 21309 <section name="Calibration"> | |
| 21310 <param name="ms1_im_calibration" value="false"/> | |
| 21311 <param name="im_correction_function" value="linear"/> | |
| 21312 <param name="debug_im_file" value=""/> | |
| 21313 <param name="debug_mz_file" value=""/> | |
| 21314 </section> | |
| 21315 <section name="Library"> | |
| 21316 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 21317 <param name="override_group_label_check" value="false"/> | |
| 21318 <param name="force_invalid_mods" value="false"/> | |
| 21319 </section> | |
| 21320 <section name="RTNormalization"> | |
| 21321 <param name="alignmentMethod" value="linear"/> | |
| 21322 <param name="outlierMethod" value="iter_residual"/> | |
| 21323 <param name="useIterativeChauvenet" value="false"/> | |
| 21324 <param name="RANSACMaxIterations" value="1000"/> | |
| 21325 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 21326 <param name="RANSACSamplingSize" value="10"/> | |
| 21327 <param name="estimateBestPeptides" value="false"/> | |
| 21328 <param name="InitialQualityCutoff" value="0.5"/> | |
| 21329 <param name="OverallQualityCutoff" value="5.5"/> | |
| 21330 <param name="NrRTBins" value="10"/> | |
| 21331 <param name="MinPeptidesPerBin" value="1"/> | |
| 21332 <param name="MinBinsFilled" value="8"/> | |
| 21333 <section name="lowess"> | |
| 21334 <param name="span" value="0.666666666666667"/> | |
| 21335 </section> | |
| 21336 <section name="b_spline"> | |
| 21337 <param name="num_nodes" value="5"/> | |
| 21338 </section> | |
| 21339 </section> | |
| 21340 <section name="Scoring"> | |
| 21341 <param name="stop_report_after_feature" value="5"/> | |
| 21342 <param name="rt_normalization_factor" value="100.0"/> | |
| 21343 <param name="quantification_cutoff" value="0.0"/> | |
| 21344 <param name="write_convex_hull" value="false"/> | |
| 21345 <param name="spectrum_addition_method" value="simple"/> | |
| 21346 <param name="add_up_spectra" value="1"/> | |
| 21347 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 21348 <param name="uis_threshold_sn" value="0"/> | |
| 21349 <param name="uis_threshold_peak_area" value="0"/> | |
| 21350 <param name="scoring_model" value="default"/> | |
| 21351 <param name="im_extra_drift" value="0.0"/> | |
| 21352 <section name="TransitionGroupPicker"> | |
| 21353 <param name="stop_after_feature" value="-1"/> | |
| 21354 <param name="min_peak_width" value="-1.0"/> | |
| 21355 <param name="peak_integration" value="original"/> | |
| 21356 <param name="background_subtraction" value="none"/> | |
| 21357 <param name="recalculate_peaks" value="true"/> | |
| 21358 <param name="use_precursors" value="false"/> | |
| 21359 <param name="use_consensus" value="true"/> | |
| 21360 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 21361 <param name="minimal_quality" value="-1.5"/> | |
| 21362 <param name="resample_boundary" value="15.0"/> | |
| 21363 <param name="compute_peak_quality" value="true"/> | |
| 21364 <param name="compute_peak_shape_metrics" value="false"/> | |
| 21365 <param name="compute_total_mi" value="false"/> | |
| 21366 <param name="boundary_selection_method" value="largest"/> | |
| 21367 <section name="PeakPickerMRM"> | |
| 21368 <param name="sgolay_frame_length" value="11"/> | |
| 21369 <param name="sgolay_polynomial_order" value="3"/> | |
| 21370 <param name="gauss_width" value="30.0"/> | |
| 21371 <param name="use_gauss" value="false"/> | |
| 21372 <param name="peak_width" value="-1.0"/> | |
| 21373 <param name="signal_to_noise" value="0.1"/> | |
| 21374 <param name="write_sn_log_messages" value="false"/> | |
| 21375 <param name="remove_overlapping_peaks" value="true"/> | |
| 21376 <param name="method" value="corrected"/> | |
| 21377 </section> | |
| 21378 <section name="PeakIntegrator"> | |
| 21379 <param name="integration_type" value="intensity_sum"/> | |
| 21380 <param name="baseline_type" value="base_to_base"/> | |
| 21381 <param name="fit_EMG" value="false"/> | |
| 21382 </section> | |
| 21383 </section> | |
| 21384 <section name="DIAScoring"> | |
| 21385 <param name="dia_extraction_window" value="0.05"/> | |
| 21386 <param name="dia_extraction_unit" value="Th"/> | |
| 21387 <param name="dia_centroided" value="false"/> | |
| 21388 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 21389 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 21390 <param name="dia_nr_isotopes" value="4"/> | |
| 21391 <param name="dia_nr_charges" value="4"/> | |
| 21392 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 21393 </section> | |
| 21394 <section name="EMGScoring"> | |
| 21395 <param name="max_iteration" value="10"/> | |
| 21396 </section> | |
| 21397 <section name="Scores"> | |
| 21398 <param name="use_shape_score" value="true"/> | |
| 21399 <param name="use_coelution_score" value="true"/> | |
| 21400 <param name="use_rt_score" value="true"/> | |
| 21401 <param name="use_library_score" value="true"/> | |
| 21402 <param name="use_intensity_score" value="true"/> | |
| 21403 <param name="use_nr_peaks_score" value="true"/> | |
| 21404 <param name="use_total_xic_score" value="true"/> | |
| 21405 <param name="use_total_mi_score" value="false"/> | |
| 21406 <param name="use_sn_score" value="true"/> | |
| 21407 <param name="use_mi_score" value="false"/> | |
| 21408 <param name="use_dia_scores" value="true"/> | |
| 21409 <param name="use_ms1_correlation" value="false"/> | |
| 21410 <param name="use_sonar_scores" value="false"/> | |
| 21411 <param name="use_ion_mobility_scores" value="false"/> | |
| 21412 <param name="use_ms1_fullscan" value="false"/> | |
| 21413 <param name="use_ms1_mi" value="false"/> | |
| 21414 <param name="use_uis_scores" value="false"/> | |
| 21415 </section> | |
| 21416 </section> | |
| 21417 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 21418 <output name="ctd_out" ftype="xml"> | |
| 21419 <assert_contents> | |
| 21420 <is_valid_xml/> | |
| 21421 </assert_contents> | |
| 21422 </output> | |
| 21423 </test> | |
| 21424 <test expect_num_outputs="2"> | |
| 21425 <conditional name="adv_opts_cond"> | |
| 21426 <param name="adv_opts_selector" value="advanced"/> | |
| 21427 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 21428 <param name="sort_swath_maps" value="false"/> | |
| 21429 <param name="use_ms1_traces" value="true"/> | |
| 21430 <param name="enable_uis_scoring" value="false"/> | |
| 21431 <param name="min_upper_edge_dist" value="0.0"/> | |
| 21432 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 21433 <param name="mz_extraction_window_unit" value="Th"/> | |
| 21434 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 21435 <param name="use_ms1_ion_mobility" value="true"/> | |
| 21436 <param name="matching_window_only" value="false"/> | |
| 21437 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 21438 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 21439 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 21440 <param name="min_rsq" value="0.95"/> | |
| 21441 <param name="min_coverage" value="0.6"/> | |
| 21442 <param name="split_file_input" value="false"/> | |
| 21443 <param name="use_elution_model_score" value="false"/> | |
| 21444 <param name="readOptions" value="normal"/> | |
| 21445 <param name="mz_correction_function" value="none"/> | |
| 21446 <param name="extraction_function" value="tophat"/> | |
| 21447 <param name="batchSize" value="250"/> | |
| 21448 <param name="ms1_isotopes" value="0"/> | |
| 21449 <param name="force" value="false"/> | |
| 21450 <param name="test" value="true"/> | |
| 21451 </conditional> | |
| 21452 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 21453 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 21454 <param name="tr_type" value=""/> | |
| 21455 <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 21456 <param name="sonar" value="false"/> | |
| 21457 <param name="rt_extraction_window" value="600.0"/> | |
| 21458 <param name="ion_mobility_window" value="-1.0"/> | |
| 21459 <param name="mz_extraction_window" value="0.05"/> | |
| 21460 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 21461 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 21462 <section name="Debugging"/> | |
| 21463 <section name="Calibration"> | |
| 21464 <param name="ms1_im_calibration" value="false"/> | |
| 21465 <param name="im_correction_function" value="linear"/> | |
| 21466 <param name="debug_im_file" value=""/> | |
| 21467 <param name="debug_mz_file" value=""/> | |
| 21468 </section> | |
| 21469 <section name="Library"> | |
| 21470 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 21471 <param name="override_group_label_check" value="false"/> | |
| 21472 <param name="force_invalid_mods" value="false"/> | |
| 21473 </section> | |
| 21474 <section name="RTNormalization"> | |
| 21475 <param name="alignmentMethod" value="linear"/> | |
| 21476 <param name="outlierMethod" value="iter_residual"/> | |
| 21477 <param name="useIterativeChauvenet" value="false"/> | |
| 21478 <param name="RANSACMaxIterations" value="1000"/> | |
| 21479 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 21480 <param name="RANSACSamplingSize" value="10"/> | |
| 21481 <param name="estimateBestPeptides" value="false"/> | |
| 21482 <param name="InitialQualityCutoff" value="0.5"/> | |
| 21483 <param name="OverallQualityCutoff" value="5.5"/> | |
| 21484 <param name="NrRTBins" value="10"/> | |
| 21485 <param name="MinPeptidesPerBin" value="1"/> | |
| 21486 <param name="MinBinsFilled" value="8"/> | |
| 21487 <section name="lowess"> | |
| 21488 <param name="span" value="0.666666666666667"/> | |
| 21489 </section> | |
| 21490 <section name="b_spline"> | |
| 21491 <param name="num_nodes" value="5"/> | |
| 21492 </section> | |
| 21493 </section> | |
| 21494 <section name="Scoring"> | |
| 21495 <param name="stop_report_after_feature" value="5"/> | |
| 21496 <param name="rt_normalization_factor" value="100.0"/> | |
| 21497 <param name="quantification_cutoff" value="0.0"/> | |
| 21498 <param name="write_convex_hull" value="false"/> | |
| 21499 <param name="spectrum_addition_method" value="simple"/> | |
| 21500 <param name="add_up_spectra" value="1"/> | |
| 21501 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 21502 <param name="uis_threshold_sn" value="0"/> | |
| 21503 <param name="uis_threshold_peak_area" value="0"/> | |
| 21504 <param name="scoring_model" value="default"/> | |
| 21505 <param name="im_extra_drift" value="0.0"/> | |
| 21506 <section name="TransitionGroupPicker"> | |
| 21507 <param name="stop_after_feature" value="-1"/> | |
| 21508 <param name="min_peak_width" value="-1.0"/> | |
| 21509 <param name="peak_integration" value="original"/> | |
| 21510 <param name="background_subtraction" value="none"/> | |
| 21511 <param name="recalculate_peaks" value="true"/> | |
| 21512 <param name="use_precursors" value="false"/> | |
| 21513 <param name="use_consensus" value="true"/> | |
| 21514 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 21515 <param name="minimal_quality" value="-1.5"/> | |
| 21516 <param name="resample_boundary" value="15.0"/> | |
| 21517 <param name="compute_peak_quality" value="true"/> | |
| 21518 <param name="compute_peak_shape_metrics" value="false"/> | |
| 21519 <param name="compute_total_mi" value="false"/> | |
| 21520 <param name="boundary_selection_method" value="largest"/> | |
| 21521 <section name="PeakPickerMRM"> | |
| 21522 <param name="sgolay_frame_length" value="11"/> | |
| 21523 <param name="sgolay_polynomial_order" value="3"/> | |
| 21524 <param name="gauss_width" value="30.0"/> | |
| 21525 <param name="use_gauss" value="false"/> | |
| 21526 <param name="peak_width" value="-1.0"/> | |
| 21527 <param name="signal_to_noise" value="0.1"/> | |
| 21528 <param name="write_sn_log_messages" value="false"/> | |
| 21529 <param name="remove_overlapping_peaks" value="true"/> | |
| 21530 <param name="method" value="corrected"/> | |
| 21531 </section> | |
| 21532 <section name="PeakIntegrator"> | |
| 21533 <param name="integration_type" value="intensity_sum"/> | |
| 21534 <param name="baseline_type" value="base_to_base"/> | |
| 21535 <param name="fit_EMG" value="false"/> | |
| 21536 </section> | |
| 21537 </section> | |
| 21538 <section name="DIAScoring"> | |
| 21539 <param name="dia_extraction_window" value="0.05"/> | |
| 21540 <param name="dia_extraction_unit" value="Th"/> | |
| 21541 <param name="dia_centroided" value="false"/> | |
| 21542 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 21543 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 21544 <param name="dia_nr_isotopes" value="4"/> | |
| 21545 <param name="dia_nr_charges" value="4"/> | |
| 21546 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 21547 </section> | |
| 21548 <section name="EMGScoring"> | |
| 21549 <param name="max_iteration" value="10"/> | |
| 21550 </section> | |
| 21551 <section name="Scores"> | |
| 21552 <param name="use_shape_score" value="true"/> | |
| 21553 <param name="use_coelution_score" value="true"/> | |
| 21554 <param name="use_rt_score" value="true"/> | |
| 21555 <param name="use_library_score" value="true"/> | |
| 21556 <param name="use_intensity_score" value="true"/> | |
| 21557 <param name="use_nr_peaks_score" value="true"/> | |
| 21558 <param name="use_total_xic_score" value="true"/> | |
| 21559 <param name="use_total_mi_score" value="false"/> | |
| 21560 <param name="use_sn_score" value="true"/> | |
| 21561 <param name="use_mi_score" value="false"/> | |
| 21562 <param name="use_dia_scores" value="true"/> | |
| 21563 <param name="use_ms1_correlation" value="false"/> | |
| 21564 <param name="use_sonar_scores" value="false"/> | |
| 21565 <param name="use_ion_mobility_scores" value="false"/> | |
| 21566 <param name="use_ms1_fullscan" value="false"/> | |
| 21567 <param name="use_ms1_mi" value="true"/> | |
| 21568 <param name="use_uis_scores" value="false"/> | |
| 21569 </section> | |
| 21570 </section> | |
| 21571 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> | |
| 21572 <output name="ctd_out" ftype="xml"> | |
| 21573 <assert_contents> | |
| 21574 <is_valid_xml/> | |
| 21575 </assert_contents> | |
| 21576 </output> | |
| 21577 </test> | |
| 21578 <test expect_num_outputs="2"> | |
| 21579 <conditional name="adv_opts_cond"> | |
| 21580 <param name="adv_opts_selector" value="advanced"/> | |
| 21581 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 21582 <param name="sort_swath_maps" value="false"/> | |
| 21583 <param name="use_ms1_traces" value="true"/> | |
| 21584 <param name="enable_uis_scoring" value="false"/> | |
| 21585 <param name="min_upper_edge_dist" value="0.0"/> | |
| 21586 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 21587 <param name="mz_extraction_window_unit" value="Th"/> | |
| 21588 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 21589 <param name="use_ms1_ion_mobility" value="true"/> | |
| 21590 <param name="matching_window_only" value="false"/> | |
| 21591 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 21592 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 21593 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 21594 <param name="min_rsq" value="0.95"/> | |
| 21595 <param name="min_coverage" value="0.6"/> | |
| 21596 <param name="split_file_input" value="false"/> | |
| 21597 <param name="use_elution_model_score" value="false"/> | |
| 21598 <param name="readOptions" value="normal"/> | |
| 21599 <param name="mz_correction_function" value="none"/> | |
| 21600 <param name="extraction_function" value="tophat"/> | |
| 21601 <param name="batchSize" value="250"/> | |
| 21602 <param name="ms1_isotopes" value="0"/> | |
| 21603 <param name="force" value="false"/> | |
| 21604 <param name="test" value="true"/> | |
| 21605 </conditional> | |
| 21606 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 21607 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 21608 <param name="tr_type" value=""/> | |
| 21609 <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 21610 <param name="sonar" value="false"/> | |
| 21611 <param name="rt_extraction_window" value="600.0"/> | |
| 21612 <param name="ion_mobility_window" value="-1.0"/> | |
| 21613 <param name="mz_extraction_window" value="0.05"/> | |
| 21614 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 21615 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 21616 <section name="Debugging"/> | |
| 21617 <section name="Calibration"> | |
| 21618 <param name="ms1_im_calibration" value="false"/> | |
| 21619 <param name="im_correction_function" value="linear"/> | |
| 21620 <param name="debug_im_file" value=""/> | |
| 21621 <param name="debug_mz_file" value=""/> | |
| 21622 </section> | |
| 21623 <section name="Library"> | |
| 21624 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 21625 <param name="override_group_label_check" value="false"/> | |
| 21626 <param name="force_invalid_mods" value="false"/> | |
| 21627 </section> | |
| 21628 <section name="RTNormalization"> | |
| 21629 <param name="alignmentMethod" value="linear"/> | |
| 21630 <param name="outlierMethod" value="iter_residual"/> | |
| 21631 <param name="useIterativeChauvenet" value="false"/> | |
| 21632 <param name="RANSACMaxIterations" value="1000"/> | |
| 21633 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 21634 <param name="RANSACSamplingSize" value="10"/> | |
| 21635 <param name="estimateBestPeptides" value="false"/> | |
| 21636 <param name="InitialQualityCutoff" value="0.5"/> | |
| 21637 <param name="OverallQualityCutoff" value="5.5"/> | |
| 21638 <param name="NrRTBins" value="10"/> | |
| 21639 <param name="MinPeptidesPerBin" value="1"/> | |
| 21640 <param name="MinBinsFilled" value="8"/> | |
| 21641 <section name="lowess"> | |
| 21642 <param name="span" value="0.666666666666667"/> | |
| 21643 </section> | |
| 21644 <section name="b_spline"> | |
| 21645 <param name="num_nodes" value="5"/> | |
| 21646 </section> | |
| 21647 </section> | |
| 21648 <section name="Scoring"> | |
| 21649 <param name="stop_report_after_feature" value="5"/> | |
| 21650 <param name="rt_normalization_factor" value="100.0"/> | |
| 21651 <param name="quantification_cutoff" value="0.0"/> | |
| 21652 <param name="write_convex_hull" value="false"/> | |
| 21653 <param name="spectrum_addition_method" value="simple"/> | |
| 21654 <param name="add_up_spectra" value="1"/> | |
| 21655 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 21656 <param name="uis_threshold_sn" value="0"/> | |
| 21657 <param name="uis_threshold_peak_area" value="0"/> | |
| 21658 <param name="scoring_model" value="default"/> | |
| 21659 <param name="im_extra_drift" value="0.0"/> | |
| 21660 <section name="TransitionGroupPicker"> | |
| 21661 <param name="stop_after_feature" value="-1"/> | |
| 21662 <param name="min_peak_width" value="-1.0"/> | |
| 21663 <param name="peak_integration" value="original"/> | |
| 21664 <param name="background_subtraction" value="none"/> | |
| 21665 <param name="recalculate_peaks" value="true"/> | |
| 21666 <param name="use_precursors" value="false"/> | |
| 21667 <param name="use_consensus" value="true"/> | |
| 21668 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 21669 <param name="minimal_quality" value="-1.5"/> | |
| 21670 <param name="resample_boundary" value="15.0"/> | |
| 21671 <param name="compute_peak_quality" value="true"/> | |
| 21672 <param name="compute_peak_shape_metrics" value="false"/> | |
| 21673 <param name="compute_total_mi" value="false"/> | |
| 21674 <param name="boundary_selection_method" value="largest"/> | |
| 21675 <section name="PeakPickerMRM"> | |
| 21676 <param name="sgolay_frame_length" value="11"/> | |
| 21677 <param name="sgolay_polynomial_order" value="3"/> | |
| 21678 <param name="gauss_width" value="30.0"/> | |
| 21679 <param name="use_gauss" value="false"/> | |
| 21680 <param name="peak_width" value="-1.0"/> | |
| 21681 <param name="signal_to_noise" value="0.1"/> | |
| 21682 <param name="write_sn_log_messages" value="false"/> | |
| 21683 <param name="remove_overlapping_peaks" value="true"/> | |
| 21684 <param name="method" value="corrected"/> | |
| 21685 </section> | |
| 21686 <section name="PeakIntegrator"> | |
| 21687 <param name="integration_type" value="intensity_sum"/> | |
| 21688 <param name="baseline_type" value="base_to_base"/> | |
| 21689 <param name="fit_EMG" value="false"/> | |
| 21690 </section> | |
| 21691 </section> | |
| 21692 <section name="DIAScoring"> | |
| 21693 <param name="dia_extraction_window" value="0.05"/> | |
| 21694 <param name="dia_extraction_unit" value="Th"/> | |
| 21695 <param name="dia_centroided" value="false"/> | |
| 21696 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 21697 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 21698 <param name="dia_nr_isotopes" value="4"/> | |
| 21699 <param name="dia_nr_charges" value="4"/> | |
| 21700 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 21701 </section> | |
| 21702 <section name="EMGScoring"> | |
| 21703 <param name="max_iteration" value="10"/> | |
| 21704 </section> | |
| 21705 <section name="Scores"> | |
| 21706 <param name="use_shape_score" value="true"/> | |
| 21707 <param name="use_coelution_score" value="true"/> | |
| 21708 <param name="use_rt_score" value="true"/> | |
| 21709 <param name="use_library_score" value="true"/> | |
| 21710 <param name="use_intensity_score" value="true"/> | |
| 21711 <param name="use_nr_peaks_score" value="true"/> | |
| 21712 <param name="use_total_xic_score" value="true"/> | |
| 21713 <param name="use_total_mi_score" value="false"/> | |
| 21714 <param name="use_sn_score" value="true"/> | |
| 21715 <param name="use_mi_score" value="true"/> | |
| 21716 <param name="use_dia_scores" value="true"/> | |
| 21717 <param name="use_ms1_correlation" value="false"/> | |
| 21718 <param name="use_sonar_scores" value="false"/> | |
| 21719 <param name="use_ion_mobility_scores" value="false"/> | |
| 21720 <param name="use_ms1_fullscan" value="false"/> | |
| 21721 <param name="use_ms1_mi" value="false"/> | |
| 21722 <param name="use_uis_scores" value="false"/> | |
| 21723 </section> | |
| 21724 </section> | |
| 21725 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> | |
| 21726 <output name="ctd_out" ftype="xml"> | |
| 21727 <assert_contents> | |
| 21728 <is_valid_xml/> | |
| 21729 </assert_contents> | |
| 21730 </output> | |
| 21731 </test> | |
| 21732 <test expect_num_outputs="2"> | |
| 21733 <conditional name="adv_opts_cond"> | |
| 21734 <param name="adv_opts_selector" value="advanced"/> | |
| 21735 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> | |
| 21736 <param name="sort_swath_maps" value="false"/> | |
| 21737 <param name="use_ms1_traces" value="true"/> | |
| 21738 <param name="enable_uis_scoring" value="false"/> | |
| 21739 <param name="min_upper_edge_dist" value="0.0"/> | |
| 21740 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 21741 <param name="mz_extraction_window_unit" value="Th"/> | |
| 21742 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 21743 <param name="use_ms1_ion_mobility" value="true"/> | |
| 21744 <param name="matching_window_only" value="false"/> | |
| 21745 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 21746 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 21747 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 21748 <param name="min_rsq" value="0.95"/> | |
| 21749 <param name="min_coverage" value="0.6"/> | |
| 21750 <param name="split_file_input" value="false"/> | |
| 21751 <param name="use_elution_model_score" value="false"/> | |
| 21752 <param name="readOptions" value="normal"/> | |
| 21753 <param name="mz_correction_function" value="none"/> | |
| 21754 <param name="extraction_function" value="tophat"/> | |
| 21755 <param name="batchSize" value="250"/> | |
| 21756 <param name="ms1_isotopes" value="0"/> | |
| 21757 <param name="force" value="false"/> | |
| 21758 <param name="test" value="true"/> | |
| 21759 </conditional> | |
| 21760 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 21761 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> | |
| 21762 <param name="tr_type" value=""/> | |
| 21763 <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 21764 <param name="sonar" value="false"/> | |
| 21765 <param name="rt_extraction_window" value="600.0"/> | |
| 21766 <param name="ion_mobility_window" value="-1.0"/> | |
| 21767 <param name="mz_extraction_window" value="0.05"/> | |
| 21768 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 21769 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 21770 <section name="Debugging"/> | |
| 21771 <section name="Calibration"> | |
| 21772 <param name="ms1_im_calibration" value="false"/> | |
| 21773 <param name="im_correction_function" value="linear"/> | |
| 21774 <param name="debug_im_file" value=""/> | |
| 21775 <param name="debug_mz_file" value=""/> | |
| 21776 </section> | |
| 21777 <section name="Library"> | |
| 21778 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 21779 <param name="override_group_label_check" value="false"/> | |
| 21780 <param name="force_invalid_mods" value="false"/> | |
| 21781 </section> | |
| 21782 <section name="RTNormalization"> | |
| 21783 <param name="alignmentMethod" value="linear"/> | |
| 21784 <param name="outlierMethod" value="iter_residual"/> | |
| 21785 <param name="useIterativeChauvenet" value="false"/> | |
| 21786 <param name="RANSACMaxIterations" value="1000"/> | |
| 21787 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 21788 <param name="RANSACSamplingSize" value="10"/> | |
| 21789 <param name="estimateBestPeptides" value="false"/> | |
| 21790 <param name="InitialQualityCutoff" value="0.5"/> | |
| 21791 <param name="OverallQualityCutoff" value="5.5"/> | |
| 21792 <param name="NrRTBins" value="10"/> | |
| 21793 <param name="MinPeptidesPerBin" value="1"/> | |
| 21794 <param name="MinBinsFilled" value="8"/> | |
| 21795 <section name="lowess"> | |
| 21796 <param name="span" value="0.666666666666667"/> | |
| 21797 </section> | |
| 21798 <section name="b_spline"> | |
| 21799 <param name="num_nodes" value="5"/> | |
| 21800 </section> | |
| 21801 </section> | |
| 21802 <section name="Scoring"> | |
| 21803 <param name="stop_report_after_feature" value="5"/> | |
| 21804 <param name="rt_normalization_factor" value="100.0"/> | |
| 21805 <param name="quantification_cutoff" value="0.0"/> | |
| 21806 <param name="write_convex_hull" value="false"/> | |
| 21807 <param name="spectrum_addition_method" value="simple"/> | |
| 21808 <param name="add_up_spectra" value="1"/> | |
| 21809 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 21810 <param name="uis_threshold_sn" value="0"/> | |
| 21811 <param name="uis_threshold_peak_area" value="0"/> | |
| 21812 <param name="scoring_model" value="default"/> | |
| 21813 <param name="im_extra_drift" value="0.0"/> | |
| 21814 <section name="TransitionGroupPicker"> | |
| 21815 <param name="stop_after_feature" value="-1"/> | |
| 21816 <param name="min_peak_width" value="-1.0"/> | |
| 21817 <param name="peak_integration" value="original"/> | |
| 21818 <param name="background_subtraction" value="none"/> | |
| 21819 <param name="recalculate_peaks" value="true"/> | |
| 21820 <param name="use_precursors" value="false"/> | |
| 21821 <param name="use_consensus" value="true"/> | |
| 21822 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 21823 <param name="minimal_quality" value="-1.5"/> | |
| 21824 <param name="resample_boundary" value="15.0"/> | |
| 21825 <param name="compute_peak_quality" value="true"/> | |
| 21826 <param name="compute_peak_shape_metrics" value="false"/> | |
| 21827 <param name="compute_total_mi" value="false"/> | |
| 21828 <param name="boundary_selection_method" value="largest"/> | |
| 21829 <section name="PeakPickerMRM"> | |
| 21830 <param name="sgolay_frame_length" value="11"/> | |
| 21831 <param name="sgolay_polynomial_order" value="3"/> | |
| 21832 <param name="gauss_width" value="30.0"/> | |
| 21833 <param name="use_gauss" value="false"/> | |
| 21834 <param name="peak_width" value="-1.0"/> | |
| 21835 <param name="signal_to_noise" value="0.1"/> | |
| 21836 <param name="write_sn_log_messages" value="false"/> | |
| 21837 <param name="remove_overlapping_peaks" value="true"/> | |
| 21838 <param name="method" value="corrected"/> | |
| 21839 </section> | |
| 21840 <section name="PeakIntegrator"> | |
| 21841 <param name="integration_type" value="intensity_sum"/> | |
| 21842 <param name="baseline_type" value="base_to_base"/> | |
| 21843 <param name="fit_EMG" value="false"/> | |
| 21844 </section> | |
| 21845 </section> | |
| 21846 <section name="DIAScoring"> | |
| 21847 <param name="dia_extraction_window" value="0.05"/> | |
| 21848 <param name="dia_extraction_unit" value="Th"/> | |
| 21849 <param name="dia_centroided" value="false"/> | |
| 21850 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 21851 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 21852 <param name="dia_nr_isotopes" value="4"/> | |
| 21853 <param name="dia_nr_charges" value="4"/> | |
| 21854 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 21855 </section> | |
| 21856 <section name="EMGScoring"> | |
| 21857 <param name="max_iteration" value="10"/> | |
| 21858 </section> | |
| 21859 <section name="Scores"> | |
| 21860 <param name="use_shape_score" value="true"/> | |
| 21861 <param name="use_coelution_score" value="true"/> | |
| 21862 <param name="use_rt_score" value="true"/> | |
| 21863 <param name="use_library_score" value="true"/> | |
| 21864 <param name="use_intensity_score" value="true"/> | |
| 21865 <param name="use_nr_peaks_score" value="true"/> | |
| 21866 <param name="use_total_xic_score" value="true"/> | |
| 21867 <param name="use_total_mi_score" value="true"/> | |
| 21868 <param name="use_sn_score" value="true"/> | |
| 21869 <param name="use_mi_score" value="true"/> | |
| 21870 <param name="use_dia_scores" value="true"/> | |
| 21871 <param name="use_ms1_correlation" value="false"/> | |
| 21872 <param name="use_sonar_scores" value="false"/> | |
| 21873 <param name="use_ion_mobility_scores" value="false"/> | |
| 21874 <param name="use_ms1_fullscan" value="false"/> | |
| 21875 <param name="use_ms1_mi" value="false"/> | |
| 21876 <param name="use_uis_scores" value="false"/> | |
| 21877 </section> | |
| 21878 </section> | |
| 21879 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> | |
| 21880 <output name="ctd_out" ftype="xml"> | |
| 21881 <assert_contents> | |
| 21882 <is_valid_xml/> | |
| 21883 </assert_contents> | |
| 21884 </output> | |
| 21885 </test> | |
| 21886 <test expect_num_outputs="4"> | |
| 21887 <conditional name="adv_opts_cond"> | |
| 21888 <param name="adv_opts_selector" value="advanced"/> | |
| 21889 <param name="sort_swath_maps" value="false"/> | |
| 21890 <param name="use_ms1_traces" value="true"/> | |
| 21891 <param name="enable_uis_scoring" value="false"/> | |
| 21892 <param name="out_chrom_type" value="mzML"/> | |
| 21893 <param name="min_upper_edge_dist" value="0.0"/> | |
| 21894 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 21895 <param name="mz_extraction_window_unit" value="Th"/> | |
| 21896 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 21897 <param name="use_ms1_ion_mobility" value="true"/> | |
| 21898 <param name="matching_window_only" value="false"/> | |
| 21899 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 21900 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 21901 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 21902 <param name="min_rsq" value="0.95"/> | |
| 21903 <param name="min_coverage" value="0.6"/> | |
| 21904 <param name="split_file_input" value="false"/> | |
| 21905 <param name="use_elution_model_score" value="false"/> | |
| 21906 <param name="readOptions" value="normal"/> | |
| 21907 <param name="mz_correction_function" value="none"/> | |
| 21908 <param name="extraction_function" value="tophat"/> | |
| 21909 <param name="batchSize" value="250"/> | |
| 21910 <param name="ms1_isotopes" value="0"/> | |
| 21911 <param name="force" value="false"/> | |
| 21912 <param name="test" value="true"/> | |
| 21913 </conditional> | |
| 21914 <param name="in" value="OpenSwathWorkflow_21_input.mzML"/> | |
| 21915 <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/> | |
| 21916 <param name="tr_type" value=""/> | |
| 21917 <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/> | |
| 21918 <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 21919 <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 21920 <param name="sonar" value="false"/> | |
| 21921 <param name="rt_extraction_window" value="600.0"/> | |
| 21922 <param name="ion_mobility_window" value="-1.0"/> | |
| 21923 <param name="mz_extraction_window" value="0.05"/> | |
| 21924 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 21925 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 21926 <section name="Debugging"/> | |
| 21927 <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> | |
| 21928 <section name="Calibration"> | |
| 21929 <param name="ms1_im_calibration" value="false"/> | |
| 21930 <param name="im_correction_function" value="linear"/> | |
| 21931 <param name="debug_im_file" value=""/> | |
| 21932 <param name="debug_mz_file" value=""/> | |
| 21933 </section> | |
| 21934 <section name="Library"> | |
| 21935 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 21936 <param name="override_group_label_check" value="false"/> | |
| 21937 <param name="force_invalid_mods" value="false"/> | |
| 21938 </section> | |
| 21939 <section name="RTNormalization"> | |
| 21940 <param name="alignmentMethod" value="linear"/> | |
| 21941 <param name="outlierMethod" value="iter_residual"/> | |
| 21942 <param name="useIterativeChauvenet" value="false"/> | |
| 21943 <param name="RANSACMaxIterations" value="1000"/> | |
| 21944 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 21945 <param name="RANSACSamplingSize" value="10"/> | |
| 21946 <param name="estimateBestPeptides" value="false"/> | |
| 21947 <param name="InitialQualityCutoff" value="0.5"/> | |
| 21948 <param name="OverallQualityCutoff" value="5.5"/> | |
| 21949 <param name="NrRTBins" value="10"/> | |
| 21950 <param name="MinPeptidesPerBin" value="1"/> | |
| 21951 <param name="MinBinsFilled" value="8"/> | |
| 21952 <section name="lowess"> | |
| 21953 <param name="span" value="0.666666666666667"/> | |
| 21954 </section> | |
| 21955 <section name="b_spline"> | |
| 21956 <param name="num_nodes" value="5"/> | |
| 21957 </section> | |
| 21958 </section> | |
| 21959 <section name="Scoring"> | |
| 21960 <param name="stop_report_after_feature" value="5"/> | |
| 21961 <param name="rt_normalization_factor" value="100.0"/> | |
| 21962 <param name="quantification_cutoff" value="0.0"/> | |
| 21963 <param name="write_convex_hull" value="false"/> | |
| 21964 <param name="spectrum_addition_method" value="simple"/> | |
| 21965 <param name="add_up_spectra" value="1"/> | |
| 21966 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 21967 <param name="uis_threshold_sn" value="0"/> | |
| 21968 <param name="uis_threshold_peak_area" value="0"/> | |
| 21969 <param name="scoring_model" value="default"/> | |
| 21970 <param name="im_extra_drift" value="0.0"/> | |
| 21971 <section name="TransitionGroupPicker"> | |
| 21972 <param name="stop_after_feature" value="-1"/> | |
| 21973 <param name="min_peak_width" value="-1.0"/> | |
| 21974 <param name="peak_integration" value="original"/> | |
| 21975 <param name="background_subtraction" value="none"/> | |
| 21976 <param name="recalculate_peaks" value="true"/> | |
| 21977 <param name="use_precursors" value="false"/> | |
| 21978 <param name="use_consensus" value="true"/> | |
| 21979 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 21980 <param name="minimal_quality" value="-1.5"/> | |
| 21981 <param name="resample_boundary" value="15.0"/> | |
| 21982 <param name="compute_peak_quality" value="true"/> | |
| 21983 <param name="compute_peak_shape_metrics" value="false"/> | |
| 21984 <param name="compute_total_mi" value="false"/> | |
| 21985 <param name="boundary_selection_method" value="largest"/> | |
| 21986 <section name="PeakPickerMRM"> | |
| 21987 <param name="sgolay_frame_length" value="11"/> | |
| 21988 <param name="sgolay_polynomial_order" value="3"/> | |
| 21989 <param name="gauss_width" value="30.0"/> | |
| 21990 <param name="use_gauss" value="false"/> | |
| 21991 <param name="peak_width" value="-1.0"/> | |
| 21992 <param name="signal_to_noise" value="0.1"/> | |
| 21993 <param name="write_sn_log_messages" value="false"/> | |
| 21994 <param name="remove_overlapping_peaks" value="true"/> | |
| 21995 <param name="method" value="corrected"/> | |
| 21996 </section> | |
| 21997 <section name="PeakIntegrator"> | |
| 21998 <param name="integration_type" value="intensity_sum"/> | |
| 21999 <param name="baseline_type" value="base_to_base"/> | |
| 22000 <param name="fit_EMG" value="false"/> | |
| 22001 </section> | |
| 22002 </section> | |
| 22003 <section name="DIAScoring"> | |
| 22004 <param name="dia_extraction_window" value="0.05"/> | |
| 22005 <param name="dia_extraction_unit" value="Th"/> | |
| 22006 <param name="dia_centroided" value="false"/> | |
| 22007 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 22008 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 22009 <param name="dia_nr_isotopes" value="4"/> | |
| 22010 <param name="dia_nr_charges" value="4"/> | |
| 22011 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 22012 </section> | |
| 22013 <section name="EMGScoring"> | |
| 22014 <param name="max_iteration" value="10"/> | |
| 22015 </section> | |
| 22016 <section name="Scores"> | |
| 22017 <param name="use_shape_score" value="true"/> | |
| 22018 <param name="use_coelution_score" value="true"/> | |
| 22019 <param name="use_rt_score" value="true"/> | |
| 22020 <param name="use_library_score" value="true"/> | |
| 22021 <param name="use_intensity_score" value="true"/> | |
| 22022 <param name="use_nr_peaks_score" value="true"/> | |
| 22023 <param name="use_total_xic_score" value="true"/> | |
| 22024 <param name="use_total_mi_score" value="true"/> | |
| 22025 <param name="use_sn_score" value="true"/> | |
| 22026 <param name="use_mi_score" value="true"/> | |
| 22027 <param name="use_dia_scores" value="true"/> | |
| 22028 <param name="use_ms1_correlation" value="false"/> | |
| 22029 <param name="use_sonar_scores" value="false"/> | |
| 22030 <param name="use_ion_mobility_scores" value="false"/> | |
| 22031 <param name="use_ms1_fullscan" value="false"/> | |
| 22032 <param name="use_ms1_mi" value="false"/> | |
| 22033 <param name="use_uis_scores" value="false"/> | |
| 22034 </section> | |
| 22035 </section> | |
| 22036 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/> | |
| 22037 <output name="ctd_out" ftype="xml"> | |
| 22038 <assert_contents> | |
| 22039 <is_valid_xml/> | |
| 22040 </assert_contents> | |
| 22041 </output> | |
| 22042 </test> | |
| 22043 <test expect_num_outputs="3"> | |
| 22044 <conditional name="adv_opts_cond"> | |
| 22045 <param name="adv_opts_selector" value="advanced"/> | |
| 22046 <param name="sort_swath_maps" value="false"/> | |
| 22047 <param name="use_ms1_traces" value="true"/> | |
| 22048 <param name="enable_uis_scoring" value="false"/> | |
| 22049 <param name="out_chrom_type" value="mzML"/> | |
| 22050 <param name="min_upper_edge_dist" value="0.0"/> | |
| 22051 <param name="extra_rt_extraction_window" value="0.0"/> | |
| 22052 <param name="mz_extraction_window_unit" value="Th"/> | |
| 22053 <param name="mz_extraction_window_ms1_unit" value="Th"/> | |
| 22054 <param name="use_ms1_ion_mobility" value="true"/> | |
| 22055 <param name="matching_window_only" value="true"/> | |
| 22056 <param name="irt_mz_extraction_window" value="0.05"/> | |
| 22057 <param name="irt_mz_extraction_window_unit" value="Th"/> | |
| 22058 <param name="irt_im_extraction_window" value="-1.0"/> | |
| 22059 <param name="min_rsq" value="0.95"/> | |
| 22060 <param name="min_coverage" value="0.6"/> | |
| 22061 <param name="split_file_input" value="false"/> | |
| 22062 <param name="use_elution_model_score" value="false"/> | |
| 22063 <param name="readOptions" value="workingInMemory"/> | |
| 22064 <param name="mz_correction_function" value="none"/> | |
| 22065 <param name="extraction_function" value="tophat"/> | |
| 22066 <param name="batchSize" value="250"/> | |
| 22067 <param name="ms1_isotopes" value="3"/> | |
| 22068 <param name="force" value="false"/> | |
| 22069 <param name="test" value="true"/> | |
| 22070 </conditional> | |
| 22071 <param name="in" value="OpenSwathWorkflow_22_input.mzML"/> | |
| 22072 <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/> | |
| 22073 <param name="tr_type" value=""/> | |
| 22074 <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 22075 <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22076 <param name="sonar" value="false"/> | |
| 22077 <param name="rt_extraction_window" value="600.0"/> | |
| 22078 <param name="ion_mobility_window" value="-1.0"/> | |
| 22079 <param name="mz_extraction_window" value="0.05"/> | |
| 22080 <param name="mz_extraction_window_ms1" value="0.05"/> | |
| 22081 <param name="im_extraction_window_ms1" value="-1.0"/> | |
| 22082 <section name="Debugging"/> | |
| 22083 <section name="Calibration"> | |
| 22084 <param name="ms1_im_calibration" value="false"/> | |
| 22085 <param name="im_correction_function" value="linear"/> | |
| 22086 <param name="debug_im_file" value=""/> | |
| 22087 <param name="debug_mz_file" value=""/> | |
| 22088 </section> | |
| 22089 <section name="Library"> | |
| 22090 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 22091 <param name="override_group_label_check" value="false"/> | |
| 22092 <param name="force_invalid_mods" value="false"/> | |
| 22093 </section> | |
| 22094 <section name="RTNormalization"> | |
| 22095 <param name="alignmentMethod" value="linear"/> | |
| 22096 <param name="outlierMethod" value="iter_residual"/> | |
| 22097 <param name="useIterativeChauvenet" value="false"/> | |
| 22098 <param name="RANSACMaxIterations" value="1000"/> | |
| 22099 <param name="RANSACMaxPercentRTThreshold" value="3"/> | |
| 22100 <param name="RANSACSamplingSize" value="10"/> | |
| 22101 <param name="estimateBestPeptides" value="false"/> | |
| 22102 <param name="InitialQualityCutoff" value="0.5"/> | |
| 22103 <param name="OverallQualityCutoff" value="5.5"/> | |
| 22104 <param name="NrRTBins" value="10"/> | |
| 22105 <param name="MinPeptidesPerBin" value="1"/> | |
| 22106 <param name="MinBinsFilled" value="8"/> | |
| 22107 <section name="lowess"> | |
| 22108 <param name="span" value="0.666666666666667"/> | |
| 22109 </section> | |
| 22110 <section name="b_spline"> | |
| 22111 <param name="num_nodes" value="5"/> | |
| 22112 </section> | |
| 22113 </section> | |
| 22114 <section name="Scoring"> | |
| 22115 <param name="stop_report_after_feature" value="5"/> | |
| 22116 <param name="rt_normalization_factor" value="100.0"/> | |
| 22117 <param name="quantification_cutoff" value="0.0"/> | |
| 22118 <param name="write_convex_hull" value="false"/> | |
| 22119 <param name="spectrum_addition_method" value="simple"/> | |
| 22120 <param name="add_up_spectra" value="1"/> | |
| 22121 <param name="spacing_for_spectra_resampling" value="0.005"/> | |
| 22122 <param name="uis_threshold_sn" value="0"/> | |
| 22123 <param name="uis_threshold_peak_area" value="0"/> | |
| 22124 <param name="scoring_model" value="default"/> | |
| 22125 <param name="im_extra_drift" value="0.0"/> | |
| 22126 <section name="TransitionGroupPicker"> | |
| 22127 <param name="stop_after_feature" value="-1"/> | |
| 22128 <param name="min_peak_width" value="-1.0"/> | |
| 22129 <param name="peak_integration" value="original"/> | |
| 22130 <param name="background_subtraction" value="none"/> | |
| 22131 <param name="recalculate_peaks" value="true"/> | |
| 22132 <param name="use_precursors" value="false"/> | |
| 22133 <param name="use_consensus" value="true"/> | |
| 22134 <param name="recalculate_peaks_max_z" value="0.75"/> | |
| 22135 <param name="minimal_quality" value="-1.5"/> | |
| 22136 <param name="resample_boundary" value="15.0"/> | |
| 22137 <param name="compute_peak_quality" value="true"/> | |
| 22138 <param name="compute_peak_shape_metrics" value="false"/> | |
| 22139 <param name="compute_total_mi" value="false"/> | |
| 22140 <param name="boundary_selection_method" value="largest"/> | |
| 22141 <section name="PeakPickerMRM"> | |
| 22142 <param name="sgolay_frame_length" value="11"/> | |
| 22143 <param name="sgolay_polynomial_order" value="3"/> | |
| 22144 <param name="gauss_width" value="30.0"/> | |
| 22145 <param name="use_gauss" value="false"/> | |
| 22146 <param name="peak_width" value="-1.0"/> | |
| 22147 <param name="signal_to_noise" value="0.1"/> | |
| 22148 <param name="write_sn_log_messages" value="false"/> | |
| 22149 <param name="remove_overlapping_peaks" value="true"/> | |
| 22150 <param name="method" value="corrected"/> | |
| 22151 </section> | |
| 22152 <section name="PeakIntegrator"> | |
| 22153 <param name="integration_type" value="intensity_sum"/> | |
| 22154 <param name="baseline_type" value="base_to_base"/> | |
| 22155 <param name="fit_EMG" value="false"/> | |
| 22156 </section> | |
| 22157 </section> | |
| 22158 <section name="DIAScoring"> | |
| 22159 <param name="dia_extraction_window" value="0.05"/> | |
| 22160 <param name="dia_extraction_unit" value="Th"/> | |
| 22161 <param name="dia_centroided" value="false"/> | |
| 22162 <param name="dia_byseries_intensity_min" value="300.0"/> | |
| 22163 <param name="dia_byseries_ppm_diff" value="10.0"/> | |
| 22164 <param name="dia_nr_isotopes" value="4"/> | |
| 22165 <param name="dia_nr_charges" value="4"/> | |
| 22166 <param name="peak_before_mono_max_ppm_diff" value="20.0"/> | |
| 22167 </section> | |
| 22168 <section name="EMGScoring"> | |
| 22169 <param name="max_iteration" value="10"/> | |
| 22170 </section> | |
| 22171 <section name="Scores"> | |
| 22172 <param name="use_shape_score" value="true"/> | |
| 22173 <param name="use_coelution_score" value="true"/> | |
| 22174 <param name="use_rt_score" value="true"/> | |
| 22175 <param name="use_library_score" value="true"/> | |
| 22176 <param name="use_intensity_score" value="true"/> | |
| 22177 <param name="use_nr_peaks_score" value="true"/> | |
| 22178 <param name="use_total_xic_score" value="true"/> | |
| 22179 <param name="use_total_mi_score" value="false"/> | |
| 22180 <param name="use_sn_score" value="true"/> | |
| 22181 <param name="use_mi_score" value="false"/> | |
| 22182 <param name="use_dia_scores" value="true"/> | |
| 22183 <param name="use_ms1_correlation" value="false"/> | |
| 22184 <param name="use_sonar_scores" value="false"/> | |
| 22185 <param name="use_ion_mobility_scores" value="false"/> | |
| 22186 <param name="use_ms1_fullscan" value="false"/> | |
| 22187 <param name="use_ms1_mi" value="false"/> | |
| 22188 <param name="use_uis_scores" value="false"/> | |
| 22189 </section> | |
| 22190 </section> | |
| 22191 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> | |
| 22192 <output name="ctd_out" ftype="xml"> | |
| 22193 <assert_contents> | |
| 22194 <is_valid_xml/> | |
| 22195 </assert_contents> | |
| 22196 </output> | |
| 22197 </test> | |
| 22198 </xml> | |
| 22199 <xml name="autotest_PeakPickerHiRes"> | |
| 22200 <test expect_num_outputs="2"> | |
| 22201 <conditional name="adv_opts_cond"> | |
| 22202 <param name="adv_opts_selector" value="advanced"/> | |
| 22203 <param name="processOption" value="inmemory"/> | |
| 22204 <param name="force" value="false"/> | |
| 22205 <param name="test" value="true"/> | |
| 22206 </conditional> | |
| 22207 <param name="in" value="PeakPickerHiRes_input.mzML"/> | |
| 22208 <output name="out" file="PeakPickerHiRes_1.tmp" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22209 <section name="algorithm"> | |
| 22210 <param name="signal_to_noise" value="1.0"/> | |
| 22211 <param name="spacing_difference_gap" value="4.0"/> | |
| 22212 <param name="spacing_difference" value="1.5"/> | |
| 22213 <param name="missing" value="1"/> | |
| 22214 <param name="ms_levels" value="1"/> | |
| 22215 <param name="report_FWHM" value="true"/> | |
| 22216 <param name="report_FWHM_unit" value="relative"/> | |
| 22217 <section name="SignalToNoise"> | |
| 22218 <param name="max_intensity" value="-1"/> | |
| 22219 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22220 <param name="auto_max_percentile" value="95"/> | |
| 22221 <param name="auto_mode" value="0"/> | |
| 22222 <param name="win_len" value="200.0"/> | |
| 22223 <param name="bin_count" value="30"/> | |
| 22224 <param name="min_required_elements" value="10"/> | |
| 22225 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22226 <param name="write_log_messages" value="true"/> | |
| 22227 </section> | |
| 22228 </section> | |
| 22229 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22230 <output name="ctd_out" ftype="xml"> | |
| 22231 <assert_contents> | |
| 22232 <is_valid_xml/> | |
| 22233 </assert_contents> | |
| 22234 </output> | |
| 22235 </test> | |
| 22236 <test expect_num_outputs="2"> | |
| 22237 <conditional name="adv_opts_cond"> | |
| 22238 <param name="adv_opts_selector" value="advanced"/> | |
| 22239 <param name="processOption" value="inmemory"/> | |
| 22240 <param name="force" value="false"/> | |
| 22241 <param name="test" value="true"/> | |
| 22242 </conditional> | |
| 22243 <param name="in" value="PeakPickerHiRes_2_input.mzML"/> | |
| 22244 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22245 <section name="algorithm"> | |
| 22246 <param name="signal_to_noise" value="1.0"/> | |
| 22247 <param name="spacing_difference_gap" value="4.0"/> | |
| 22248 <param name="spacing_difference" value="1.5"/> | |
| 22249 <param name="missing" value="1"/> | |
| 22250 <param name="ms_levels" value="1"/> | |
| 22251 <param name="report_FWHM" value="true"/> | |
| 22252 <param name="report_FWHM_unit" value="relative"/> | |
| 22253 <section name="SignalToNoise"> | |
| 22254 <param name="max_intensity" value="-1"/> | |
| 22255 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22256 <param name="auto_max_percentile" value="95"/> | |
| 22257 <param name="auto_mode" value="0"/> | |
| 22258 <param name="win_len" value="200.0"/> | |
| 22259 <param name="bin_count" value="30"/> | |
| 22260 <param name="min_required_elements" value="10"/> | |
| 22261 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22262 <param name="write_log_messages" value="true"/> | |
| 22263 </section> | |
| 22264 </section> | |
| 22265 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22266 <output name="ctd_out" ftype="xml"> | |
| 22267 <assert_contents> | |
| 22268 <is_valid_xml/> | |
| 22269 </assert_contents> | |
| 22270 </output> | |
| 22271 </test> | |
| 22272 <test expect_num_outputs="2"> | |
| 22273 <conditional name="adv_opts_cond"> | |
| 22274 <param name="adv_opts_selector" value="advanced"/> | |
| 22275 <param name="processOption" value="lowmemory"/> | |
| 22276 <param name="force" value="false"/> | |
| 22277 <param name="test" value="true"/> | |
| 22278 </conditional> | |
| 22279 <param name="in" value="PeakPickerHiRes_input.mzML"/> | |
| 22280 <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22281 <section name="algorithm"> | |
| 22282 <param name="signal_to_noise" value="1.0"/> | |
| 22283 <param name="spacing_difference_gap" value="4.0"/> | |
| 22284 <param name="spacing_difference" value="1.5"/> | |
| 22285 <param name="missing" value="1"/> | |
| 22286 <param name="ms_levels" value="1"/> | |
| 22287 <param name="report_FWHM" value="true"/> | |
| 22288 <param name="report_FWHM_unit" value="relative"/> | |
| 22289 <section name="SignalToNoise"> | |
| 22290 <param name="max_intensity" value="-1"/> | |
| 22291 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22292 <param name="auto_max_percentile" value="95"/> | |
| 22293 <param name="auto_mode" value="0"/> | |
| 22294 <param name="win_len" value="200.0"/> | |
| 22295 <param name="bin_count" value="30"/> | |
| 22296 <param name="min_required_elements" value="10"/> | |
| 22297 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22298 <param name="write_log_messages" value="true"/> | |
| 22299 </section> | |
| 22300 </section> | |
| 22301 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22302 <output name="ctd_out" ftype="xml"> | |
| 22303 <assert_contents> | |
| 22304 <is_valid_xml/> | |
| 22305 </assert_contents> | |
| 22306 </output> | |
| 22307 </test> | |
| 22308 <test expect_num_outputs="2"> | |
| 22309 <conditional name="adv_opts_cond"> | |
| 22310 <param name="adv_opts_selector" value="advanced"/> | |
| 22311 <param name="processOption" value="lowmemory"/> | |
| 22312 <param name="force" value="false"/> | |
| 22313 <param name="test" value="true"/> | |
| 22314 </conditional> | |
| 22315 <param name="in" value="PeakPickerHiRes_2_input.mzML"/> | |
| 22316 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22317 <section name="algorithm"> | |
| 22318 <param name="signal_to_noise" value="1.0"/> | |
| 22319 <param name="spacing_difference_gap" value="4.0"/> | |
| 22320 <param name="spacing_difference" value="1.5"/> | |
| 22321 <param name="missing" value="1"/> | |
| 22322 <param name="ms_levels" value="1"/> | |
| 22323 <param name="report_FWHM" value="true"/> | |
| 22324 <param name="report_FWHM_unit" value="relative"/> | |
| 22325 <section name="SignalToNoise"> | |
| 22326 <param name="max_intensity" value="-1"/> | |
| 22327 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22328 <param name="auto_max_percentile" value="95"/> | |
| 22329 <param name="auto_mode" value="0"/> | |
| 22330 <param name="win_len" value="200.0"/> | |
| 22331 <param name="bin_count" value="30"/> | |
| 22332 <param name="min_required_elements" value="10"/> | |
| 22333 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22334 <param name="write_log_messages" value="true"/> | |
| 22335 </section> | |
| 22336 </section> | |
| 22337 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22338 <output name="ctd_out" ftype="xml"> | |
| 22339 <assert_contents> | |
| 22340 <is_valid_xml/> | |
| 22341 </assert_contents> | |
| 22342 </output> | |
| 22343 </test> | |
| 22344 <test expect_num_outputs="2"> | |
| 22345 <conditional name="adv_opts_cond"> | |
| 22346 <param name="adv_opts_selector" value="advanced"/> | |
| 22347 <param name="processOption" value="inmemory"/> | |
| 22348 <param name="force" value="false"/> | |
| 22349 <param name="test" value="true"/> | |
| 22350 </conditional> | |
| 22351 <param name="in" value="PeakPickerHiRes_5_input.mzML"/> | |
| 22352 <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22353 <section name="algorithm"> | |
| 22354 <param name="signal_to_noise" value="0.0"/> | |
| 22355 <param name="spacing_difference_gap" value="4.0"/> | |
| 22356 <param name="spacing_difference" value="1.5"/> | |
| 22357 <param name="missing" value="1"/> | |
| 22358 <param name="ms_levels" value=""/> | |
| 22359 <param name="report_FWHM" value="false"/> | |
| 22360 <param name="report_FWHM_unit" value="relative"/> | |
| 22361 <section name="SignalToNoise"> | |
| 22362 <param name="max_intensity" value="-1"/> | |
| 22363 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22364 <param name="auto_max_percentile" value="95"/> | |
| 22365 <param name="auto_mode" value="0"/> | |
| 22366 <param name="win_len" value="200.0"/> | |
| 22367 <param name="bin_count" value="30"/> | |
| 22368 <param name="min_required_elements" value="10"/> | |
| 22369 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22370 <param name="write_log_messages" value="true"/> | |
| 22371 </section> | |
| 22372 </section> | |
| 22373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22374 <output name="ctd_out" ftype="xml"> | |
| 22375 <assert_contents> | |
| 22376 <is_valid_xml/> | |
| 22377 </assert_contents> | |
| 22378 </output> | |
| 22379 </test> | |
| 22380 </xml> | |
| 22381 <xml name="autotest_PeakPickerIterative"> | |
| 22382 <test expect_num_outputs="2"> | |
| 22383 <conditional name="adv_opts_cond"> | |
| 22384 <param name="adv_opts_selector" value="advanced"/> | |
| 22385 <param name="force" value="false"/> | |
| 22386 <param name="test" value="true"/> | |
| 22387 </conditional> | |
| 22388 <param name="in" value="PeakPickerIterative_1_input.mzML"/> | |
| 22389 <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22390 <section name="algorithm"> | |
| 22391 <param name="signal_to_noise_" value="1.0"/> | |
| 22392 <param name="peak_width" value="0.04"/> | |
| 22393 <param name="spacing_difference" value="1.5"/> | |
| 22394 <param name="sn_bin_count_" value="30"/> | |
| 22395 <param name="nr_iterations_" value="5"/> | |
| 22396 <param name="sn_win_len_" value="20.0"/> | |
| 22397 <param name="check_width_internally" value="false"/> | |
| 22398 <param name="ms1_only" value="false"/> | |
| 22399 <param name="clear_meta_data" value="false"/> | |
| 22400 </section> | |
| 22401 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22402 <output name="ctd_out" ftype="xml"> | |
| 22403 <assert_contents> | |
| 22404 <is_valid_xml/> | |
| 22405 </assert_contents> | |
| 22406 </output> | |
| 22407 </test> | |
| 22408 <test expect_num_outputs="2"> | |
| 22409 <conditional name="adv_opts_cond"> | |
| 22410 <param name="adv_opts_selector" value="advanced"/> | |
| 22411 <param name="force" value="false"/> | |
| 22412 <param name="test" value="true"/> | |
| 22413 </conditional> | |
| 22414 <param name="in" value="PeakPickerIterative_2_input.mzML"/> | |
| 22415 <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22416 <section name="algorithm"> | |
| 22417 <param name="signal_to_noise_" value="0.0"/> | |
| 22418 <param name="peak_width" value="0.04"/> | |
| 22419 <param name="spacing_difference" value="2.5"/> | |
| 22420 <param name="sn_bin_count_" value="30"/> | |
| 22421 <param name="nr_iterations_" value="5"/> | |
| 22422 <param name="sn_win_len_" value="20.0"/> | |
| 22423 <param name="check_width_internally" value="true"/> | |
| 22424 <param name="ms1_only" value="false"/> | |
| 22425 <param name="clear_meta_data" value="false"/> | |
| 22426 </section> | |
| 22427 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22428 <output name="ctd_out" ftype="xml"> | |
| 22429 <assert_contents> | |
| 22430 <is_valid_xml/> | |
| 22431 </assert_contents> | |
| 22432 </output> | |
| 22433 </test> | |
| 22434 </xml> | |
| 22435 <xml name="autotest_PeakPickerWavelet"> | |
| 22436 <test expect_num_outputs="2"> | |
| 22437 <conditional name="adv_opts_cond"> | |
| 22438 <param name="adv_opts_selector" value="advanced"/> | |
| 22439 <param name="write_peak_meta_data" value="true"/> | |
| 22440 <param name="force" value="false"/> | |
| 22441 <param name="test" value="true"/> | |
| 22442 </conditional> | |
| 22443 <param name="in" value="PeakPickerWavelet_input.mzML"/> | |
| 22444 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22445 <section name="algorithm"> | |
| 22446 <param name="signal_to_noise" value="3.0"/> | |
| 22447 <param name="centroid_percentage" value="0.6"/> | |
| 22448 <param name="peak_width" value="0.2"/> | |
| 22449 <param name="estimate_peak_width" value="false"/> | |
| 22450 <param name="fwhm_lower_bound_factor" value="0.5"/> | |
| 22451 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
| 22452 <section name="optimization"> | |
| 22453 <param name="iterations" value="400"/> | |
| 22454 <section name="penalties"> | |
| 22455 <param name="position" value="0.0"/> | |
| 22456 <param name="left_width" value="1.0"/> | |
| 22457 <param name="right_width" value="1.0"/> | |
| 22458 <param name="height" value="1.0"/> | |
| 22459 </section> | |
| 22460 <section name="2d"> | |
| 22461 <param name="tolerance_mz" value="2.2"/> | |
| 22462 <param name="max_peak_distance" value="1.2"/> | |
| 22463 </section> | |
| 22464 </section> | |
| 22465 <section name="thresholds"> | |
| 22466 <param name="peak_bound" value="100.0"/> | |
| 22467 <param name="peak_bound_ms2_level" value="10.0"/> | |
| 22468 <param name="correlation" value="0.5"/> | |
| 22469 <param name="noise_level" value="0.1"/> | |
| 22470 <param name="search_radius" value="3"/> | |
| 22471 </section> | |
| 22472 <section name="wavelet_transform"> | |
| 22473 <param name="spacing" value="0.001"/> | |
| 22474 </section> | |
| 22475 <section name="deconvolution"> | |
| 22476 <param name="deconvolution" value="false"/> | |
| 22477 <param name="asym_threshold" value="0.3"/> | |
| 22478 <param name="left_width" value="2.0"/> | |
| 22479 <param name="right_width" value="2.0"/> | |
| 22480 <param name="scaling" value="0.12"/> | |
| 22481 <section name="fitting"> | |
| 22482 <param name="fwhm_threshold" value="0.7"/> | |
| 22483 <param name="eps_abs" value="9.999999747378752e-06"/> | |
| 22484 <param name="eps_rel" value="9.999999747378752e-06"/> | |
| 22485 <param name="max_iteration" value="10"/> | |
| 22486 <section name="penalties"> | |
| 22487 <param name="position" value="0.0"/> | |
| 22488 <param name="height" value="1.0"/> | |
| 22489 <param name="left_width" value="0.0"/> | |
| 22490 <param name="right_width" value="0.0"/> | |
| 22491 </section> | |
| 22492 </section> | |
| 22493 </section> | |
| 22494 <section name="SignalToNoiseEstimationParameter"> | |
| 22495 <param name="max_intensity" value="-1"/> | |
| 22496 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22497 <param name="auto_max_percentile" value="95"/> | |
| 22498 <param name="auto_mode" value="0"/> | |
| 22499 <param name="win_len" value="200.0"/> | |
| 22500 <param name="bin_count" value="30"/> | |
| 22501 <param name="stdev_mp" value="3.0"/> | |
| 22502 <param name="min_required_elements" value="10"/> | |
| 22503 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22504 </section> | |
| 22505 </section> | |
| 22506 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22507 <output name="ctd_out" ftype="xml"> | |
| 22508 <assert_contents> | |
| 22509 <is_valid_xml/> | |
| 22510 </assert_contents> | |
| 22511 </output> | |
| 22512 </test> | |
| 22513 <test expect_num_outputs="2"> | |
| 22514 <conditional name="adv_opts_cond"> | |
| 22515 <param name="adv_opts_selector" value="advanced"/> | |
| 22516 <param name="write_peak_meta_data" value="true"/> | |
| 22517 <param name="force" value="false"/> | |
| 22518 <param name="test" value="true"/> | |
| 22519 </conditional> | |
| 22520 <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/> | |
| 22521 <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22522 <section name="algorithm"> | |
| 22523 <param name="signal_to_noise" value="2.0"/> | |
| 22524 <param name="centroid_percentage" value="0.8"/> | |
| 22525 <param name="peak_width" value="0.15"/> | |
| 22526 <param name="estimate_peak_width" value="false"/> | |
| 22527 <param name="fwhm_lower_bound_factor" value="1.0"/> | |
| 22528 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
| 22529 <section name="optimization"> | |
| 22530 <param name="iterations" value="400"/> | |
| 22531 <section name="penalties"> | |
| 22532 <param name="position" value="0.0"/> | |
| 22533 <param name="left_width" value="1.0"/> | |
| 22534 <param name="right_width" value="1.0"/> | |
| 22535 <param name="height" value="1.0"/> | |
| 22536 </section> | |
| 22537 <section name="2d"> | |
| 22538 <param name="tolerance_mz" value="2.2"/> | |
| 22539 <param name="max_peak_distance" value="1.2"/> | |
| 22540 </section> | |
| 22541 </section> | |
| 22542 <section name="thresholds"> | |
| 22543 <param name="peak_bound" value="200.0"/> | |
| 22544 <param name="peak_bound_ms2_level" value="50.0"/> | |
| 22545 <param name="correlation" value="0.5"/> | |
| 22546 <param name="noise_level" value="0.1"/> | |
| 22547 <param name="search_radius" value="3"/> | |
| 22548 </section> | |
| 22549 <section name="wavelet_transform"> | |
| 22550 <param name="spacing" value="0.001"/> | |
| 22551 </section> | |
| 22552 <section name="deconvolution"> | |
| 22553 <param name="deconvolution" value="true"/> | |
| 22554 <param name="asym_threshold" value="0.3"/> | |
| 22555 <param name="left_width" value="2.0"/> | |
| 22556 <param name="right_width" value="2.0"/> | |
| 22557 <param name="scaling" value="0.1"/> | |
| 22558 <section name="fitting"> | |
| 22559 <param name="fwhm_threshold" value="0.7"/> | |
| 22560 <param name="eps_abs" value="9.999999747378752e-06"/> | |
| 22561 <param name="eps_rel" value="9.999999747378752e-06"/> | |
| 22562 <param name="max_iteration" value="100"/> | |
| 22563 <section name="penalties"> | |
| 22564 <param name="position" value="1.0"/> | |
| 22565 <param name="height" value="1.0"/> | |
| 22566 <param name="left_width" value="0.0"/> | |
| 22567 <param name="right_width" value="0.0"/> | |
| 22568 </section> | |
| 22569 </section> | |
| 22570 </section> | |
| 22571 <section name="SignalToNoiseEstimationParameter"> | |
| 22572 <param name="max_intensity" value="-1"/> | |
| 22573 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22574 <param name="auto_max_percentile" value="95"/> | |
| 22575 <param name="auto_mode" value="0"/> | |
| 22576 <param name="win_len" value="200.0"/> | |
| 22577 <param name="bin_count" value="30"/> | |
| 22578 <param name="stdev_mp" value="3.0"/> | |
| 22579 <param name="min_required_elements" value="10"/> | |
| 22580 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22581 </section> | |
| 22582 </section> | |
| 22583 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22584 <output name="ctd_out" ftype="xml"> | |
| 22585 <assert_contents> | |
| 22586 <is_valid_xml/> | |
| 22587 </assert_contents> | |
| 22588 </output> | |
| 22589 </test> | |
| 22590 <test expect_num_outputs="2"> | |
| 22591 <conditional name="adv_opts_cond"> | |
| 22592 <param name="adv_opts_selector" value="advanced"/> | |
| 22593 <param name="write_peak_meta_data" value="true"/> | |
| 22594 <param name="force" value="false"/> | |
| 22595 <param name="test" value="true"/> | |
| 22596 </conditional> | |
| 22597 <param name="in" value="PeakPickerWavelet_input.mzML"/> | |
| 22598 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22599 <section name="algorithm"> | |
| 22600 <param name="signal_to_noise" value="3.0"/> | |
| 22601 <param name="centroid_percentage" value="0.6"/> | |
| 22602 <param name="peak_width" value="0.2"/> | |
| 22603 <param name="estimate_peak_width" value="false"/> | |
| 22604 <param name="fwhm_lower_bound_factor" value="0.5"/> | |
| 22605 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
| 22606 <section name="optimization"> | |
| 22607 <param name="iterations" value="400"/> | |
| 22608 <section name="penalties"> | |
| 22609 <param name="position" value="0.0"/> | |
| 22610 <param name="left_width" value="1.0"/> | |
| 22611 <param name="right_width" value="1.0"/> | |
| 22612 <param name="height" value="1.0"/> | |
| 22613 </section> | |
| 22614 <section name="2d"> | |
| 22615 <param name="tolerance_mz" value="2.2"/> | |
| 22616 <param name="max_peak_distance" value="1.2"/> | |
| 22617 </section> | |
| 22618 </section> | |
| 22619 <section name="thresholds"> | |
| 22620 <param name="peak_bound" value="100.0"/> | |
| 22621 <param name="peak_bound_ms2_level" value="10.0"/> | |
| 22622 <param name="correlation" value="0.5"/> | |
| 22623 <param name="noise_level" value="0.1"/> | |
| 22624 <param name="search_radius" value="3"/> | |
| 22625 </section> | |
| 22626 <section name="wavelet_transform"> | |
| 22627 <param name="spacing" value="0.001"/> | |
| 22628 </section> | |
| 22629 <section name="deconvolution"> | |
| 22630 <param name="deconvolution" value="false"/> | |
| 22631 <param name="asym_threshold" value="0.3"/> | |
| 22632 <param name="left_width" value="2.0"/> | |
| 22633 <param name="right_width" value="2.0"/> | |
| 22634 <param name="scaling" value="0.12"/> | |
| 22635 <section name="fitting"> | |
| 22636 <param name="fwhm_threshold" value="0.7"/> | |
| 22637 <param name="eps_abs" value="9.999999747378752e-06"/> | |
| 22638 <param name="eps_rel" value="9.999999747378752e-06"/> | |
| 22639 <param name="max_iteration" value="10"/> | |
| 22640 <section name="penalties"> | |
| 22641 <param name="position" value="0.0"/> | |
| 22642 <param name="height" value="1.0"/> | |
| 22643 <param name="left_width" value="0.0"/> | |
| 22644 <param name="right_width" value="0.0"/> | |
| 22645 </section> | |
| 22646 </section> | |
| 22647 </section> | |
| 22648 <section name="SignalToNoiseEstimationParameter"> | |
| 22649 <param name="max_intensity" value="-1"/> | |
| 22650 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22651 <param name="auto_max_percentile" value="95"/> | |
| 22652 <param name="auto_mode" value="0"/> | |
| 22653 <param name="win_len" value="200.0"/> | |
| 22654 <param name="bin_count" value="30"/> | |
| 22655 <param name="stdev_mp" value="3.0"/> | |
| 22656 <param name="min_required_elements" value="10"/> | |
| 22657 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22658 </section> | |
| 22659 </section> | |
| 22660 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22661 <output name="ctd_out" ftype="xml"> | |
| 22662 <assert_contents> | |
| 22663 <is_valid_xml/> | |
| 22664 </assert_contents> | |
| 22665 </output> | |
| 22666 </test> | |
| 22667 <test expect_num_outputs="2"> | |
| 22668 <conditional name="adv_opts_cond"> | |
| 22669 <param name="adv_opts_selector" value="advanced"/> | |
| 22670 <param name="write_peak_meta_data" value="false"/> | |
| 22671 <param name="force" value="false"/> | |
| 22672 <param name="test" value="true"/> | |
| 22673 </conditional> | |
| 22674 <param name="in" value="PeakPickerWavelet_input.mzML"/> | |
| 22675 <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 22676 <section name="algorithm"> | |
| 22677 <param name="signal_to_noise" value="3.0"/> | |
| 22678 <param name="centroid_percentage" value="0.6"/> | |
| 22679 <param name="peak_width" value="0.2"/> | |
| 22680 <param name="estimate_peak_width" value="false"/> | |
| 22681 <param name="fwhm_lower_bound_factor" value="0.5"/> | |
| 22682 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
| 22683 <section name="optimization"> | |
| 22684 <param name="iterations" value="400"/> | |
| 22685 <section name="penalties"> | |
| 22686 <param name="position" value="0.0"/> | |
| 22687 <param name="left_width" value="1.0"/> | |
| 22688 <param name="right_width" value="1.0"/> | |
| 22689 <param name="height" value="1.0"/> | |
| 22690 </section> | |
| 22691 <section name="2d"> | |
| 22692 <param name="tolerance_mz" value="2.2"/> | |
| 22693 <param name="max_peak_distance" value="1.2"/> | |
| 22694 </section> | |
| 22695 </section> | |
| 22696 <section name="thresholds"> | |
| 22697 <param name="peak_bound" value="100.0"/> | |
| 22698 <param name="peak_bound_ms2_level" value="10.0"/> | |
| 22699 <param name="correlation" value="0.5"/> | |
| 22700 <param name="noise_level" value="0.1"/> | |
| 22701 <param name="search_radius" value="3"/> | |
| 22702 </section> | |
| 22703 <section name="wavelet_transform"> | |
| 22704 <param name="spacing" value="0.001"/> | |
| 22705 </section> | |
| 22706 <section name="deconvolution"> | |
| 22707 <param name="deconvolution" value="false"/> | |
| 22708 <param name="asym_threshold" value="0.3"/> | |
| 22709 <param name="left_width" value="2.0"/> | |
| 22710 <param name="right_width" value="2.0"/> | |
| 22711 <param name="scaling" value="0.12"/> | |
| 22712 <section name="fitting"> | |
| 22713 <param name="fwhm_threshold" value="0.7"/> | |
| 22714 <param name="eps_abs" value="9.999999747378752e-06"/> | |
| 22715 <param name="eps_rel" value="9.999999747378752e-06"/> | |
| 22716 <param name="max_iteration" value="10"/> | |
| 22717 <section name="penalties"> | |
| 22718 <param name="position" value="0.0"/> | |
| 22719 <param name="height" value="1.0"/> | |
| 22720 <param name="left_width" value="0.0"/> | |
| 22721 <param name="right_width" value="0.0"/> | |
| 22722 </section> | |
| 22723 </section> | |
| 22724 </section> | |
| 22725 <section name="SignalToNoiseEstimationParameter"> | |
| 22726 <param name="max_intensity" value="-1"/> | |
| 22727 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 22728 <param name="auto_max_percentile" value="95"/> | |
| 22729 <param name="auto_mode" value="0"/> | |
| 22730 <param name="win_len" value="200.0"/> | |
| 22731 <param name="bin_count" value="30"/> | |
| 22732 <param name="stdev_mp" value="3.0"/> | |
| 22733 <param name="min_required_elements" value="10"/> | |
| 22734 <param name="noise_for_empty_window" value="1e+20"/> | |
| 22735 </section> | |
| 22736 </section> | |
| 22737 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22738 <output name="ctd_out" ftype="xml"> | |
| 22739 <assert_contents> | |
| 22740 <is_valid_xml/> | |
| 22741 </assert_contents> | |
| 22742 </output> | |
| 22743 </test> | |
| 22744 </xml> | |
| 22745 <xml name="autotest_PepNovoAdapter"> | |
| 22746 </xml> | |
| 22747 <xml name="autotest_PeptideIndexer"> | |
| 22748 <test expect_num_outputs="2"> | |
| 22749 <conditional name="adv_opts_cond"> | |
| 22750 <param name="adv_opts_selector" value="advanced"/> | |
| 22751 <param name="force" value="false"/> | |
| 22752 <param name="test" value="true"/> | |
| 22753 </conditional> | |
| 22754 <param name="in" value="PeptideIndexer_1.idXML"/> | |
| 22755 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22756 <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22757 <param name="decoy_string" value=""/> | |
| 22758 <param name="decoy_string_position" value="prefix"/> | |
| 22759 <param name="missing_decoy_action" value="error"/> | |
| 22760 <param name="write_protein_sequence" value="false"/> | |
| 22761 <param name="write_protein_description" value="false"/> | |
| 22762 <param name="keep_unreferenced_proteins" value="false"/> | |
| 22763 <param name="allow_unmatched" value="true"/> | |
| 22764 <param name="aaa_max" value="4"/> | |
| 22765 <param name="mismatches_max" value="0"/> | |
| 22766 <param name="IL_equivalent" value="false"/> | |
| 22767 <section name="enzyme"> | |
| 22768 <param name="name" value="Trypsin"/> | |
| 22769 <param name="specificity" value="none"/> | |
| 22770 </section> | |
| 22771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22772 <output name="ctd_out" ftype="xml"> | |
| 22773 <assert_contents> | |
| 22774 <is_valid_xml/> | |
| 22775 </assert_contents> | |
| 22776 </output> | |
| 22777 </test> | |
| 22778 <test expect_num_outputs="2"> | |
| 22779 <conditional name="adv_opts_cond"> | |
| 22780 <param name="adv_opts_selector" value="advanced"/> | |
| 22781 <param name="force" value="false"/> | |
| 22782 <param name="test" value="true"/> | |
| 22783 </conditional> | |
| 22784 <param name="in" value="PeptideIndexer_1.idXML"/> | |
| 22785 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22786 <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22787 <param name="decoy_string" value=""/> | |
| 22788 <param name="decoy_string_position" value="prefix"/> | |
| 22789 <param name="missing_decoy_action" value="error"/> | |
| 22790 <param name="write_protein_sequence" value="true"/> | |
| 22791 <param name="write_protein_description" value="false"/> | |
| 22792 <param name="keep_unreferenced_proteins" value="false"/> | |
| 22793 <param name="allow_unmatched" value="true"/> | |
| 22794 <param name="aaa_max" value="4"/> | |
| 22795 <param name="mismatches_max" value="0"/> | |
| 22796 <param name="IL_equivalent" value="false"/> | |
| 22797 <section name="enzyme"> | |
| 22798 <param name="name" value="Trypsin"/> | |
| 22799 <param name="specificity" value="none"/> | |
| 22800 </section> | |
| 22801 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22802 <output name="ctd_out" ftype="xml"> | |
| 22803 <assert_contents> | |
| 22804 <is_valid_xml/> | |
| 22805 </assert_contents> | |
| 22806 </output> | |
| 22807 </test> | |
| 22808 <test expect_num_outputs="2"> | |
| 22809 <conditional name="adv_opts_cond"> | |
| 22810 <param name="adv_opts_selector" value="advanced"/> | |
| 22811 <param name="force" value="false"/> | |
| 22812 <param name="test" value="true"/> | |
| 22813 </conditional> | |
| 22814 <param name="in" value="PeptideIndexer_1.idXML"/> | |
| 22815 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22816 <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22817 <param name="decoy_string" value=""/> | |
| 22818 <param name="decoy_string_position" value="prefix"/> | |
| 22819 <param name="missing_decoy_action" value="error"/> | |
| 22820 <param name="write_protein_sequence" value="false"/> | |
| 22821 <param name="write_protein_description" value="false"/> | |
| 22822 <param name="keep_unreferenced_proteins" value="true"/> | |
| 22823 <param name="allow_unmatched" value="true"/> | |
| 22824 <param name="aaa_max" value="4"/> | |
| 22825 <param name="mismatches_max" value="0"/> | |
| 22826 <param name="IL_equivalent" value="false"/> | |
| 22827 <section name="enzyme"> | |
| 22828 <param name="name" value="Trypsin"/> | |
| 22829 <param name="specificity" value="none"/> | |
| 22830 </section> | |
| 22831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22832 <output name="ctd_out" ftype="xml"> | |
| 22833 <assert_contents> | |
| 22834 <is_valid_xml/> | |
| 22835 </assert_contents> | |
| 22836 </output> | |
| 22837 </test> | |
| 22838 <test expect_num_outputs="2"> | |
| 22839 <conditional name="adv_opts_cond"> | |
| 22840 <param name="adv_opts_selector" value="advanced"/> | |
| 22841 <param name="force" value="false"/> | |
| 22842 <param name="test" value="true"/> | |
| 22843 </conditional> | |
| 22844 <param name="in" value="PeptideIndexer_1.idXML"/> | |
| 22845 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22846 <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22847 <param name="decoy_string" value=""/> | |
| 22848 <param name="decoy_string_position" value="prefix"/> | |
| 22849 <param name="missing_decoy_action" value="error"/> | |
| 22850 <param name="write_protein_sequence" value="true"/> | |
| 22851 <param name="write_protein_description" value="false"/> | |
| 22852 <param name="keep_unreferenced_proteins" value="false"/> | |
| 22853 <param name="allow_unmatched" value="true"/> | |
| 22854 <param name="aaa_max" value="0"/> | |
| 22855 <param name="mismatches_max" value="0"/> | |
| 22856 <param name="IL_equivalent" value="false"/> | |
| 22857 <section name="enzyme"> | |
| 22858 <param name="name" value="Trypsin"/> | |
| 22859 <param name="specificity" value="none"/> | |
| 22860 </section> | |
| 22861 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22862 <output name="ctd_out" ftype="xml"> | |
| 22863 <assert_contents> | |
| 22864 <is_valid_xml/> | |
| 22865 </assert_contents> | |
| 22866 </output> | |
| 22867 </test> | |
| 22868 <test expect_num_outputs="2"> | |
| 22869 <conditional name="adv_opts_cond"> | |
| 22870 <param name="adv_opts_selector" value="advanced"/> | |
| 22871 <param name="force" value="false"/> | |
| 22872 <param name="test" value="true"/> | |
| 22873 </conditional> | |
| 22874 <param name="in" value="PeptideIndexer_1.idXML"/> | |
| 22875 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22876 <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22877 <param name="decoy_string" value=""/> | |
| 22878 <param name="decoy_string_position" value="prefix"/> | |
| 22879 <param name="missing_decoy_action" value="error"/> | |
| 22880 <param name="write_protein_sequence" value="false"/> | |
| 22881 <param name="write_protein_description" value="false"/> | |
| 22882 <param name="keep_unreferenced_proteins" value="false"/> | |
| 22883 <param name="allow_unmatched" value="true"/> | |
| 22884 <param name="aaa_max" value="4"/> | |
| 22885 <param name="mismatches_max" value="0"/> | |
| 22886 <param name="IL_equivalent" value="false"/> | |
| 22887 <section name="enzyme"> | |
| 22888 <param name="name" value="Trypsin"/> | |
| 22889 <param name="specificity" value="none"/> | |
| 22890 </section> | |
| 22891 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22892 <output name="ctd_out" ftype="xml"> | |
| 22893 <assert_contents> | |
| 22894 <is_valid_xml/> | |
| 22895 </assert_contents> | |
| 22896 </output> | |
| 22897 </test> | |
| 22898 <test expect_num_outputs="2"> | |
| 22899 <conditional name="adv_opts_cond"> | |
| 22900 <param name="adv_opts_selector" value="advanced"/> | |
| 22901 <param name="force" value="false"/> | |
| 22902 <param name="test" value="true"/> | |
| 22903 </conditional> | |
| 22904 <param name="in" value="PeptideIndexer_2.idXML"/> | |
| 22905 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22906 <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22907 <param name="decoy_string" value=""/> | |
| 22908 <param name="decoy_string_position" value="prefix"/> | |
| 22909 <param name="missing_decoy_action" value="error"/> | |
| 22910 <param name="write_protein_sequence" value="false"/> | |
| 22911 <param name="write_protein_description" value="false"/> | |
| 22912 <param name="keep_unreferenced_proteins" value="false"/> | |
| 22913 <param name="allow_unmatched" value="true"/> | |
| 22914 <param name="aaa_max" value="3"/> | |
| 22915 <param name="mismatches_max" value="0"/> | |
| 22916 <param name="IL_equivalent" value="false"/> | |
| 22917 <section name="enzyme"> | |
| 22918 <param name="name" value="Trypsin"/> | |
| 22919 <param name="specificity" value="none"/> | |
| 22920 </section> | |
| 22921 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22922 <output name="ctd_out" ftype="xml"> | |
| 22923 <assert_contents> | |
| 22924 <is_valid_xml/> | |
| 22925 </assert_contents> | |
| 22926 </output> | |
| 22927 </test> | |
| 22928 <test expect_num_outputs="2"> | |
| 22929 <conditional name="adv_opts_cond"> | |
| 22930 <param name="adv_opts_selector" value="advanced"/> | |
| 22931 <param name="force" value="false"/> | |
| 22932 <param name="test" value="true"/> | |
| 22933 </conditional> | |
| 22934 <param name="in" value="PeptideIndexer_3.idXML"/> | |
| 22935 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22936 <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22937 <param name="decoy_string" value="DECOY_"/> | |
| 22938 <param name="decoy_string_position" value="prefix"/> | |
| 22939 <param name="missing_decoy_action" value="error"/> | |
| 22940 <param name="write_protein_sequence" value="false"/> | |
| 22941 <param name="write_protein_description" value="false"/> | |
| 22942 <param name="keep_unreferenced_proteins" value="false"/> | |
| 22943 <param name="allow_unmatched" value="true"/> | |
| 22944 <param name="aaa_max" value="4"/> | |
| 22945 <param name="mismatches_max" value="0"/> | |
| 22946 <param name="IL_equivalent" value="false"/> | |
| 22947 <section name="enzyme"> | |
| 22948 <param name="name" value="Trypsin"/> | |
| 22949 <param name="specificity" value="full"/> | |
| 22950 </section> | |
| 22951 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22952 <output name="ctd_out" ftype="xml"> | |
| 22953 <assert_contents> | |
| 22954 <is_valid_xml/> | |
| 22955 </assert_contents> | |
| 22956 </output> | |
| 22957 </test> | |
| 22958 <test expect_num_outputs="2"> | |
| 22959 <conditional name="adv_opts_cond"> | |
| 22960 <param name="adv_opts_selector" value="advanced"/> | |
| 22961 <param name="force" value="false"/> | |
| 22962 <param name="test" value="true"/> | |
| 22963 </conditional> | |
| 22964 <param name="in" value="PeptideIndexer_3.idXML"/> | |
| 22965 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22966 <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22967 <param name="decoy_string" value=""/> | |
| 22968 <param name="decoy_string_position" value="prefix"/> | |
| 22969 <param name="missing_decoy_action" value="error"/> | |
| 22970 <param name="write_protein_sequence" value="false"/> | |
| 22971 <param name="write_protein_description" value="false"/> | |
| 22972 <param name="keep_unreferenced_proteins" value="false"/> | |
| 22973 <param name="allow_unmatched" value="true"/> | |
| 22974 <param name="aaa_max" value="4"/> | |
| 22975 <param name="mismatches_max" value="0"/> | |
| 22976 <param name="IL_equivalent" value="false"/> | |
| 22977 <section name="enzyme"> | |
| 22978 <param name="name" value="Trypsin"/> | |
| 22979 <param name="specificity" value="semi"/> | |
| 22980 </section> | |
| 22981 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 22982 <output name="ctd_out" ftype="xml"> | |
| 22983 <assert_contents> | |
| 22984 <is_valid_xml/> | |
| 22985 </assert_contents> | |
| 22986 </output> | |
| 22987 </test> | |
| 22988 <test expect_num_outputs="2"> | |
| 22989 <conditional name="adv_opts_cond"> | |
| 22990 <param name="adv_opts_selector" value="advanced"/> | |
| 22991 <param name="force" value="false"/> | |
| 22992 <param name="test" value="true"/> | |
| 22993 </conditional> | |
| 22994 <param name="in" value="PeptideIndexer_3.idXML"/> | |
| 22995 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 22996 <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 22997 <param name="decoy_string" value=""/> | |
| 22998 <param name="decoy_string_position" value="prefix"/> | |
| 22999 <param name="missing_decoy_action" value="error"/> | |
| 23000 <param name="write_protein_sequence" value="false"/> | |
| 23001 <param name="write_protein_description" value="false"/> | |
| 23002 <param name="keep_unreferenced_proteins" value="false"/> | |
| 23003 <param name="allow_unmatched" value="true"/> | |
| 23004 <param name="aaa_max" value="4"/> | |
| 23005 <param name="mismatches_max" value="0"/> | |
| 23006 <param name="IL_equivalent" value="false"/> | |
| 23007 <section name="enzyme"> | |
| 23008 <param name="name" value="Trypsin"/> | |
| 23009 <param name="specificity" value="none"/> | |
| 23010 </section> | |
| 23011 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23012 <output name="ctd_out" ftype="xml"> | |
| 23013 <assert_contents> | |
| 23014 <is_valid_xml/> | |
| 23015 </assert_contents> | |
| 23016 </output> | |
| 23017 </test> | |
| 23018 <test expect_num_outputs="2"> | |
| 23019 <conditional name="adv_opts_cond"> | |
| 23020 <param name="adv_opts_selector" value="advanced"/> | |
| 23021 <param name="force" value="false"/> | |
| 23022 <param name="test" value="true"/> | |
| 23023 </conditional> | |
| 23024 <param name="in" value="PeptideIndexer_10_input.idXML"/> | |
| 23025 <param name="fasta" value="PeptideIndexer_10_input.fasta"/> | |
| 23026 <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 23027 <param name="decoy_string" value=""/> | |
| 23028 <param name="decoy_string_position" value="prefix"/> | |
| 23029 <param name="missing_decoy_action" value="error"/> | |
| 23030 <param name="write_protein_sequence" value="true"/> | |
| 23031 <param name="write_protein_description" value="false"/> | |
| 23032 <param name="keep_unreferenced_proteins" value="false"/> | |
| 23033 <param name="allow_unmatched" value="false"/> | |
| 23034 <param name="aaa_max" value="3"/> | |
| 23035 <param name="mismatches_max" value="0"/> | |
| 23036 <param name="IL_equivalent" value="true"/> | |
| 23037 <section name="enzyme"> | |
| 23038 <param name="name" value="Trypsin"/> | |
| 23039 <param name="specificity" value="full"/> | |
| 23040 </section> | |
| 23041 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23042 <output name="ctd_out" ftype="xml"> | |
| 23043 <assert_contents> | |
| 23044 <is_valid_xml/> | |
| 23045 </assert_contents> | |
| 23046 </output> | |
| 23047 </test> | |
| 23048 <test expect_num_outputs="2"> | |
| 23049 <conditional name="adv_opts_cond"> | |
| 23050 <param name="adv_opts_selector" value="advanced"/> | |
| 23051 <param name="force" value="false"/> | |
| 23052 <param name="test" value="true"/> | |
| 23053 </conditional> | |
| 23054 <param name="in" value="PeptideIndexer_1.idXML"/> | |
| 23055 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 23056 <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 23057 <param name="decoy_string" value=""/> | |
| 23058 <param name="decoy_string_position" value="prefix"/> | |
| 23059 <param name="missing_decoy_action" value="error"/> | |
| 23060 <param name="write_protein_sequence" value="false"/> | |
| 23061 <param name="write_protein_description" value="false"/> | |
| 23062 <param name="keep_unreferenced_proteins" value="false"/> | |
| 23063 <param name="allow_unmatched" value="true"/> | |
| 23064 <param name="aaa_max" value="4"/> | |
| 23065 <param name="mismatches_max" value="0"/> | |
| 23066 <param name="IL_equivalent" value="false"/> | |
| 23067 <section name="enzyme"> | |
| 23068 <param name="name" value="Trypsin"/> | |
| 23069 <param name="specificity" value="none"/> | |
| 23070 </section> | |
| 23071 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23072 <output name="ctd_out" ftype="xml"> | |
| 23073 <assert_contents> | |
| 23074 <is_valid_xml/> | |
| 23075 </assert_contents> | |
| 23076 </output> | |
| 23077 </test> | |
| 23078 <test expect_num_outputs="2"> | |
| 23079 <conditional name="adv_opts_cond"> | |
| 23080 <param name="adv_opts_selector" value="advanced"/> | |
| 23081 <param name="force" value="false"/> | |
| 23082 <param name="test" value="true"/> | |
| 23083 </conditional> | |
| 23084 <param name="in" value="empty.idXML"/> | |
| 23085 <param name="fasta" value="PeptideIndexer_1.fasta"/> | |
| 23086 <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 23087 <param name="decoy_string" value=""/> | |
| 23088 <param name="decoy_string_position" value="prefix"/> | |
| 23089 <param name="missing_decoy_action" value="error"/> | |
| 23090 <param name="write_protein_sequence" value="false"/> | |
| 23091 <param name="write_protein_description" value="false"/> | |
| 23092 <param name="keep_unreferenced_proteins" value="false"/> | |
| 23093 <param name="allow_unmatched" value="false"/> | |
| 23094 <param name="aaa_max" value="4"/> | |
| 23095 <param name="mismatches_max" value="0"/> | |
| 23096 <param name="IL_equivalent" value="false"/> | |
| 23097 <section name="enzyme"> | |
| 23098 <param name="name" value="Trypsin"/> | |
| 23099 <param name="specificity" value="full"/> | |
| 23100 </section> | |
| 23101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23102 <output name="ctd_out" ftype="xml"> | |
| 23103 <assert_contents> | |
| 23104 <is_valid_xml/> | |
| 23105 </assert_contents> | |
| 23106 </output> | |
| 23107 </test> | |
| 23108 <test expect_num_outputs="2"> | |
| 23109 <conditional name="adv_opts_cond"> | |
| 23110 <param name="adv_opts_selector" value="advanced"/> | |
| 23111 <param name="force" value="false"/> | |
| 23112 <param name="test" value="true"/> | |
| 23113 </conditional> | |
| 23114 <param name="in" value="PeptideIndexer_14.idXML"/> | |
| 23115 <param name="fasta" value="PeptideIndexer_2.fasta"/> | |
| 23116 <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 23117 <param name="decoy_string" value=""/> | |
| 23118 <param name="decoy_string_position" value="prefix"/> | |
| 23119 <param name="missing_decoy_action" value="error"/> | |
| 23120 <param name="write_protein_sequence" value="true"/> | |
| 23121 <param name="write_protein_description" value="false"/> | |
| 23122 <param name="keep_unreferenced_proteins" value="false"/> | |
| 23123 <param name="allow_unmatched" value="false"/> | |
| 23124 <param name="aaa_max" value="4"/> | |
| 23125 <param name="mismatches_max" value="0"/> | |
| 23126 <param name="IL_equivalent" value="false"/> | |
| 23127 <section name="enzyme"> | |
| 23128 <param name="name" value="Trypsin"/> | |
| 23129 <param name="specificity" value="none"/> | |
| 23130 </section> | |
| 23131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23132 <output name="ctd_out" ftype="xml"> | |
| 23133 <assert_contents> | |
| 23134 <is_valid_xml/> | |
| 23135 </assert_contents> | |
| 23136 </output> | |
| 23137 </test> | |
| 23138 </xml> | |
| 23139 <xml name="autotest_PercolatorAdapter"> | |
| 23140 <test expect_num_outputs="2"> | |
| 23141 <conditional name="adv_opts_cond"> | |
| 23142 <param name="adv_opts_selector" value="advanced"/> | |
| 23143 <param name="generic_feature_set" value="false"/> | |
| 23144 <param name="subset_max_train" value="0"/> | |
| 23145 <param name="cpos" value="0.0"/> | |
| 23146 <param name="cneg" value="0.0"/> | |
| 23147 <param name="testFDR" value="0.5"/> | |
| 23148 <param name="trainFDR" value="0.5"/> | |
| 23149 <param name="maxiter" value="10"/> | |
| 23150 <param name="quick_validation" value="false"/> | |
| 23151 <param name="default_direction" value=""/> | |
| 23152 <param name="verbose" value="2"/> | |
| 23153 <param name="unitnorm" value="false"/> | |
| 23154 <param name="test_each_iteration" value="false"/> | |
| 23155 <param name="override" value="false"/> | |
| 23156 <param name="seed" value="1"/> | |
| 23157 <param name="doc" value="0"/> | |
| 23158 <param name="klammer" value="false"/> | |
| 23159 <param name="decoy_pattern" value="random"/> | |
| 23160 <param name="post_processing_tdc" value="false"/> | |
| 23161 <param name="train_best_positive" value="false"/> | |
| 23162 <param name="ipf_max_peakgroup_pep" value="0.7"/> | |
| 23163 <param name="ipf_max_transition_isotope_overlap" value="0.5"/> | |
| 23164 <param name="ipf_min_transition_sn" value="0.0"/> | |
| 23165 <param name="force" value="false"/> | |
| 23166 <param name="test" value="true"/> | |
| 23167 </conditional> | |
| 23168 <param name="in" value="PercolatorAdapter_1.idXML"/> | |
| 23169 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 23170 <param name="out_type" value="idXML"/> | |
| 23171 <param name="enzyme" value="trypsin"/> | |
| 23172 <param name="peptide_level_fdrs" value="false"/> | |
| 23173 <param name="protein_level_fdrs" value="false"/> | |
| 23174 <param name="osw_level" value="ms2"/> | |
| 23175 <param name="score_type" value="q-value"/> | |
| 23176 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23177 <output name="ctd_out" ftype="xml"> | |
| 23178 <assert_contents> | |
| 23179 <is_valid_xml/> | |
| 23180 </assert_contents> | |
| 23181 </output> | |
| 23182 </test> | |
| 23183 <test expect_num_outputs="2"> | |
| 23184 <conditional name="adv_opts_cond"> | |
| 23185 <param name="adv_opts_selector" value="advanced"/> | |
| 23186 <param name="generic_feature_set" value="false"/> | |
| 23187 <param name="subset_max_train" value="0"/> | |
| 23188 <param name="cpos" value="0.0"/> | |
| 23189 <param name="cneg" value="0.0"/> | |
| 23190 <param name="testFDR" value="0.01"/> | |
| 23191 <param name="trainFDR" value="0.01"/> | |
| 23192 <param name="maxiter" value="10"/> | |
| 23193 <param name="quick_validation" value="false"/> | |
| 23194 <param name="default_direction" value=""/> | |
| 23195 <param name="verbose" value="2"/> | |
| 23196 <param name="unitnorm" value="false"/> | |
| 23197 <param name="test_each_iteration" value="false"/> | |
| 23198 <param name="override" value="false"/> | |
| 23199 <param name="seed" value="1"/> | |
| 23200 <param name="doc" value="0"/> | |
| 23201 <param name="klammer" value="false"/> | |
| 23202 <param name="decoy_pattern" value="random"/> | |
| 23203 <param name="post_processing_tdc" value="false"/> | |
| 23204 <param name="train_best_positive" value="false"/> | |
| 23205 <param name="ipf_max_peakgroup_pep" value="0.7"/> | |
| 23206 <param name="ipf_max_transition_isotope_overlap" value="0.5"/> | |
| 23207 <param name="ipf_min_transition_sn" value="0.0"/> | |
| 23208 <param name="force" value="false"/> | |
| 23209 <param name="test" value="true"/> | |
| 23210 </conditional> | |
| 23211 <param name="in_osw" value="PercolatorAdapter_2.osw"/> | |
| 23212 <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> | |
| 23213 <param name="out_type" value="osw"/> | |
| 23214 <param name="enzyme" value="trypsin"/> | |
| 23215 <param name="peptide_level_fdrs" value="false"/> | |
| 23216 <param name="protein_level_fdrs" value="false"/> | |
| 23217 <param name="osw_level" value="ms1"/> | |
| 23218 <param name="score_type" value="q-value"/> | |
| 23219 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23220 <output name="ctd_out" ftype="xml"> | |
| 23221 <assert_contents> | |
| 23222 <is_valid_xml/> | |
| 23223 </assert_contents> | |
| 23224 </output> | |
| 23225 </test> | |
| 23226 <test expect_num_outputs="2"> | |
| 23227 <conditional name="adv_opts_cond"> | |
| 23228 <param name="adv_opts_selector" value="advanced"/> | |
| 23229 <param name="generic_feature_set" value="false"/> | |
| 23230 <param name="subset_max_train" value="0"/> | |
| 23231 <param name="cpos" value="0.0"/> | |
| 23232 <param name="cneg" value="0.0"/> | |
| 23233 <param name="testFDR" value="0.01"/> | |
| 23234 <param name="trainFDR" value="0.01"/> | |
| 23235 <param name="maxiter" value="10"/> | |
| 23236 <param name="quick_validation" value="false"/> | |
| 23237 <param name="default_direction" value=""/> | |
| 23238 <param name="verbose" value="2"/> | |
| 23239 <param name="unitnorm" value="false"/> | |
| 23240 <param name="test_each_iteration" value="false"/> | |
| 23241 <param name="override" value="false"/> | |
| 23242 <param name="seed" value="1"/> | |
| 23243 <param name="doc" value="0"/> | |
| 23244 <param name="klammer" value="false"/> | |
| 23245 <param name="decoy_pattern" value="random"/> | |
| 23246 <param name="post_processing_tdc" value="false"/> | |
| 23247 <param name="train_best_positive" value="false"/> | |
| 23248 <param name="ipf_max_peakgroup_pep" value="0.7"/> | |
| 23249 <param name="ipf_max_transition_isotope_overlap" value="0.5"/> | |
| 23250 <param name="ipf_min_transition_sn" value="0.0"/> | |
| 23251 <param name="force" value="false"/> | |
| 23252 <param name="test" value="true"/> | |
| 23253 </conditional> | |
| 23254 <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/> | |
| 23255 <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> | |
| 23256 <param name="out_type" value="osw"/> | |
| 23257 <param name="enzyme" value="trypsin"/> | |
| 23258 <param name="peptide_level_fdrs" value="false"/> | |
| 23259 <param name="protein_level_fdrs" value="false"/> | |
| 23260 <param name="osw_level" value="ms2"/> | |
| 23261 <param name="score_type" value="q-value"/> | |
| 23262 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23263 <output name="ctd_out" ftype="xml"> | |
| 23264 <assert_contents> | |
| 23265 <is_valid_xml/> | |
| 23266 </assert_contents> | |
| 23267 </output> | |
| 23268 </test> | |
| 23269 <test expect_num_outputs="2"> | |
| 23270 <conditional name="adv_opts_cond"> | |
| 23271 <param name="adv_opts_selector" value="advanced"/> | |
| 23272 <param name="generic_feature_set" value="false"/> | |
| 23273 <param name="subset_max_train" value="0"/> | |
| 23274 <param name="cpos" value="0.0"/> | |
| 23275 <param name="cneg" value="0.0"/> | |
| 23276 <param name="testFDR" value="0.01"/> | |
| 23277 <param name="trainFDR" value="0.01"/> | |
| 23278 <param name="maxiter" value="10"/> | |
| 23279 <param name="quick_validation" value="false"/> | |
| 23280 <param name="default_direction" value=""/> | |
| 23281 <param name="verbose" value="2"/> | |
| 23282 <param name="unitnorm" value="false"/> | |
| 23283 <param name="test_each_iteration" value="false"/> | |
| 23284 <param name="override" value="false"/> | |
| 23285 <param name="seed" value="1"/> | |
| 23286 <param name="doc" value="0"/> | |
| 23287 <param name="klammer" value="false"/> | |
| 23288 <param name="decoy_pattern" value="random"/> | |
| 23289 <param name="post_processing_tdc" value="false"/> | |
| 23290 <param name="train_best_positive" value="false"/> | |
| 23291 <param name="ipf_max_peakgroup_pep" value="0.7"/> | |
| 23292 <param name="ipf_max_transition_isotope_overlap" value="0.5"/> | |
| 23293 <param name="ipf_min_transition_sn" value="0.0"/> | |
| 23294 <param name="force" value="false"/> | |
| 23295 <param name="test" value="true"/> | |
| 23296 </conditional> | |
| 23297 <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/> | |
| 23298 <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> | |
| 23299 <param name="out_type" value="osw"/> | |
| 23300 <param name="enzyme" value="trypsin"/> | |
| 23301 <param name="peptide_level_fdrs" value="false"/> | |
| 23302 <param name="protein_level_fdrs" value="false"/> | |
| 23303 <param name="osw_level" value="transition"/> | |
| 23304 <param name="score_type" value="q-value"/> | |
| 23305 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23306 <output name="ctd_out" ftype="xml"> | |
| 23307 <assert_contents> | |
| 23308 <is_valid_xml/> | |
| 23309 </assert_contents> | |
| 23310 </output> | |
| 23311 </test> | |
| 23312 <test expect_num_outputs="3"> | |
| 23313 <conditional name="adv_opts_cond"> | |
| 23314 <param name="adv_opts_selector" value="advanced"/> | |
| 23315 <param name="generic_feature_set" value="false"/> | |
| 23316 <param name="subset_max_train" value="0"/> | |
| 23317 <param name="cpos" value="0.0"/> | |
| 23318 <param name="cneg" value="0.0"/> | |
| 23319 <param name="testFDR" value="0.5"/> | |
| 23320 <param name="trainFDR" value="0.5"/> | |
| 23321 <param name="maxiter" value="10"/> | |
| 23322 <param name="quick_validation" value="false"/> | |
| 23323 <param name="default_direction" value=""/> | |
| 23324 <param name="verbose" value="2"/> | |
| 23325 <param name="unitnorm" value="false"/> | |
| 23326 <param name="test_each_iteration" value="false"/> | |
| 23327 <param name="override" value="false"/> | |
| 23328 <param name="seed" value="1"/> | |
| 23329 <param name="doc" value="0"/> | |
| 23330 <param name="klammer" value="false"/> | |
| 23331 <param name="decoy_pattern" value="random"/> | |
| 23332 <param name="post_processing_tdc" value="false"/> | |
| 23333 <param name="train_best_positive" value="false"/> | |
| 23334 <param name="ipf_max_peakgroup_pep" value="0.7"/> | |
| 23335 <param name="ipf_max_transition_isotope_overlap" value="0.5"/> | |
| 23336 <param name="ipf_min_transition_sn" value="0.0"/> | |
| 23337 <param name="force" value="false"/> | |
| 23338 <param name="test" value="true"/> | |
| 23339 </conditional> | |
| 23340 <param name="in" value="PercolatorAdapter_1.idXML"/> | |
| 23341 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 23342 <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 23343 <param name="out_type" value="idXML"/> | |
| 23344 <param name="enzyme" value="trypsin"/> | |
| 23345 <param name="peptide_level_fdrs" value="false"/> | |
| 23346 <param name="protein_level_fdrs" value="false"/> | |
| 23347 <param name="osw_level" value="ms2"/> | |
| 23348 <param name="score_type" value="q-value"/> | |
| 23349 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/> | |
| 23350 <output name="ctd_out" ftype="xml"> | |
| 23351 <assert_contents> | |
| 23352 <is_valid_xml/> | |
| 23353 </assert_contents> | |
| 23354 </output> | |
| 23355 </test> | |
| 23356 </xml> | |
| 23357 <xml name="autotest_PhosphoScoring"> | |
| 23358 </xml> | |
| 23359 <xml name="autotest_PrecursorIonSelector"> | |
| 23360 <test expect_num_outputs="2"> | |
| 23361 <conditional name="adv_opts_cond"> | |
| 23362 <param name="adv_opts_selector" value="advanced"/> | |
| 23363 <param name="solver" value="GLPK"/> | |
| 23364 <param name="force" value="false"/> | |
| 23365 <param name="test" value="true"/> | |
| 23366 </conditional> | |
| 23367 <param name="in" value="PrecursorIonSelector_features.featureXML"/> | |
| 23368 <param name="ids" value="PrecursorIonSelector_ids.idXML"/> | |
| 23369 <param name="num_precursors" value="1"/> | |
| 23370 <param name="load_preprocessing" value="false"/> | |
| 23371 <param name="store_preprocessing" value="false"/> | |
| 23372 <param name="simulation" value="true"/> | |
| 23373 <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 23374 <param name="db_path" value="PrecursorIonSelector_db.fasta"/> | |
| 23375 <param name="fixed_modifications" value=""/> | |
| 23376 <section name="algorithm"> | |
| 23377 <param name="type" value="IPS"/> | |
| 23378 <param name="max_iteration" value="10"/> | |
| 23379 <param name="rt_bin_capacity" value="10"/> | |
| 23380 <param name="step_size" value="1"/> | |
| 23381 <param name="peptide_min_prob" value="0.2"/> | |
| 23382 <param name="sequential_spectrum_order" value="false"/> | |
| 23383 <section name="MIPFormulation"> | |
| 23384 <section name="thresholds"> | |
| 23385 <param name="min_protein_probability" value="0.2"/> | |
| 23386 <param name="min_protein_id_probability" value="0.95"/> | |
| 23387 <param name="min_pt_weight" value="0.5"/> | |
| 23388 <param name="min_mz" value="500.0"/> | |
| 23389 <param name="max_mz" value="5000.0"/> | |
| 23390 <param name="min_pred_pep_prob" value="0.5"/> | |
| 23391 <param name="min_rt_weight" value="0.5"/> | |
| 23392 <param name="use_peptide_rule" value="true"/> | |
| 23393 <param name="min_peptide_ids" value="2"/> | |
| 23394 <param name="min_peptide_probability" value="0.95"/> | |
| 23395 </section> | |
| 23396 <section name="combined_ilp"> | |
| 23397 <param name="k1" value="0.2"/> | |
| 23398 <param name="k2" value="0.2"/> | |
| 23399 <param name="k3" value="0.4"/> | |
| 23400 <param name="scale_matching_probs" value="true"/> | |
| 23401 </section> | |
| 23402 <section name="feature_based"> | |
| 23403 <param name="no_intensity_normalization" value="false"/> | |
| 23404 <param name="max_number_precursors_per_feature" value="1"/> | |
| 23405 </section> | |
| 23406 </section> | |
| 23407 <section name="Preprocessing"> | |
| 23408 <param name="precursor_mass_tolerance" value="0.9"/> | |
| 23409 <param name="precursor_mass_tolerance_unit" value="Da"/> | |
| 23410 <param name="preprocessed_db_path" value=""/> | |
| 23411 <param name="preprocessed_db_pred_rt_path" value=""/> | |
| 23412 <param name="preprocessed_db_pred_dt_path" value=""/> | |
| 23413 <param name="max_peptides_per_run" value="100000"/> | |
| 23414 <param name="missed_cleavages" value="1"/> | |
| 23415 <param name="taxonomy" value=""/> | |
| 23416 <param name="store_peptide_sequences" value="false"/> | |
| 23417 <section name="rt_settings"> | |
| 23418 <param name="min_rt" value="960.0"/> | |
| 23419 <param name="max_rt" value="3840.0"/> | |
| 23420 <param name="rt_step_size" value="30.0"/> | |
| 23421 <param name="gauss_mean" value="-1.0"/> | |
| 23422 <param name="gauss_sigma" value="3.0"/> | |
| 23423 </section> | |
| 23424 </section> | |
| 23425 </section> | |
| 23426 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/> | |
| 23427 <output name="ctd_out" ftype="xml"> | |
| 23428 <assert_contents> | |
| 23429 <is_valid_xml/> | |
| 23430 </assert_contents> | |
| 23431 </output> | |
| 23432 </test> | |
| 23433 <test expect_num_outputs="2"> | |
| 23434 <conditional name="adv_opts_cond"> | |
| 23435 <param name="adv_opts_selector" value="advanced"/> | |
| 23436 <param name="solver" value="GLPK"/> | |
| 23437 <param name="force" value="false"/> | |
| 23438 <param name="test" value="true"/> | |
| 23439 </conditional> | |
| 23440 <param name="in" value="PrecursorIonSelector_features.featureXML"/> | |
| 23441 <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 23442 <param name="ids" value="PrecursorIonSelector_ids.idXML"/> | |
| 23443 <param name="num_precursors" value="1"/> | |
| 23444 <param name="load_preprocessing" value="false"/> | |
| 23445 <param name="store_preprocessing" value="false"/> | |
| 23446 <param name="simulation" value="false"/> | |
| 23447 <param name="db_path" value="PrecursorIonSelector_db.fasta"/> | |
| 23448 <param name="fixed_modifications" value=""/> | |
| 23449 <section name="algorithm"> | |
| 23450 <param name="type" value="IPS"/> | |
| 23451 <param name="max_iteration" value="10"/> | |
| 23452 <param name="rt_bin_capacity" value="10"/> | |
| 23453 <param name="step_size" value="1"/> | |
| 23454 <param name="peptide_min_prob" value="0.2"/> | |
| 23455 <param name="sequential_spectrum_order" value="false"/> | |
| 23456 <section name="MIPFormulation"> | |
| 23457 <section name="thresholds"> | |
| 23458 <param name="min_protein_probability" value="0.2"/> | |
| 23459 <param name="min_protein_id_probability" value="0.95"/> | |
| 23460 <param name="min_pt_weight" value="0.5"/> | |
| 23461 <param name="min_mz" value="500.0"/> | |
| 23462 <param name="max_mz" value="5000.0"/> | |
| 23463 <param name="min_pred_pep_prob" value="0.5"/> | |
| 23464 <param name="min_rt_weight" value="0.5"/> | |
| 23465 <param name="use_peptide_rule" value="true"/> | |
| 23466 <param name="min_peptide_ids" value="2"/> | |
| 23467 <param name="min_peptide_probability" value="0.95"/> | |
| 23468 </section> | |
| 23469 <section name="combined_ilp"> | |
| 23470 <param name="k1" value="0.2"/> | |
| 23471 <param name="k2" value="0.2"/> | |
| 23472 <param name="k3" value="0.4"/> | |
| 23473 <param name="scale_matching_probs" value="true"/> | |
| 23474 </section> | |
| 23475 <section name="feature_based"> | |
| 23476 <param name="no_intensity_normalization" value="false"/> | |
| 23477 <param name="max_number_precursors_per_feature" value="1"/> | |
| 23478 </section> | |
| 23479 </section> | |
| 23480 <section name="Preprocessing"> | |
| 23481 <param name="precursor_mass_tolerance" value="0.9"/> | |
| 23482 <param name="precursor_mass_tolerance_unit" value="Da"/> | |
| 23483 <param name="preprocessed_db_path" value=""/> | |
| 23484 <param name="preprocessed_db_pred_rt_path" value=""/> | |
| 23485 <param name="preprocessed_db_pred_dt_path" value=""/> | |
| 23486 <param name="max_peptides_per_run" value="100000"/> | |
| 23487 <param name="missed_cleavages" value="1"/> | |
| 23488 <param name="taxonomy" value=""/> | |
| 23489 <param name="store_peptide_sequences" value="false"/> | |
| 23490 <section name="rt_settings"> | |
| 23491 <param name="min_rt" value="960.0"/> | |
| 23492 <param name="max_rt" value="3840.0"/> | |
| 23493 <param name="rt_step_size" value="30.0"/> | |
| 23494 <param name="gauss_mean" value="-1.0"/> | |
| 23495 <param name="gauss_sigma" value="3.0"/> | |
| 23496 </section> | |
| 23497 </section> | |
| 23498 </section> | |
| 23499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23500 <output name="ctd_out" ftype="xml"> | |
| 23501 <assert_contents> | |
| 23502 <is_valid_xml/> | |
| 23503 </assert_contents> | |
| 23504 </output> | |
| 23505 </test> | |
| 23506 </xml> | |
| 23507 <xml name="autotest_PrecursorMassCorrector"> | |
| 23508 <test expect_num_outputs="2"> | |
| 23509 <conditional name="adv_opts_cond"> | |
| 23510 <param name="adv_opts_selector" value="advanced"/> | |
| 23511 <param name="max_charge" value="3"/> | |
| 23512 <param name="intensity_threshold" value="-1.0"/> | |
| 23513 <param name="force" value="false"/> | |
| 23514 <param name="test" value="true"/> | |
| 23515 </conditional> | |
| 23516 <param name="in" value="PrecursorMassCorrector_1_input.mzML"/> | |
| 23517 <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 23518 <param name="precursor_mass_tolerance" value="1.5"/> | |
| 23519 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23520 <output name="ctd_out" ftype="xml"> | |
| 23521 <assert_contents> | |
| 23522 <is_valid_xml/> | |
| 23523 </assert_contents> | |
| 23524 </output> | |
| 23525 </test> | |
| 23526 </xml> | |
| 23527 <xml name="autotest_ProteinInference"> | |
| 23528 <test expect_num_outputs="2"> | |
| 23529 <conditional name="adv_opts_cond"> | |
| 23530 <param name="adv_opts_selector" value="advanced"/> | |
| 23531 <param name="force" value="false"/> | |
| 23532 <param name="test" value="true"/> | |
| 23533 </conditional> | |
| 23534 <param name="in" value="ProteinInference_1_input.idXML"/> | |
| 23535 <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 23536 <param name="merge_runs" value="all"/> | |
| 23537 <param name="annotate_indist_groups" value="true"/> | |
| 23538 <section name="Merging"> | |
| 23539 <param name="annotate_origin" value="false"/> | |
| 23540 </section> | |
| 23541 <section name="Algorithm"> | |
| 23542 <param name="min_peptides_per_protein" value="1"/> | |
| 23543 <param name="score_aggregation_method" value="maximum"/> | |
| 23544 <param name="treat_charge_variants_separately" value="true"/> | |
| 23545 <param name="treat_modification_variants_separately" value="true"/> | |
| 23546 <param name="use_shared_peptides" value="false"/> | |
| 23547 <param name="skip_count_annotation" value="false"/> | |
| 23548 </section> | |
| 23549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 23550 <output name="ctd_out" ftype="xml"> | |
| 23551 <assert_contents> | |
| 23552 <is_valid_xml/> | |
| 23553 </assert_contents> | |
| 23554 </output> | |
| 23555 </test> | |
| 23556 </xml> | |
| 23557 <xml name="autotest_ProteinQuantifier"> | |
| 23558 <test expect_num_outputs="3"> | |
| 23559 <conditional name="adv_opts_cond"> | |
| 23560 <param name="adv_opts_selector" value="advanced"/> | |
| 23561 <param name="force" value="false"/> | |
| 23562 <param name="test" value="true"/> | |
| 23563 </conditional> | |
| 23564 <param name="in" value="ProteinQuantifier_input.featureXML"/> | |
| 23565 <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23566 <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23567 <param name="top" value="3"/> | |
| 23568 <param name="average" value="median"/> | |
| 23569 <param name="include_all" value="false"/> | |
| 23570 <param name="best_charge_and_fraction" value="false"/> | |
| 23571 <param name="greedy_group_resolution" value="false"/> | |
| 23572 <param name="ratios" value="false"/> | |
| 23573 <param name="ratiosSILAC" value="false"/> | |
| 23574 <section name="consensus"> | |
| 23575 <param name="normalize" value="false"/> | |
| 23576 <param name="fix_peptides" value="false"/> | |
| 23577 </section> | |
| 23578 <section name="format"> | |
| 23579 <param name="separator" value=""/> | |
| 23580 <param name="quoting" value="double"/> | |
| 23581 <param name="replacement" value="_"/> | |
| 23582 </section> | |
| 23583 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> | |
| 23584 <output name="ctd_out" ftype="xml"> | |
| 23585 <assert_contents> | |
| 23586 <is_valid_xml/> | |
| 23587 </assert_contents> | |
| 23588 </output> | |
| 23589 </test> | |
| 23590 <test expect_num_outputs="3"> | |
| 23591 <conditional name="adv_opts_cond"> | |
| 23592 <param name="adv_opts_selector" value="advanced"/> | |
| 23593 <param name="force" value="false"/> | |
| 23594 <param name="test" value="true"/> | |
| 23595 </conditional> | |
| 23596 <param name="in" value="ProteinQuantifier_input.featureXML"/> | |
| 23597 <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23598 <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23599 <param name="top" value="2"/> | |
| 23600 <param name="average" value="sum"/> | |
| 23601 <param name="include_all" value="true"/> | |
| 23602 <param name="best_charge_and_fraction" value="true"/> | |
| 23603 <param name="greedy_group_resolution" value="false"/> | |
| 23604 <param name="ratios" value="false"/> | |
| 23605 <param name="ratiosSILAC" value="false"/> | |
| 23606 <section name="consensus"> | |
| 23607 <param name="normalize" value="false"/> | |
| 23608 <param name="fix_peptides" value="false"/> | |
| 23609 </section> | |
| 23610 <section name="format"> | |
| 23611 <param name="separator" value=""/> | |
| 23612 <param name="quoting" value="double"/> | |
| 23613 <param name="replacement" value="_"/> | |
| 23614 </section> | |
| 23615 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> | |
| 23616 <output name="ctd_out" ftype="xml"> | |
| 23617 <assert_contents> | |
| 23618 <is_valid_xml/> | |
| 23619 </assert_contents> | |
| 23620 </output> | |
| 23621 </test> | |
| 23622 <test expect_num_outputs="3"> | |
| 23623 <conditional name="adv_opts_cond"> | |
| 23624 <param name="adv_opts_selector" value="advanced"/> | |
| 23625 <param name="force" value="false"/> | |
| 23626 <param name="test" value="true"/> | |
| 23627 </conditional> | |
| 23628 <param name="in" value="ProteinQuantifier_3_input.featureXML"/> | |
| 23629 <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23630 <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23631 <param name="top" value="2"/> | |
| 23632 <param name="average" value="mean"/> | |
| 23633 <param name="include_all" value="true"/> | |
| 23634 <param name="best_charge_and_fraction" value="false"/> | |
| 23635 <param name="greedy_group_resolution" value="false"/> | |
| 23636 <param name="ratios" value="false"/> | |
| 23637 <param name="ratiosSILAC" value="false"/> | |
| 23638 <section name="consensus"> | |
| 23639 <param name="normalize" value="false"/> | |
| 23640 <param name="fix_peptides" value="false"/> | |
| 23641 </section> | |
| 23642 <section name="format"> | |
| 23643 <param name="separator" value=""/> | |
| 23644 <param name="quoting" value="double"/> | |
| 23645 <param name="replacement" value="_"/> | |
| 23646 </section> | |
| 23647 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> | |
| 23648 <output name="ctd_out" ftype="xml"> | |
| 23649 <assert_contents> | |
| 23650 <is_valid_xml/> | |
| 23651 </assert_contents> | |
| 23652 </output> | |
| 23653 </test> | |
| 23654 <test expect_num_outputs="2"> | |
| 23655 <conditional name="adv_opts_cond"> | |
| 23656 <param name="adv_opts_selector" value="advanced"/> | |
| 23657 <param name="force" value="false"/> | |
| 23658 <param name="test" value="true"/> | |
| 23659 </conditional> | |
| 23660 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23661 <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23662 <param name="top" value="0"/> | |
| 23663 <param name="average" value="sum"/> | |
| 23664 <param name="include_all" value="false"/> | |
| 23665 <param name="best_charge_and_fraction" value="false"/> | |
| 23666 <param name="greedy_group_resolution" value="false"/> | |
| 23667 <param name="ratios" value="false"/> | |
| 23668 <param name="ratiosSILAC" value="false"/> | |
| 23669 <section name="consensus"> | |
| 23670 <param name="normalize" value="false"/> | |
| 23671 <param name="fix_peptides" value="false"/> | |
| 23672 </section> | |
| 23673 <section name="format"> | |
| 23674 <param name="separator" value=""/> | |
| 23675 <param name="quoting" value="double"/> | |
| 23676 <param name="replacement" value="_"/> | |
| 23677 </section> | |
| 23678 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23679 <output name="ctd_out" ftype="xml"> | |
| 23680 <assert_contents> | |
| 23681 <is_valid_xml/> | |
| 23682 </assert_contents> | |
| 23683 </output> | |
| 23684 </test> | |
| 23685 <test expect_num_outputs="2"> | |
| 23686 <conditional name="adv_opts_cond"> | |
| 23687 <param name="adv_opts_selector" value="advanced"/> | |
| 23688 <param name="force" value="false"/> | |
| 23689 <param name="test" value="true"/> | |
| 23690 </conditional> | |
| 23691 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23692 <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23693 <param name="top" value="3"/> | |
| 23694 <param name="average" value="sum"/> | |
| 23695 <param name="include_all" value="false"/> | |
| 23696 <param name="best_charge_and_fraction" value="false"/> | |
| 23697 <param name="greedy_group_resolution" value="false"/> | |
| 23698 <param name="ratios" value="false"/> | |
| 23699 <param name="ratiosSILAC" value="false"/> | |
| 23700 <section name="consensus"> | |
| 23701 <param name="normalize" value="false"/> | |
| 23702 <param name="fix_peptides" value="false"/> | |
| 23703 </section> | |
| 23704 <section name="format"> | |
| 23705 <param name="separator" value=""/> | |
| 23706 <param name="quoting" value="double"/> | |
| 23707 <param name="replacement" value="_"/> | |
| 23708 </section> | |
| 23709 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23710 <output name="ctd_out" ftype="xml"> | |
| 23711 <assert_contents> | |
| 23712 <is_valid_xml/> | |
| 23713 </assert_contents> | |
| 23714 </output> | |
| 23715 </test> | |
| 23716 <test expect_num_outputs="2"> | |
| 23717 <conditional name="adv_opts_cond"> | |
| 23718 <param name="adv_opts_selector" value="advanced"/> | |
| 23719 <param name="force" value="false"/> | |
| 23720 <param name="test" value="true"/> | |
| 23721 </conditional> | |
| 23722 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23723 <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23724 <param name="top" value="3"/> | |
| 23725 <param name="average" value="sum"/> | |
| 23726 <param name="include_all" value="true"/> | |
| 23727 <param name="best_charge_and_fraction" value="false"/> | |
| 23728 <param name="greedy_group_resolution" value="false"/> | |
| 23729 <param name="ratios" value="false"/> | |
| 23730 <param name="ratiosSILAC" value="false"/> | |
| 23731 <section name="consensus"> | |
| 23732 <param name="normalize" value="false"/> | |
| 23733 <param name="fix_peptides" value="false"/> | |
| 23734 </section> | |
| 23735 <section name="format"> | |
| 23736 <param name="separator" value=""/> | |
| 23737 <param name="quoting" value="double"/> | |
| 23738 <param name="replacement" value="_"/> | |
| 23739 </section> | |
| 23740 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23741 <output name="ctd_out" ftype="xml"> | |
| 23742 <assert_contents> | |
| 23743 <is_valid_xml/> | |
| 23744 </assert_contents> | |
| 23745 </output> | |
| 23746 </test> | |
| 23747 <test expect_num_outputs="2"> | |
| 23748 <conditional name="adv_opts_cond"> | |
| 23749 <param name="adv_opts_selector" value="advanced"/> | |
| 23750 <param name="force" value="false"/> | |
| 23751 <param name="test" value="true"/> | |
| 23752 </conditional> | |
| 23753 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23754 <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23755 <param name="top" value="0"/> | |
| 23756 <param name="average" value="sum"/> | |
| 23757 <param name="include_all" value="false"/> | |
| 23758 <param name="best_charge_and_fraction" value="false"/> | |
| 23759 <param name="greedy_group_resolution" value="false"/> | |
| 23760 <param name="ratios" value="false"/> | |
| 23761 <param name="ratiosSILAC" value="false"/> | |
| 23762 <section name="consensus"> | |
| 23763 <param name="normalize" value="false"/> | |
| 23764 <param name="fix_peptides" value="true"/> | |
| 23765 </section> | |
| 23766 <section name="format"> | |
| 23767 <param name="separator" value=""/> | |
| 23768 <param name="quoting" value="double"/> | |
| 23769 <param name="replacement" value="_"/> | |
| 23770 </section> | |
| 23771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23772 <output name="ctd_out" ftype="xml"> | |
| 23773 <assert_contents> | |
| 23774 <is_valid_xml/> | |
| 23775 </assert_contents> | |
| 23776 </output> | |
| 23777 </test> | |
| 23778 <test expect_num_outputs="2"> | |
| 23779 <conditional name="adv_opts_cond"> | |
| 23780 <param name="adv_opts_selector" value="advanced"/> | |
| 23781 <param name="force" value="false"/> | |
| 23782 <param name="test" value="true"/> | |
| 23783 </conditional> | |
| 23784 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23785 <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23786 <param name="top" value="3"/> | |
| 23787 <param name="average" value="sum"/> | |
| 23788 <param name="include_all" value="false"/> | |
| 23789 <param name="best_charge_and_fraction" value="false"/> | |
| 23790 <param name="greedy_group_resolution" value="false"/> | |
| 23791 <param name="ratios" value="false"/> | |
| 23792 <param name="ratiosSILAC" value="false"/> | |
| 23793 <section name="consensus"> | |
| 23794 <param name="normalize" value="false"/> | |
| 23795 <param name="fix_peptides" value="true"/> | |
| 23796 </section> | |
| 23797 <section name="format"> | |
| 23798 <param name="separator" value=""/> | |
| 23799 <param name="quoting" value="double"/> | |
| 23800 <param name="replacement" value="_"/> | |
| 23801 </section> | |
| 23802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23803 <output name="ctd_out" ftype="xml"> | |
| 23804 <assert_contents> | |
| 23805 <is_valid_xml/> | |
| 23806 </assert_contents> | |
| 23807 </output> | |
| 23808 </test> | |
| 23809 <test expect_num_outputs="2"> | |
| 23810 <conditional name="adv_opts_cond"> | |
| 23811 <param name="adv_opts_selector" value="advanced"/> | |
| 23812 <param name="force" value="false"/> | |
| 23813 <param name="test" value="true"/> | |
| 23814 </conditional> | |
| 23815 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23816 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23817 <param name="top" value="3"/> | |
| 23818 <param name="average" value="sum"/> | |
| 23819 <param name="include_all" value="true"/> | |
| 23820 <param name="best_charge_and_fraction" value="false"/> | |
| 23821 <param name="greedy_group_resolution" value="false"/> | |
| 23822 <param name="ratios" value="false"/> | |
| 23823 <param name="ratiosSILAC" value="false"/> | |
| 23824 <section name="consensus"> | |
| 23825 <param name="normalize" value="false"/> | |
| 23826 <param name="fix_peptides" value="true"/> | |
| 23827 </section> | |
| 23828 <section name="format"> | |
| 23829 <param name="separator" value=""/> | |
| 23830 <param name="quoting" value="double"/> | |
| 23831 <param name="replacement" value="_"/> | |
| 23832 </section> | |
| 23833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23834 <output name="ctd_out" ftype="xml"> | |
| 23835 <assert_contents> | |
| 23836 <is_valid_xml/> | |
| 23837 </assert_contents> | |
| 23838 </output> | |
| 23839 </test> | |
| 23840 <test expect_num_outputs="2"> | |
| 23841 <conditional name="adv_opts_cond"> | |
| 23842 <param name="adv_opts_selector" value="advanced"/> | |
| 23843 <param name="force" value="false"/> | |
| 23844 <param name="test" value="true"/> | |
| 23845 </conditional> | |
| 23846 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23847 <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23848 <param name="top" value="3"/> | |
| 23849 <param name="average" value="sum"/> | |
| 23850 <param name="include_all" value="true"/> | |
| 23851 <param name="best_charge_and_fraction" value="false"/> | |
| 23852 <param name="greedy_group_resolution" value="false"/> | |
| 23853 <param name="ratios" value="true"/> | |
| 23854 <param name="ratiosSILAC" value="false"/> | |
| 23855 <section name="consensus"> | |
| 23856 <param name="normalize" value="false"/> | |
| 23857 <param name="fix_peptides" value="true"/> | |
| 23858 </section> | |
| 23859 <section name="format"> | |
| 23860 <param name="separator" value=""/> | |
| 23861 <param name="quoting" value="double"/> | |
| 23862 <param name="replacement" value="_"/> | |
| 23863 </section> | |
| 23864 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23865 <output name="ctd_out" ftype="xml"> | |
| 23866 <assert_contents> | |
| 23867 <is_valid_xml/> | |
| 23868 </assert_contents> | |
| 23869 </output> | |
| 23870 </test> | |
| 23871 <test expect_num_outputs="2"> | |
| 23872 <conditional name="adv_opts_cond"> | |
| 23873 <param name="adv_opts_selector" value="advanced"/> | |
| 23874 <param name="force" value="false"/> | |
| 23875 <param name="test" value="true"/> | |
| 23876 </conditional> | |
| 23877 <param name="in" value="ProteinQuantifier_input.consensusXML"/> | |
| 23878 <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23879 <param name="top" value="3"/> | |
| 23880 <param name="average" value="sum"/> | |
| 23881 <param name="include_all" value="true"/> | |
| 23882 <param name="best_charge_and_fraction" value="false"/> | |
| 23883 <param name="greedy_group_resolution" value="false"/> | |
| 23884 <param name="ratios" value="false"/> | |
| 23885 <param name="ratiosSILAC" value="true"/> | |
| 23886 <section name="consensus"> | |
| 23887 <param name="normalize" value="false"/> | |
| 23888 <param name="fix_peptides" value="true"/> | |
| 23889 </section> | |
| 23890 <section name="format"> | |
| 23891 <param name="separator" value=""/> | |
| 23892 <param name="quoting" value="double"/> | |
| 23893 <param name="replacement" value="_"/> | |
| 23894 </section> | |
| 23895 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 23896 <output name="ctd_out" ftype="xml"> | |
| 23897 <assert_contents> | |
| 23898 <is_valid_xml/> | |
| 23899 </assert_contents> | |
| 23900 </output> | |
| 23901 </test> | |
| 23902 <test expect_num_outputs="3"> | |
| 23903 <conditional name="adv_opts_cond"> | |
| 23904 <param name="adv_opts_selector" value="advanced"/> | |
| 23905 <param name="force" value="false"/> | |
| 23906 <param name="test" value="true"/> | |
| 23907 </conditional> | |
| 23908 <param name="in" value="ProteinQuantifier_input.idXML"/> | |
| 23909 <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23910 <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23911 <param name="top" value="0"/> | |
| 23912 <param name="average" value="sum"/> | |
| 23913 <param name="include_all" value="false"/> | |
| 23914 <param name="best_charge_and_fraction" value="false"/> | |
| 23915 <param name="greedy_group_resolution" value="false"/> | |
| 23916 <param name="ratios" value="false"/> | |
| 23917 <param name="ratiosSILAC" value="false"/> | |
| 23918 <section name="consensus"> | |
| 23919 <param name="normalize" value="false"/> | |
| 23920 <param name="fix_peptides" value="false"/> | |
| 23921 </section> | |
| 23922 <section name="format"> | |
| 23923 <param name="separator" value=""/> | |
| 23924 <param name="quoting" value="double"/> | |
| 23925 <param name="replacement" value="_"/> | |
| 23926 </section> | |
| 23927 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> | |
| 23928 <output name="ctd_out" ftype="xml"> | |
| 23929 <assert_contents> | |
| 23930 <is_valid_xml/> | |
| 23931 </assert_contents> | |
| 23932 </output> | |
| 23933 </test> | |
| 23934 </xml> | |
| 23935 <xml name="autotest_ProteinResolver"> | |
| 23936 <test expect_num_outputs="4"> | |
| 23937 <conditional name="adv_opts_cond"> | |
| 23938 <param name="adv_opts_selector" value="advanced"/> | |
| 23939 <param name="force" value="false"/> | |
| 23940 <param name="test" value="true"/> | |
| 23941 </conditional> | |
| 23942 <param name="fasta" value="ProteinResolver_1_input.fasta"/> | |
| 23943 <param name="in" value="ProteinResolver_1_input.consensusXML"/> | |
| 23944 <param name="in_path" value=""/> | |
| 23945 <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23946 <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23947 <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 23948 <section name="resolver"> | |
| 23949 <param name="missed_cleavages" value="2"/> | |
| 23950 <param name="min_length" value="6"/> | |
| 23951 <param name="enzyme" value="Trypsin"/> | |
| 23952 </section> | |
| 23953 <section name="designer"> | |
| 23954 <param name="experiment" value="ExperimentalSetting"/> | |
| 23955 <param name="file" value="File"/> | |
| 23956 <param name="separator" value="tab"/> | |
| 23957 </section> | |
| 23958 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/> | |
| 23959 <output name="ctd_out" ftype="xml"> | |
| 23960 <assert_contents> | |
| 23961 <is_valid_xml/> | |
| 23962 </assert_contents> | |
| 23963 </output> | |
| 23964 </test> | |
| 23965 </xml> | |
| 23966 <xml name="autotest_PSMFeatureExtractor"> | |
| 23967 </xml> | |
| 23968 <xml name="autotest_PTModel"> | |
| 23969 <test expect_num_outputs="2"> | |
| 23970 <conditional name="adv_opts_cond"> | |
| 23971 <param name="adv_opts_selector" value="advanced"/> | |
| 23972 <param name="force" value="false"/> | |
| 23973 <param name="test" value="true"/> | |
| 23974 </conditional> | |
| 23975 <param name="in_positive" value="PTModel_1_input_positive.idXML"/> | |
| 23976 <param name="in_negative" value="PTModel_1_input_negative.idXML"/> | |
| 23977 <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> | |
| 23978 <param name="c" value="0.5"/> | |
| 23979 <param name="svm_type" value="C_SVC"/> | |
| 23980 <param name="nu" value="0.5"/> | |
| 23981 <param name="kernel_type" value="OLIGO"/> | |
| 23982 <param name="degree" value="1"/> | |
| 23983 <param name="border_length" value="22"/> | |
| 23984 <param name="k_mer_length" value="1"/> | |
| 23985 <param name="sigma" value="5.0"/> | |
| 23986 <param name="max_positive_count" value="1000"/> | |
| 23987 <param name="max_negative_count" value="1000"/> | |
| 23988 <param name="redundant" value="false"/> | |
| 23989 <param name="additive_cv" value="false"/> | |
| 23990 <section name="cv"> | |
| 23991 <param name="skip_cv" value="true"/> | |
| 23992 <param name="number_of_runs" value="10"/> | |
| 23993 <param name="number_of_partitions" value="10"/> | |
| 23994 <param name="degree_start" value="1"/> | |
| 23995 <param name="degree_step_size" value="2"/> | |
| 23996 <param name="degree_stop" value="4"/> | |
| 23997 <param name="c_start" value="1.0"/> | |
| 23998 <param name="c_step_size" value="100.0"/> | |
| 23999 <param name="c_stop" value="1000.0"/> | |
| 24000 <param name="nu_start" value="0.1"/> | |
| 24001 <param name="nu_step_size" value="1.3"/> | |
| 24002 <param name="nu_stop" value="0.9"/> | |
| 24003 <param name="sigma_start" value="1.0"/> | |
| 24004 <param name="sigma_step_size" value="1.3"/> | |
| 24005 <param name="sigma_stop" value="15.0"/> | |
| 24006 </section> | |
| 24007 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24008 <output name="ctd_out" ftype="xml"> | |
| 24009 <assert_contents> | |
| 24010 <is_valid_xml/> | |
| 24011 </assert_contents> | |
| 24012 </output> | |
| 24013 </test> | |
| 24014 </xml> | |
| 24015 <xml name="autotest_QCCalculator"> | |
| 24016 </xml> | |
| 24017 <xml name="autotest_QCEmbedder"> | |
| 24018 </xml> | |
| 24019 <xml name="autotest_QCExporter"> | |
| 24020 </xml> | |
| 24021 <xml name="autotest_QCExtractor"> | |
| 24022 </xml> | |
| 24023 <xml name="autotest_QCImporter"> | |
| 24024 </xml> | |
| 24025 <xml name="autotest_QCMerger"> | |
| 24026 </xml> | |
| 24027 <xml name="autotest_QCShrinker"> | |
| 24028 </xml> | |
| 24029 <xml name="autotest_QualityControl"> | |
| 24030 <test expect_num_outputs="3"> | |
| 24031 <conditional name="adv_opts_cond"> | |
| 24032 <param name="adv_opts_selector" value="advanced"/> | |
| 24033 <param name="force" value="false"/> | |
| 24034 <param name="test" value="true"/> | |
| 24035 </conditional> | |
| 24036 <param name="in_cm" value="QualityControl_1_in.consensusXML"/> | |
| 24037 <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/> | |
| 24038 <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/> | |
| 24039 <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 24040 <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> | |
| 24041 <param name="in_contaminants" value="QualityControl_1.fasta"/> | |
| 24042 <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/> | |
| 24043 <section name="FragmentMassError"> | |
| 24044 <param name="unit" value="auto"/> | |
| 24045 <param name="tolerance" value="20.0"/> | |
| 24046 </section> | |
| 24047 <section name="MS2_id_rate"> | |
| 24048 <param name="force_no_fdr" value="false"/> | |
| 24049 </section> | |
| 24050 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG"/> | |
| 24051 <output name="ctd_out" ftype="xml"> | |
| 24052 <assert_contents> | |
| 24053 <is_valid_xml/> | |
| 24054 </assert_contents> | |
| 24055 </output> | |
| 24056 </test> | |
| 24057 </xml> | |
| 24058 <xml name="autotest_RNADigestor"> | |
| 24059 </xml> | |
| 24060 <xml name="autotest_RNAMassCalculator"> | |
| 24061 <test expect_num_outputs="2"> | |
| 24062 <conditional name="adv_opts_cond"> | |
| 24063 <param name="adv_opts_selector" value="advanced"/> | |
| 24064 <param name="force" value="false"/> | |
| 24065 <param name="test" value="true"/> | |
| 24066 </conditional> | |
| 24067 <param name="in_seq" value=""AUCGGC""/> | |
| 24068 <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/> | |
| 24069 <param name="charge" value="-1 -2"/> | |
| 24070 <param name="format" value="list"/> | |
| 24071 <param name="average_mass" value="false"/> | |
| 24072 <param name="fragment_type" value="full"/> | |
| 24073 <param name="separator" value=""/> | |
| 24074 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 24075 <output name="ctd_out" ftype="xml"> | |
| 24076 <assert_contents> | |
| 24077 <is_valid_xml/> | |
| 24078 </assert_contents> | |
| 24079 </output> | |
| 24080 </test> | |
| 24081 </xml> | |
| 24082 <xml name="autotest_RNPxlSearch"> | |
| 24083 <test expect_num_outputs="2"> | |
| 24084 <conditional name="adv_opts_cond"> | |
| 24085 <param name="adv_opts_selector" value="advanced"/> | |
| 24086 <param name="force" value="false"/> | |
| 24087 <param name="test" value="true"/> | |
| 24088 </conditional> | |
| 24089 <param name="in" value="RNPxlSearch_1_input.mzML"/> | |
| 24090 <param name="database" value="RNPxlSearch_1_input.fasta"/> | |
| 24091 <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 24092 <section name="precursor"> | |
| 24093 <param name="mass_tolerance" value="20.0"/> | |
| 24094 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24095 <param name="min_charge" value="2"/> | |
| 24096 <param name="max_charge" value="5"/> | |
| 24097 <param name="isotopes" value="0 1"/> | |
| 24098 </section> | |
| 24099 <section name="fragment"> | |
| 24100 <param name="mass_tolerance" value="20.0"/> | |
| 24101 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24102 </section> | |
| 24103 <section name="modifications"> | |
| 24104 <param name="fixed" value=""/> | |
| 24105 <param name="variable" value="Oxidation (M)"/> | |
| 24106 <param name="variable_max_per_peptide" value="2"/> | |
| 24107 </section> | |
| 24108 <section name="peptide"> | |
| 24109 <param name="min_size" value="6"/> | |
| 24110 <param name="max_size" value="1000000"/> | |
| 24111 <param name="missed_cleavages" value="1"/> | |
| 24112 <param name="enzyme" value="Trypsin"/> | |
| 24113 </section> | |
| 24114 <section name="report"> | |
| 24115 <param name="top_hits" value="1"/> | |
| 24116 </section> | |
| 24117 <section name="RNPxl"> | |
| 24118 <param name="length" value="2"/> | |
| 24119 <param name="sequence" value="GUA"/> | |
| 24120 <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> | |
| 24121 <param name="nt_groups" value=""/> | |
| 24122 <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> | |
| 24123 <param name="can_cross_link" value="U"/> | |
| 24124 <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> | |
| 24125 <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> | |
| 24126 <param name="scoring" value="fast"/> | |
| 24127 <param name="decoys" value="false"/> | |
| 24128 <param name="CysteineAdduct" value="false"/> | |
| 24129 <param name="filter_fractional_mass" value="false"/> | |
| 24130 <param name="carbon_labeled_fragments" value="false"/> | |
| 24131 <param name="only_xl" value="false"/> | |
| 24132 <param name="filter_small_peptide_mass" value="600.0"/> | |
| 24133 <param name="marker_ions_tolerance" value="0.05"/> | |
| 24134 </section> | |
| 24135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24136 <output name="ctd_out" ftype="xml"> | |
| 24137 <assert_contents> | |
| 24138 <is_valid_xml/> | |
| 24139 </assert_contents> | |
| 24140 </output> | |
| 24141 </test> | |
| 24142 <test expect_num_outputs="2"> | |
| 24143 <conditional name="adv_opts_cond"> | |
| 24144 <param name="adv_opts_selector" value="advanced"/> | |
| 24145 <param name="force" value="false"/> | |
| 24146 <param name="test" value="true"/> | |
| 24147 </conditional> | |
| 24148 <param name="in" value="RNPxlSearch_1_input.mzML"/> | |
| 24149 <param name="database" value="RNPxlSearch_1_input.fasta"/> | |
| 24150 <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 24151 <section name="precursor"> | |
| 24152 <param name="mass_tolerance" value="20.0"/> | |
| 24153 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24154 <param name="min_charge" value="2"/> | |
| 24155 <param name="max_charge" value="5"/> | |
| 24156 <param name="isotopes" value="0 1"/> | |
| 24157 </section> | |
| 24158 <section name="fragment"> | |
| 24159 <param name="mass_tolerance" value="20.0"/> | |
| 24160 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24161 </section> | |
| 24162 <section name="modifications"> | |
| 24163 <param name="fixed" value=""/> | |
| 24164 <param name="variable" value="Oxidation (M)"/> | |
| 24165 <param name="variable_max_per_peptide" value="2"/> | |
| 24166 </section> | |
| 24167 <section name="peptide"> | |
| 24168 <param name="min_size" value="6"/> | |
| 24169 <param name="max_size" value="1000000"/> | |
| 24170 <param name="missed_cleavages" value="1"/> | |
| 24171 <param name="enzyme" value="Trypsin"/> | |
| 24172 </section> | |
| 24173 <section name="report"> | |
| 24174 <param name="top_hits" value="1"/> | |
| 24175 </section> | |
| 24176 <section name="RNPxl"> | |
| 24177 <param name="length" value="2"/> | |
| 24178 <param name="sequence" value="GUA"/> | |
| 24179 <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> | |
| 24180 <param name="nt_groups" value=""/> | |
| 24181 <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> | |
| 24182 <param name="can_cross_link" value="U"/> | |
| 24183 <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> | |
| 24184 <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> | |
| 24185 <param name="scoring" value="fast"/> | |
| 24186 <param name="decoys" value="true"/> | |
| 24187 <param name="CysteineAdduct" value="false"/> | |
| 24188 <param name="filter_fractional_mass" value="false"/> | |
| 24189 <param name="carbon_labeled_fragments" value="false"/> | |
| 24190 <param name="only_xl" value="false"/> | |
| 24191 <param name="filter_small_peptide_mass" value="600.0"/> | |
| 24192 <param name="marker_ions_tolerance" value="0.05"/> | |
| 24193 </section> | |
| 24194 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24195 <output name="ctd_out" ftype="xml"> | |
| 24196 <assert_contents> | |
| 24197 <is_valid_xml/> | |
| 24198 </assert_contents> | |
| 24199 </output> | |
| 24200 </test> | |
| 24201 <test expect_num_outputs="3"> | |
| 24202 <conditional name="adv_opts_cond"> | |
| 24203 <param name="adv_opts_selector" value="advanced"/> | |
| 24204 <param name="force" value="false"/> | |
| 24205 <param name="test" value="true"/> | |
| 24206 </conditional> | |
| 24207 <param name="in" value="RNPxlSearch_1_input.mzML"/> | |
| 24208 <param name="database" value="RNPxlSearch_1_input.fasta"/> | |
| 24209 <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 24210 <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 24211 <section name="precursor"> | |
| 24212 <param name="mass_tolerance" value="10.0"/> | |
| 24213 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24214 <param name="min_charge" value="2"/> | |
| 24215 <param name="max_charge" value="5"/> | |
| 24216 <param name="isotopes" value="0 1"/> | |
| 24217 </section> | |
| 24218 <section name="fragment"> | |
| 24219 <param name="mass_tolerance" value="10.0"/> | |
| 24220 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24221 </section> | |
| 24222 <section name="modifications"> | |
| 24223 <param name="fixed" value=""/> | |
| 24224 <param name="variable" value=""/> | |
| 24225 <param name="variable_max_per_peptide" value="2"/> | |
| 24226 </section> | |
| 24227 <section name="peptide"> | |
| 24228 <param name="min_size" value="6"/> | |
| 24229 <param name="max_size" value="1000000"/> | |
| 24230 <param name="missed_cleavages" value="1"/> | |
| 24231 <param name="enzyme" value="Trypsin"/> | |
| 24232 </section> | |
| 24233 <section name="report"> | |
| 24234 <param name="top_hits" value="3"/> | |
| 24235 </section> | |
| 24236 <section name="RNPxl"> | |
| 24237 <param name="length" value="2"/> | |
| 24238 <param name="sequence" value=""/> | |
| 24239 <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> | |
| 24240 <param name="nt_groups" value=""/> | |
| 24241 <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> | |
| 24242 <param name="can_cross_link" value="U"/> | |
| 24243 <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> | |
| 24244 <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> | |
| 24245 <param name="scoring" value="fast"/> | |
| 24246 <param name="decoys" value="false"/> | |
| 24247 <param name="CysteineAdduct" value="false"/> | |
| 24248 <param name="filter_fractional_mass" value="false"/> | |
| 24249 <param name="carbon_labeled_fragments" value="false"/> | |
| 24250 <param name="only_xl" value="false"/> | |
| 24251 <param name="filter_small_peptide_mass" value="600.0"/> | |
| 24252 <param name="marker_ions_tolerance" value="0.05"/> | |
| 24253 </section> | |
| 24254 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> | |
| 24255 <output name="ctd_out" ftype="xml"> | |
| 24256 <assert_contents> | |
| 24257 <is_valid_xml/> | |
| 24258 </assert_contents> | |
| 24259 </output> | |
| 24260 </test> | |
| 24261 <test expect_num_outputs="3"> | |
| 24262 <conditional name="adv_opts_cond"> | |
| 24263 <param name="adv_opts_selector" value="advanced"/> | |
| 24264 <param name="force" value="false"/> | |
| 24265 <param name="test" value="true"/> | |
| 24266 </conditional> | |
| 24267 <param name="in" value="RNPxlSearch_1_input.mzML"/> | |
| 24268 <param name="database" value="RNPxlSearch_1_input.fasta"/> | |
| 24269 <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 24270 <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 24271 <section name="precursor"> | |
| 24272 <param name="mass_tolerance" value="10.0"/> | |
| 24273 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24274 <param name="min_charge" value="2"/> | |
| 24275 <param name="max_charge" value="5"/> | |
| 24276 <param name="isotopes" value="0 1"/> | |
| 24277 </section> | |
| 24278 <section name="fragment"> | |
| 24279 <param name="mass_tolerance" value="10.0"/> | |
| 24280 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24281 </section> | |
| 24282 <section name="modifications"> | |
| 24283 <param name="fixed" value=""/> | |
| 24284 <param name="variable" value=""/> | |
| 24285 <param name="variable_max_per_peptide" value="2"/> | |
| 24286 </section> | |
| 24287 <section name="peptide"> | |
| 24288 <param name="min_size" value="6"/> | |
| 24289 <param name="max_size" value="1000000"/> | |
| 24290 <param name="missed_cleavages" value="1"/> | |
| 24291 <param name="enzyme" value="Trypsin"/> | |
| 24292 </section> | |
| 24293 <section name="report"> | |
| 24294 <param name="top_hits" value="2"/> | |
| 24295 </section> | |
| 24296 <section name="RNPxl"> | |
| 24297 <param name="length" value="2"/> | |
| 24298 <param name="sequence" value=""/> | |
| 24299 <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> | |
| 24300 <param name="nt_groups" value=""/> | |
| 24301 <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> | |
| 24302 <param name="can_cross_link" value="U"/> | |
| 24303 <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> | |
| 24304 <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> | |
| 24305 <param name="scoring" value="fast"/> | |
| 24306 <param name="decoys" value="true"/> | |
| 24307 <param name="CysteineAdduct" value="false"/> | |
| 24308 <param name="filter_fractional_mass" value="false"/> | |
| 24309 <param name="carbon_labeled_fragments" value="false"/> | |
| 24310 <param name="only_xl" value="false"/> | |
| 24311 <param name="filter_small_peptide_mass" value="600.0"/> | |
| 24312 <param name="marker_ions_tolerance" value="0.05"/> | |
| 24313 </section> | |
| 24314 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> | |
| 24315 <output name="ctd_out" ftype="xml"> | |
| 24316 <assert_contents> | |
| 24317 <is_valid_xml/> | |
| 24318 </assert_contents> | |
| 24319 </output> | |
| 24320 </test> | |
| 24321 </xml> | |
| 24322 <xml name="autotest_RNPxlXICFilter"> | |
| 24323 </xml> | |
| 24324 <xml name="autotest_RTEvaluation"> | |
| 24325 </xml> | |
| 24326 <xml name="autotest_RTModel"> | |
| 24327 <test expect_num_outputs="2"> | |
| 24328 <conditional name="adv_opts_cond"> | |
| 24329 <param name="adv_opts_selector" value="advanced"/> | |
| 24330 <param name="force" value="false"/> | |
| 24331 <param name="test" value="true"/> | |
| 24332 </conditional> | |
| 24333 <param name="in" value="RTModel_1_input.idXML"/> | |
| 24334 <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/> | |
| 24335 <param name="svm_type" value="NU_SVR"/> | |
| 24336 <param name="nu" value="0.5"/> | |
| 24337 <param name="p" value="0.1"/> | |
| 24338 <param name="c" value="0.1"/> | |
| 24339 <param name="kernel_type" value="POLY"/> | |
| 24340 <param name="degree" value="1"/> | |
| 24341 <param name="border_length" value="22"/> | |
| 24342 <param name="max_std" value="10.0"/> | |
| 24343 <param name="k_mer_length" value="1"/> | |
| 24344 <param name="sigma" value="5.0"/> | |
| 24345 <param name="total_gradient_time" value="3000.0"/> | |
| 24346 <param name="first_dim_rt" value="false"/> | |
| 24347 <param name="additive_cv" value="false"/> | |
| 24348 <section name="cv"> | |
| 24349 <param name="skip_cv" value="true"/> | |
| 24350 <param name="number_of_runs" value="10"/> | |
| 24351 <param name="number_of_partitions" value="10"/> | |
| 24352 <param name="degree_start" value="1"/> | |
| 24353 <param name="degree_step_size" value="2"/> | |
| 24354 <param name="degree_stop" value="4"/> | |
| 24355 <param name="p_start" value="1.0"/> | |
| 24356 <param name="p_step_size" value="10.0"/> | |
| 24357 <param name="p_stop" value="1000.0"/> | |
| 24358 <param name="c_start" value="1.0"/> | |
| 24359 <param name="c_step_size" value="10.0"/> | |
| 24360 <param name="c_stop" value="1000.0"/> | |
| 24361 <param name="nu_start" value="0.3"/> | |
| 24362 <param name="nu_step_size" value="1.2"/> | |
| 24363 <param name="nu_stop" value="0.7"/> | |
| 24364 <param name="sigma_start" value="1.0"/> | |
| 24365 <param name="sigma_step_size" value="1.3"/> | |
| 24366 <param name="sigma_stop" value="15.0"/> | |
| 24367 </section> | |
| 24368 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24369 <output name="ctd_out" ftype="xml"> | |
| 24370 <assert_contents> | |
| 24371 <is_valid_xml/> | |
| 24372 </assert_contents> | |
| 24373 </output> | |
| 24374 </test> | |
| 24375 <test expect_num_outputs="2"> | |
| 24376 <conditional name="adv_opts_cond"> | |
| 24377 <param name="adv_opts_selector" value="advanced"/> | |
| 24378 <param name="force" value="false"/> | |
| 24379 <param name="test" value="true"/> | |
| 24380 </conditional> | |
| 24381 <param name="in_positive" value="RTModel_2_input_positive.idXML"/> | |
| 24382 <param name="in_negative" value="RTModel_2_input_negative.idXML"/> | |
| 24383 <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> | |
| 24384 <param name="svm_type" value="NU_SVR"/> | |
| 24385 <param name="nu" value="0.5"/> | |
| 24386 <param name="p" value="0.1"/> | |
| 24387 <param name="c" value="0.5"/> | |
| 24388 <param name="kernel_type" value="OLIGO"/> | |
| 24389 <param name="degree" value="1"/> | |
| 24390 <param name="border_length" value="22"/> | |
| 24391 <param name="max_std" value="10.0"/> | |
| 24392 <param name="k_mer_length" value="1"/> | |
| 24393 <param name="sigma" value="5.0"/> | |
| 24394 <param name="total_gradient_time" value="1.0"/> | |
| 24395 <param name="first_dim_rt" value="false"/> | |
| 24396 <param name="additive_cv" value="false"/> | |
| 24397 <section name="cv"> | |
| 24398 <param name="skip_cv" value="true"/> | |
| 24399 <param name="number_of_runs" value="10"/> | |
| 24400 <param name="number_of_partitions" value="10"/> | |
| 24401 <param name="degree_start" value="1"/> | |
| 24402 <param name="degree_step_size" value="2"/> | |
| 24403 <param name="degree_stop" value="4"/> | |
| 24404 <param name="p_start" value="1.0"/> | |
| 24405 <param name="p_step_size" value="10.0"/> | |
| 24406 <param name="p_stop" value="1000.0"/> | |
| 24407 <param name="c_start" value="1.0"/> | |
| 24408 <param name="c_step_size" value="10.0"/> | |
| 24409 <param name="c_stop" value="1000.0"/> | |
| 24410 <param name="nu_start" value="0.3"/> | |
| 24411 <param name="nu_step_size" value="1.2"/> | |
| 24412 <param name="nu_stop" value="0.7"/> | |
| 24413 <param name="sigma_start" value="1.0"/> | |
| 24414 <param name="sigma_step_size" value="1.3"/> | |
| 24415 <param name="sigma_stop" value="15.0"/> | |
| 24416 </section> | |
| 24417 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24418 <output name="ctd_out" ftype="xml"> | |
| 24419 <assert_contents> | |
| 24420 <is_valid_xml/> | |
| 24421 </assert_contents> | |
| 24422 </output> | |
| 24423 </test> | |
| 24424 <test expect_num_outputs="2"> | |
| 24425 <conditional name="adv_opts_cond"> | |
| 24426 <param name="adv_opts_selector" value="advanced"/> | |
| 24427 <param name="force" value="false"/> | |
| 24428 <param name="test" value="true"/> | |
| 24429 </conditional> | |
| 24430 <param name="in" value="RTModel_3_input.idXML"/> | |
| 24431 <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> | |
| 24432 <param name="svm_type" value="NU_SVR"/> | |
| 24433 <param name="nu" value="0.5"/> | |
| 24434 <param name="p" value="0.1"/> | |
| 24435 <param name="c" value="0.001953125"/> | |
| 24436 <param name="kernel_type" value="OLIGO"/> | |
| 24437 <param name="degree" value="1"/> | |
| 24438 <param name="border_length" value="22"/> | |
| 24439 <param name="max_std" value="10.0"/> | |
| 24440 <param name="k_mer_length" value="1"/> | |
| 24441 <param name="sigma" value="1.0"/> | |
| 24442 <param name="total_gradient_time" value="1.0"/> | |
| 24443 <param name="first_dim_rt" value="false"/> | |
| 24444 <param name="additive_cv" value="false"/> | |
| 24445 <section name="cv"> | |
| 24446 <param name="skip_cv" value="false"/> | |
| 24447 <param name="number_of_runs" value="1"/> | |
| 24448 <param name="number_of_partitions" value="5"/> | |
| 24449 <param name="degree_start" value="1"/> | |
| 24450 <param name="degree_step_size" value="2"/> | |
| 24451 <param name="degree_stop" value="4"/> | |
| 24452 <param name="p_start" value="1.0"/> | |
| 24453 <param name="p_step_size" value="10.0"/> | |
| 24454 <param name="p_stop" value="1000.0"/> | |
| 24455 <param name="c_start" value="0.001953125"/> | |
| 24456 <param name="c_step_size" value="2.0"/> | |
| 24457 <param name="c_stop" value="0.001953125"/> | |
| 24458 <param name="nu_start" value="0.4"/> | |
| 24459 <param name="nu_step_size" value="1.2"/> | |
| 24460 <param name="nu_stop" value="0.4"/> | |
| 24461 <param name="sigma_start" value="5.0"/> | |
| 24462 <param name="sigma_step_size" value="1.221055"/> | |
| 24463 <param name="sigma_stop" value="5.0"/> | |
| 24464 </section> | |
| 24465 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24466 <output name="ctd_out" ftype="xml"> | |
| 24467 <assert_contents> | |
| 24468 <is_valid_xml/> | |
| 24469 </assert_contents> | |
| 24470 </output> | |
| 24471 </test> | |
| 24472 <test expect_num_outputs="2"> | |
| 24473 <conditional name="adv_opts_cond"> | |
| 24474 <param name="adv_opts_selector" value="advanced"/> | |
| 24475 <param name="force" value="false"/> | |
| 24476 <param name="test" value="true"/> | |
| 24477 </conditional> | |
| 24478 <param name="in" value="RTModel_4_input.txt" ftype="txt"/> | |
| 24479 <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> | |
| 24480 <param name="svm_type" value="NU_SVR"/> | |
| 24481 <param name="nu" value="0.5"/> | |
| 24482 <param name="p" value="0.1"/> | |
| 24483 <param name="c" value="0.001953125"/> | |
| 24484 <param name="kernel_type" value="OLIGO"/> | |
| 24485 <param name="degree" value="1"/> | |
| 24486 <param name="border_length" value="22"/> | |
| 24487 <param name="max_std" value="10.0"/> | |
| 24488 <param name="k_mer_length" value="1"/> | |
| 24489 <param name="sigma" value="1.0"/> | |
| 24490 <param name="total_gradient_time" value="1.0"/> | |
| 24491 <param name="first_dim_rt" value="false"/> | |
| 24492 <param name="additive_cv" value="false"/> | |
| 24493 <section name="cv"> | |
| 24494 <param name="skip_cv" value="false"/> | |
| 24495 <param name="number_of_runs" value="1"/> | |
| 24496 <param name="number_of_partitions" value="5"/> | |
| 24497 <param name="degree_start" value="1"/> | |
| 24498 <param name="degree_step_size" value="2"/> | |
| 24499 <param name="degree_stop" value="4"/> | |
| 24500 <param name="p_start" value="1.0"/> | |
| 24501 <param name="p_step_size" value="10.0"/> | |
| 24502 <param name="p_stop" value="1000.0"/> | |
| 24503 <param name="c_start" value="0.001953125"/> | |
| 24504 <param name="c_step_size" value="2.0"/> | |
| 24505 <param name="c_stop" value="0.001953125"/> | |
| 24506 <param name="nu_start" value="0.4"/> | |
| 24507 <param name="nu_step_size" value="1.2"/> | |
| 24508 <param name="nu_stop" value="0.4"/> | |
| 24509 <param name="sigma_start" value="5.0"/> | |
| 24510 <param name="sigma_step_size" value="1.221055"/> | |
| 24511 <param name="sigma_stop" value="5.0"/> | |
| 24512 </section> | |
| 24513 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24514 <output name="ctd_out" ftype="xml"> | |
| 24515 <assert_contents> | |
| 24516 <is_valid_xml/> | |
| 24517 </assert_contents> | |
| 24518 </output> | |
| 24519 </test> | |
| 24520 </xml> | |
| 24521 <xml name="autotest_SeedListGenerator"> | |
| 24522 <test expect_num_outputs="2"> | |
| 24523 <conditional name="adv_opts_cond"> | |
| 24524 <param name="adv_opts_selector" value="advanced"/> | |
| 24525 <param name="force" value="false"/> | |
| 24526 <param name="test" value="true"/> | |
| 24527 </conditional> | |
| 24528 <param name="in" value="PepXMLFile_test.mzML"/> | |
| 24529 <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 24530 <param name="use_peptide_mass" value="false"/> | |
| 24531 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24532 <output name="ctd_out" ftype="xml"> | |
| 24533 <assert_contents> | |
| 24534 <is_valid_xml/> | |
| 24535 </assert_contents> | |
| 24536 </output> | |
| 24537 </test> | |
| 24538 <test expect_num_outputs="2"> | |
| 24539 <conditional name="adv_opts_cond"> | |
| 24540 <param name="adv_opts_selector" value="advanced"/> | |
| 24541 <param name="force" value="false"/> | |
| 24542 <param name="test" value="true"/> | |
| 24543 </conditional> | |
| 24544 <param name="in" value="IDMapper_1_output.featureXML"/> | |
| 24545 <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> | |
| 24546 <param name="use_peptide_mass" value="false"/> | |
| 24547 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24548 <output name="ctd_out" ftype="xml"> | |
| 24549 <assert_contents> | |
| 24550 <is_valid_xml/> | |
| 24551 </assert_contents> | |
| 24552 </output> | |
| 24553 </test> | |
| 24554 </xml> | |
| 24555 <xml name="autotest_SemanticValidator"> | |
| 24556 </xml> | |
| 24557 <xml name="autotest_SequenceCoverageCalculator"> | |
| 24558 </xml> | |
| 24559 <xml name="autotest_SimpleSearchEngine"> | |
| 24560 <test expect_num_outputs="2"> | |
| 24561 <conditional name="adv_opts_cond"> | |
| 24562 <param name="adv_opts_selector" value="advanced"/> | |
| 24563 <param name="force" value="false"/> | |
| 24564 <param name="test" value="true"/> | |
| 24565 </conditional> | |
| 24566 <param name="in" value="SimpleSearchEngine_1.mzML"/> | |
| 24567 <param name="database" value="SimpleSearchEngine_1.fasta"/> | |
| 24568 <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 24569 <section name="Search"> | |
| 24570 <param name="enzyme" value="Trypsin"/> | |
| 24571 <section name="precursor"> | |
| 24572 <param name="mass_tolerance" value="5.0"/> | |
| 24573 <param name="mass_tolerance_unit" value="ppm"/> | |
| 24574 <param name="min_charge" value="2"/> | |
| 24575 <param name="max_charge" value="5"/> | |
| 24576 <param name="isotopes" value="0 1"/> | |
| 24577 </section> | |
| 24578 <section name="fragment"> | |
| 24579 <param name="mass_tolerance" value="0.3"/> | |
| 24580 <param name="mass_tolerance_unit" value="Da"/> | |
| 24581 </section> | |
| 24582 <section name="modifications"> | |
| 24583 <param name="fixed" value=""/> | |
| 24584 <param name="variable" value="Oxidation (M)"/> | |
| 24585 <param name="variable_max_per_peptide" value="2"/> | |
| 24586 </section> | |
| 24587 <section name="peptide"> | |
| 24588 <param name="min_size" value="7"/> | |
| 24589 <param name="max_size" value="40"/> | |
| 24590 <param name="missed_cleavages" value="1"/> | |
| 24591 <param name="motif" value=""/> | |
| 24592 </section> | |
| 24593 <section name="report"> | |
| 24594 <param name="top_hits" value="1"/> | |
| 24595 </section> | |
| 24596 </section> | |
| 24597 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24598 <output name="ctd_out" ftype="xml"> | |
| 24599 <assert_contents> | |
| 24600 <is_valid_xml/> | |
| 24601 </assert_contents> | |
| 24602 </output> | |
| 24603 </test> | |
| 24604 </xml> | |
| 24605 <xml name="autotest_SiriusAdapter"> | |
| 24606 <test expect_num_outputs="2"> | |
| 24607 <conditional name="adv_opts_cond"> | |
| 24608 <param name="adv_opts_selector" value="advanced"/> | |
| 24609 <param name="converter_mode" value="false"/> | |
| 24610 <param name="force" value="false"/> | |
| 24611 <param name="test" value="true"/> | |
| 24612 </conditional> | |
| 24613 <param name="in" value="SiriusAdapter_1_input.mzML"/> | |
| 24614 <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 24615 <param name="out_workspace_directory" value=""/> | |
| 24616 <section name="preprocessing"> | |
| 24617 <param name="filter_by_num_masstraces" value="1"/> | |
| 24618 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 24619 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 24620 <param name="precursor_rt_tolerance" value="5"/> | |
| 24621 <param name="isotope_pattern_iterations" value="3"/> | |
| 24622 <param name="feature_only" value="false"/> | |
| 24623 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 24624 </section> | |
| 24625 <section name="sirius"> | |
| 24626 <param name="profile" value="qtof"/> | |
| 24627 <param name="candidates" value="5"/> | |
| 24628 <param name="database" value="all"/> | |
| 24629 <param name="noise" value="0"/> | |
| 24630 <param name="ppm_max" value="10"/> | |
| 24631 <param name="isotope" value="both"/> | |
| 24632 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 24633 <param name="compound_timeout" value="10"/> | |
| 24634 <param name="tree_timeout" value="0"/> | |
| 24635 <param name="top_n_hits" value="10"/> | |
| 24636 <param name="cores" value="1"/> | |
| 24637 <param name="auto_charge" value="true"/> | |
| 24638 <param name="ion_tree" value="false"/> | |
| 24639 <param name="no_recalibration" value="false"/> | |
| 24640 <param name="most_intense_ms2" value="false"/> | |
| 24641 </section> | |
| 24642 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> | |
| 24643 <output name="ctd_out" ftype="xml"> | |
| 24644 <assert_contents> | |
| 24645 <is_valid_xml/> | |
| 24646 </assert_contents> | |
| 24647 </output> | |
| 24648 </test> | |
| 24649 <test expect_num_outputs="2"> | |
| 24650 <conditional name="adv_opts_cond"> | |
| 24651 <param name="adv_opts_selector" value="advanced"/> | |
| 24652 <param name="converter_mode" value="false"/> | |
| 24653 <param name="force" value="false"/> | |
| 24654 <param name="test" value="true"/> | |
| 24655 </conditional> | |
| 24656 <param name="in" value="SiriusAdapter_2_input.mzML"/> | |
| 24657 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> | |
| 24658 <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 24659 <param name="out_workspace_directory" value=""/> | |
| 24660 <section name="preprocessing"> | |
| 24661 <param name="filter_by_num_masstraces" value="3"/> | |
| 24662 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 24663 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 24664 <param name="precursor_rt_tolerance" value="5"/> | |
| 24665 <param name="isotope_pattern_iterations" value="3"/> | |
| 24666 <param name="feature_only" value="true"/> | |
| 24667 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 24668 </section> | |
| 24669 <section name="sirius"> | |
| 24670 <param name="profile" value="qtof"/> | |
| 24671 <param name="candidates" value="5"/> | |
| 24672 <param name="database" value="all"/> | |
| 24673 <param name="noise" value="0"/> | |
| 24674 <param name="ppm_max" value="10"/> | |
| 24675 <param name="isotope" value="both"/> | |
| 24676 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 24677 <param name="compound_timeout" value="10"/> | |
| 24678 <param name="tree_timeout" value="0"/> | |
| 24679 <param name="top_n_hits" value="10"/> | |
| 24680 <param name="cores" value="1"/> | |
| 24681 <param name="auto_charge" value="true"/> | |
| 24682 <param name="ion_tree" value="false"/> | |
| 24683 <param name="no_recalibration" value="false"/> | |
| 24684 <param name="most_intense_ms2" value="false"/> | |
| 24685 </section> | |
| 24686 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> | |
| 24687 <output name="ctd_out" ftype="xml"> | |
| 24688 <assert_contents> | |
| 24689 <is_valid_xml/> | |
| 24690 </assert_contents> | |
| 24691 </output> | |
| 24692 </test> | |
| 24693 <test expect_num_outputs="2"> | |
| 24694 <conditional name="adv_opts_cond"> | |
| 24695 <param name="adv_opts_selector" value="advanced"/> | |
| 24696 <param name="converter_mode" value="false"/> | |
| 24697 <param name="force" value="false"/> | |
| 24698 <param name="test" value="true"/> | |
| 24699 </conditional> | |
| 24700 <param name="in" value="SiriusAdapter_3_input.mzML"/> | |
| 24701 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> | |
| 24702 <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 24703 <param name="out_workspace_directory" value=""/> | |
| 24704 <section name="preprocessing"> | |
| 24705 <param name="filter_by_num_masstraces" value="3"/> | |
| 24706 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 24707 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 24708 <param name="precursor_rt_tolerance" value="5"/> | |
| 24709 <param name="isotope_pattern_iterations" value="3"/> | |
| 24710 <param name="feature_only" value="false"/> | |
| 24711 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 24712 </section> | |
| 24713 <section name="sirius"> | |
| 24714 <param name="profile" value="qtof"/> | |
| 24715 <param name="candidates" value="5"/> | |
| 24716 <param name="database" value="all"/> | |
| 24717 <param name="noise" value="0"/> | |
| 24718 <param name="ppm_max" value="10"/> | |
| 24719 <param name="isotope" value="both"/> | |
| 24720 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 24721 <param name="compound_timeout" value="10"/> | |
| 24722 <param name="tree_timeout" value="0"/> | |
| 24723 <param name="top_n_hits" value="10"/> | |
| 24724 <param name="cores" value="1"/> | |
| 24725 <param name="auto_charge" value="true"/> | |
| 24726 <param name="ion_tree" value="false"/> | |
| 24727 <param name="no_recalibration" value="false"/> | |
| 24728 <param name="most_intense_ms2" value="false"/> | |
| 24729 </section> | |
| 24730 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> | |
| 24731 <output name="ctd_out" ftype="xml"> | |
| 24732 <assert_contents> | |
| 24733 <is_valid_xml/> | |
| 24734 </assert_contents> | |
| 24735 </output> | |
| 24736 </test> | |
| 24737 <test expect_num_outputs="2"> | |
| 24738 <conditional name="adv_opts_cond"> | |
| 24739 <param name="adv_opts_selector" value="advanced"/> | |
| 24740 <param name="converter_mode" value="true"/> | |
| 24741 <param name="force" value="false"/> | |
| 24742 <param name="test" value="true"/> | |
| 24743 </conditional> | |
| 24744 <param name="in" value="SiriusAdapter_3_input.mzML"/> | |
| 24745 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> | |
| 24746 <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> | |
| 24747 <param name="out_workspace_directory" value=""/> | |
| 24748 <section name="preprocessing"> | |
| 24749 <param name="filter_by_num_masstraces" value="1"/> | |
| 24750 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 24751 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 24752 <param name="precursor_rt_tolerance" value="5"/> | |
| 24753 <param name="isotope_pattern_iterations" value="3"/> | |
| 24754 <param name="feature_only" value="false"/> | |
| 24755 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 24756 </section> | |
| 24757 <section name="sirius"> | |
| 24758 <param name="profile" value="qtof"/> | |
| 24759 <param name="candidates" value="5"/> | |
| 24760 <param name="database" value="all"/> | |
| 24761 <param name="noise" value="0"/> | |
| 24762 <param name="ppm_max" value="10"/> | |
| 24763 <param name="isotope" value="both"/> | |
| 24764 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 24765 <param name="compound_timeout" value="10"/> | |
| 24766 <param name="tree_timeout" value="0"/> | |
| 24767 <param name="top_n_hits" value="10"/> | |
| 24768 <param name="cores" value="1"/> | |
| 24769 <param name="auto_charge" value="false"/> | |
| 24770 <param name="ion_tree" value="false"/> | |
| 24771 <param name="no_recalibration" value="false"/> | |
| 24772 <param name="most_intense_ms2" value="false"/> | |
| 24773 </section> | |
| 24774 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> | |
| 24775 <output name="ctd_out" ftype="xml"> | |
| 24776 <assert_contents> | |
| 24777 <is_valid_xml/> | |
| 24778 </assert_contents> | |
| 24779 </output> | |
| 24780 </test> | |
| 24781 <test expect_num_outputs="2"> | |
| 24782 <conditional name="adv_opts_cond"> | |
| 24783 <param name="adv_opts_selector" value="advanced"/> | |
| 24784 <param name="converter_mode" value="true"/> | |
| 24785 <param name="force" value="false"/> | |
| 24786 <param name="test" value="true"/> | |
| 24787 </conditional> | |
| 24788 <param name="in" value="SiriusAdapter_4_input.mzML"/> | |
| 24789 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> | |
| 24790 <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> | |
| 24791 <param name="out_workspace_directory" value=""/> | |
| 24792 <section name="preprocessing"> | |
| 24793 <param name="filter_by_num_masstraces" value="1"/> | |
| 24794 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 24795 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 24796 <param name="precursor_rt_tolerance" value="5"/> | |
| 24797 <param name="isotope_pattern_iterations" value="3"/> | |
| 24798 <param name="feature_only" value="false"/> | |
| 24799 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 24800 </section> | |
| 24801 <section name="sirius"> | |
| 24802 <param name="profile" value="qtof"/> | |
| 24803 <param name="candidates" value="5"/> | |
| 24804 <param name="database" value="all"/> | |
| 24805 <param name="noise" value="0"/> | |
| 24806 <param name="ppm_max" value="10"/> | |
| 24807 <param name="isotope" value="both"/> | |
| 24808 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 24809 <param name="compound_timeout" value="10"/> | |
| 24810 <param name="tree_timeout" value="0"/> | |
| 24811 <param name="top_n_hits" value="10"/> | |
| 24812 <param name="cores" value="1"/> | |
| 24813 <param name="auto_charge" value="false"/> | |
| 24814 <param name="ion_tree" value="false"/> | |
| 24815 <param name="no_recalibration" value="false"/> | |
| 24816 <param name="most_intense_ms2" value="false"/> | |
| 24817 </section> | |
| 24818 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> | |
| 24819 <output name="ctd_out" ftype="xml"> | |
| 24820 <assert_contents> | |
| 24821 <is_valid_xml/> | |
| 24822 </assert_contents> | |
| 24823 </output> | |
| 24824 </test> | |
| 24825 <test expect_num_outputs="2"> | |
| 24826 <conditional name="adv_opts_cond"> | |
| 24827 <param name="adv_opts_selector" value="advanced"/> | |
| 24828 <param name="converter_mode" value="false"/> | |
| 24829 <param name="force" value="false"/> | |
| 24830 <param name="test" value="true"/> | |
| 24831 </conditional> | |
| 24832 <param name="in" value="SiriusAdapter_4_input.mzML"/> | |
| 24833 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> | |
| 24834 <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 24835 <param name="out_workspace_directory" value=""/> | |
| 24836 <section name="preprocessing"> | |
| 24837 <param name="filter_by_num_masstraces" value="1"/> | |
| 24838 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 24839 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 24840 <param name="precursor_rt_tolerance" value="5"/> | |
| 24841 <param name="isotope_pattern_iterations" value="3"/> | |
| 24842 <param name="feature_only" value="true"/> | |
| 24843 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 24844 </section> | |
| 24845 <section name="sirius"> | |
| 24846 <param name="profile" value="qtof"/> | |
| 24847 <param name="candidates" value="5"/> | |
| 24848 <param name="database" value="all"/> | |
| 24849 <param name="noise" value="0"/> | |
| 24850 <param name="ppm_max" value="10"/> | |
| 24851 <param name="isotope" value="both"/> | |
| 24852 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 24853 <param name="compound_timeout" value="10"/> | |
| 24854 <param name="tree_timeout" value="0"/> | |
| 24855 <param name="top_n_hits" value="10"/> | |
| 24856 <param name="cores" value="1"/> | |
| 24857 <param name="auto_charge" value="false"/> | |
| 24858 <param name="ion_tree" value="false"/> | |
| 24859 <param name="no_recalibration" value="false"/> | |
| 24860 <param name="most_intense_ms2" value="false"/> | |
| 24861 </section> | |
| 24862 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> | |
| 24863 <output name="ctd_out" ftype="xml"> | |
| 24864 <assert_contents> | |
| 24865 <is_valid_xml/> | |
| 24866 </assert_contents> | |
| 24867 </output> | |
| 24868 </test> | |
| 24869 <test expect_num_outputs="3"> | |
| 24870 <conditional name="adv_opts_cond"> | |
| 24871 <param name="adv_opts_selector" value="advanced"/> | |
| 24872 <param name="converter_mode" value="false"/> | |
| 24873 <param name="force" value="false"/> | |
| 24874 <param name="test" value="true"/> | |
| 24875 </conditional> | |
| 24876 <param name="in" value="SiriusAdapter_2_input.mzML"/> | |
| 24877 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> | |
| 24878 <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 24879 <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | |
| 24880 <param name="out_workspace_directory" value=""/> | |
| 24881 <section name="preprocessing"> | |
| 24882 <param name="filter_by_num_masstraces" value="1"/> | |
| 24883 <param name="precursor_mz_tolerance" value="0.005"/> | |
| 24884 <param name="precursor_mz_tolerance_unit" value="Da"/> | |
| 24885 <param name="precursor_rt_tolerance" value="5"/> | |
| 24886 <param name="isotope_pattern_iterations" value="3"/> | |
| 24887 <param name="feature_only" value="false"/> | |
| 24888 <param name="no_masstrace_info_isotope_pattern" value="false"/> | |
| 24889 </section> | |
| 24890 <section name="sirius"> | |
| 24891 <param name="profile" value="qtof"/> | |
| 24892 <param name="candidates" value="5"/> | |
| 24893 <param name="database" value="all"/> | |
| 24894 <param name="noise" value="0"/> | |
| 24895 <param name="ppm_max" value="10"/> | |
| 24896 <param name="isotope" value="both"/> | |
| 24897 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> | |
| 24898 <param name="compound_timeout" value="10"/> | |
| 24899 <param name="tree_timeout" value="0"/> | |
| 24900 <param name="top_n_hits" value="10"/> | |
| 24901 <param name="cores" value="1"/> | |
| 24902 <param name="auto_charge" value="true"/> | |
| 24903 <param name="ion_tree" value="false"/> | |
| 24904 <param name="no_recalibration" value="false"/> | |
| 24905 <param name="most_intense_ms2" value="false"/> | |
| 24906 </section> | |
| 24907 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/> | |
| 24908 <output name="ctd_out" ftype="xml"> | |
| 24909 <assert_contents> | |
| 24910 <is_valid_xml/> | |
| 24911 </assert_contents> | |
| 24912 </output> | |
| 24913 </test> | |
| 24914 </xml> | |
| 24915 <xml name="autotest_SpecLibCreator"> | |
| 24916 </xml> | |
| 24917 <xml name="autotest_SpecLibSearcher"> | |
| 24918 <test expect_num_outputs="2"> | |
| 24919 <conditional name="adv_opts_cond"> | |
| 24920 <param name="adv_opts_selector" value="advanced"/> | |
| 24921 <param name="force" value="false"/> | |
| 24922 <param name="test" value="true"/> | |
| 24923 </conditional> | |
| 24924 <param name="in" value="SpecLibSearcher_1.mzML"/> | |
| 24925 <param name="lib" value="SpecLibSearcher_1.MSP"/> | |
| 24926 <output_collection name="out" count="1"/> | |
| 24927 <param name="compare_function" value="ZhangSimilarityScore"/> | |
| 24928 <section name="precursor"> | |
| 24929 <param name="mass_tolerance" value="3.0"/> | |
| 24930 <param name="mass_tolerance_unit" value="Da"/> | |
| 24931 <param name="min_charge" value="1"/> | |
| 24932 <param name="max_charge" value="5"/> | |
| 24933 <param name="isotopes" value="0 1"/> | |
| 24934 </section> | |
| 24935 <section name="fragment"> | |
| 24936 <param name="mass_tolerance" value="10.0"/> | |
| 24937 </section> | |
| 24938 <section name="report"> | |
| 24939 <param name="top_hits" value="10"/> | |
| 24940 </section> | |
| 24941 <section name="filter"> | |
| 24942 <param name="remove_peaks_below_threshold" value="2.01"/> | |
| 24943 <param name="min_peaks" value="5"/> | |
| 24944 <param name="max_peaks" value="150"/> | |
| 24945 <param name="cut_peaks_below" value="1000"/> | |
| 24946 </section> | |
| 24947 <section name="modifications"> | |
| 24948 <param name="fixed" value=""/> | |
| 24949 <param name="variable" value=""/> | |
| 24950 <param name="variable_max_per_peptide" value="2"/> | |
| 24951 </section> | |
| 24952 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24953 <output name="ctd_out" ftype="xml"> | |
| 24954 <assert_contents> | |
| 24955 <is_valid_xml/> | |
| 24956 </assert_contents> | |
| 24957 </output> | |
| 24958 </test> | |
| 24959 </xml> | |
| 24960 <xml name="autotest_SpectraFilterBernNorm"> | |
| 24961 </xml> | |
| 24962 <xml name="autotest_SpectraFilterMarkerMower"> | |
| 24963 </xml> | |
| 24964 <xml name="autotest_SpectraFilterNLargest"> | |
| 24965 </xml> | |
| 24966 <xml name="autotest_SpectraFilterNormalizer"> | |
| 24967 </xml> | |
| 24968 <xml name="autotest_SpectraFilterParentPeakMower"> | |
| 24969 </xml> | |
| 24970 <xml name="autotest_SpectraFilterScaler"> | |
| 24971 </xml> | |
| 24972 <xml name="autotest_SpectraFilterSqrtMower"> | |
| 24973 <test expect_num_outputs="2"> | |
| 24974 <conditional name="adv_opts_cond"> | |
| 24975 <param name="adv_opts_selector" value="advanced"/> | |
| 24976 <param name="force" value="false"/> | |
| 24977 <param name="test" value="true"/> | |
| 24978 </conditional> | |
| 24979 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
| 24980 <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 24981 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 24982 <output name="ctd_out" ftype="xml"> | |
| 24983 <assert_contents> | |
| 24984 <is_valid_xml/> | |
| 24985 </assert_contents> | |
| 24986 </output> | |
| 24987 </test> | |
| 24988 </xml> | |
| 24989 <xml name="autotest_SpectraFilterThresholdMower"> | |
| 24990 </xml> | |
| 24991 <xml name="autotest_SpectraFilterWindowMower"> | |
| 24992 <test expect_num_outputs="2"> | |
| 24993 <conditional name="adv_opts_cond"> | |
| 24994 <param name="adv_opts_selector" value="advanced"/> | |
| 24995 <param name="force" value="false"/> | |
| 24996 <param name="test" value="true"/> | |
| 24997 </conditional> | |
| 24998 <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/> | |
| 24999 <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 25000 <section name="algorithm"> | |
| 25001 <param name="windowsize" value="50.0"/> | |
| 25002 <param name="peakcount" value="2"/> | |
| 25003 <param name="movetype" value="slide"/> | |
| 25004 </section> | |
| 25005 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25006 <output name="ctd_out" ftype="xml"> | |
| 25007 <assert_contents> | |
| 25008 <is_valid_xml/> | |
| 25009 </assert_contents> | |
| 25010 </output> | |
| 25011 </test> | |
| 25012 <test expect_num_outputs="2"> | |
| 25013 <conditional name="adv_opts_cond"> | |
| 25014 <param name="adv_opts_selector" value="advanced"/> | |
| 25015 <param name="force" value="false"/> | |
| 25016 <param name="test" value="true"/> | |
| 25017 </conditional> | |
| 25018 <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/> | |
| 25019 <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 25020 <section name="algorithm"> | |
| 25021 <param name="windowsize" value="20.0"/> | |
| 25022 <param name="peakcount" value="4"/> | |
| 25023 <param name="movetype" value="slide"/> | |
| 25024 </section> | |
| 25025 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25026 <output name="ctd_out" ftype="xml"> | |
| 25027 <assert_contents> | |
| 25028 <is_valid_xml/> | |
| 25029 </assert_contents> | |
| 25030 </output> | |
| 25031 </test> | |
| 25032 </xml> | |
| 25033 <xml name="autotest_SpectraMerger"> | |
| 25034 </xml> | |
| 25035 <xml name="autotest_SpectraSTSearchAdapter"/> | |
| 25036 <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer"> | |
| 25037 </xml> | |
| 25038 <xml name="autotest_TargetedFileConverter"> | |
| 25039 <test expect_num_outputs="2"> | |
| 25040 <conditional name="adv_opts_cond"> | |
| 25041 <param name="adv_opts_selector" value="advanced"/> | |
| 25042 <param name="legacy_traml_id" value="false"/> | |
| 25043 <param name="force" value="false"/> | |
| 25044 <param name="test" value="true"/> | |
| 25045 </conditional> | |
| 25046 <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> | |
| 25047 <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25048 <param name="out_type" value="TraML"/> | |
| 25049 <section name="algorithm"> | |
| 25050 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25051 <param name="override_group_label_check" value="false"/> | |
| 25052 <param name="force_invalid_mods" value="false"/> | |
| 25053 </section> | |
| 25054 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25055 <output name="ctd_out" ftype="xml"> | |
| 25056 <assert_contents> | |
| 25057 <is_valid_xml/> | |
| 25058 </assert_contents> | |
| 25059 </output> | |
| 25060 </test> | |
| 25061 <test expect_num_outputs="2"> | |
| 25062 <conditional name="adv_opts_cond"> | |
| 25063 <param name="adv_opts_selector" value="advanced"/> | |
| 25064 <param name="legacy_traml_id" value="false"/> | |
| 25065 <param name="force" value="false"/> | |
| 25066 <param name="test" value="true"/> | |
| 25067 </conditional> | |
| 25068 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> | |
| 25069 <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25070 <param name="out_type" value="TraML"/> | |
| 25071 <section name="algorithm"> | |
| 25072 <param name="retentionTimeInterpretation" value="minutes"/> | |
| 25073 <param name="override_group_label_check" value="false"/> | |
| 25074 <param name="force_invalid_mods" value="false"/> | |
| 25075 </section> | |
| 25076 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25077 <output name="ctd_out" ftype="xml"> | |
| 25078 <assert_contents> | |
| 25079 <is_valid_xml/> | |
| 25080 </assert_contents> | |
| 25081 </output> | |
| 25082 </test> | |
| 25083 <test expect_num_outputs="2"> | |
| 25084 <conditional name="adv_opts_cond"> | |
| 25085 <param name="adv_opts_selector" value="advanced"/> | |
| 25086 <param name="legacy_traml_id" value="false"/> | |
| 25087 <param name="force" value="false"/> | |
| 25088 <param name="test" value="true"/> | |
| 25089 </conditional> | |
| 25090 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> | |
| 25091 <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25092 <param name="out_type" value="TraML"/> | |
| 25093 <section name="algorithm"> | |
| 25094 <param name="retentionTimeInterpretation" value="seconds"/> | |
| 25095 <param name="override_group_label_check" value="false"/> | |
| 25096 <param name="force_invalid_mods" value="false"/> | |
| 25097 </section> | |
| 25098 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25099 <output name="ctd_out" ftype="xml"> | |
| 25100 <assert_contents> | |
| 25101 <is_valid_xml/> | |
| 25102 </assert_contents> | |
| 25103 </output> | |
| 25104 </test> | |
| 25105 <test expect_num_outputs="2"> | |
| 25106 <conditional name="adv_opts_cond"> | |
| 25107 <param name="adv_opts_selector" value="advanced"/> | |
| 25108 <param name="legacy_traml_id" value="false"/> | |
| 25109 <param name="force" value="false"/> | |
| 25110 <param name="test" value="true"/> | |
| 25111 </conditional> | |
| 25112 <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> | |
| 25113 <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25114 <param name="out_type" value="TraML"/> | |
| 25115 <section name="algorithm"> | |
| 25116 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25117 <param name="override_group_label_check" value="false"/> | |
| 25118 <param name="force_invalid_mods" value="false"/> | |
| 25119 </section> | |
| 25120 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25121 <output name="ctd_out" ftype="xml"> | |
| 25122 <assert_contents> | |
| 25123 <is_valid_xml/> | |
| 25124 </assert_contents> | |
| 25125 </output> | |
| 25126 </test> | |
| 25127 <test expect_num_outputs="2"> | |
| 25128 <conditional name="adv_opts_cond"> | |
| 25129 <param name="adv_opts_selector" value="advanced"/> | |
| 25130 <param name="legacy_traml_id" value="false"/> | |
| 25131 <param name="force" value="false"/> | |
| 25132 <param name="test" value="true"/> | |
| 25133 </conditional> | |
| 25134 <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> | |
| 25135 <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25136 <param name="out_type" value="TraML"/> | |
| 25137 <section name="algorithm"> | |
| 25138 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25139 <param name="override_group_label_check" value="false"/> | |
| 25140 <param name="force_invalid_mods" value="false"/> | |
| 25141 </section> | |
| 25142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25143 <output name="ctd_out" ftype="xml"> | |
| 25144 <assert_contents> | |
| 25145 <is_valid_xml/> | |
| 25146 </assert_contents> | |
| 25147 </output> | |
| 25148 </test> | |
| 25149 <test expect_num_outputs="2"> | |
| 25150 <conditional name="adv_opts_cond"> | |
| 25151 <param name="adv_opts_selector" value="advanced"/> | |
| 25152 <param name="legacy_traml_id" value="false"/> | |
| 25153 <param name="force" value="false"/> | |
| 25154 <param name="test" value="true"/> | |
| 25155 </conditional> | |
| 25156 <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> | |
| 25157 <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25158 <param name="out_type" value="TraML"/> | |
| 25159 <section name="algorithm"> | |
| 25160 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25161 <param name="override_group_label_check" value="false"/> | |
| 25162 <param name="force_invalid_mods" value="false"/> | |
| 25163 </section> | |
| 25164 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25165 <output name="ctd_out" ftype="xml"> | |
| 25166 <assert_contents> | |
| 25167 <is_valid_xml/> | |
| 25168 </assert_contents> | |
| 25169 </output> | |
| 25170 </test> | |
| 25171 <test expect_num_outputs="2"> | |
| 25172 <conditional name="adv_opts_cond"> | |
| 25173 <param name="adv_opts_selector" value="advanced"/> | |
| 25174 <param name="legacy_traml_id" value="false"/> | |
| 25175 <param name="force" value="false"/> | |
| 25176 <param name="test" value="true"/> | |
| 25177 </conditional> | |
| 25178 <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> | |
| 25179 <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25180 <param name="out_type" value="TraML"/> | |
| 25181 <section name="algorithm"> | |
| 25182 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25183 <param name="override_group_label_check" value="false"/> | |
| 25184 <param name="force_invalid_mods" value="false"/> | |
| 25185 </section> | |
| 25186 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25187 <output name="ctd_out" ftype="xml"> | |
| 25188 <assert_contents> | |
| 25189 <is_valid_xml/> | |
| 25190 </assert_contents> | |
| 25191 </output> | |
| 25192 </test> | |
| 25193 <test expect_num_outputs="2"> | |
| 25194 <conditional name="adv_opts_cond"> | |
| 25195 <param name="adv_opts_selector" value="advanced"/> | |
| 25196 <param name="legacy_traml_id" value="false"/> | |
| 25197 <param name="force" value="false"/> | |
| 25198 <param name="test" value="true"/> | |
| 25199 </conditional> | |
| 25200 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> | |
| 25201 <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25202 <param name="out_type" value="TraML"/> | |
| 25203 <section name="algorithm"> | |
| 25204 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25205 <param name="override_group_label_check" value="false"/> | |
| 25206 <param name="force_invalid_mods" value="false"/> | |
| 25207 </section> | |
| 25208 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25209 <output name="ctd_out" ftype="xml"> | |
| 25210 <assert_contents> | |
| 25211 <is_valid_xml/> | |
| 25212 </assert_contents> | |
| 25213 </output> | |
| 25214 </test> | |
| 25215 <test expect_num_outputs="2"> | |
| 25216 <conditional name="adv_opts_cond"> | |
| 25217 <param name="adv_opts_selector" value="advanced"/> | |
| 25218 <param name="legacy_traml_id" value="true"/> | |
| 25219 <param name="force" value="false"/> | |
| 25220 <param name="test" value="true"/> | |
| 25221 </conditional> | |
| 25222 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> | |
| 25223 <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25224 <param name="out_type" value="TraML"/> | |
| 25225 <section name="algorithm"> | |
| 25226 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25227 <param name="override_group_label_check" value="false"/> | |
| 25228 <param name="force_invalid_mods" value="false"/> | |
| 25229 </section> | |
| 25230 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25231 <output name="ctd_out" ftype="xml"> | |
| 25232 <assert_contents> | |
| 25233 <is_valid_xml/> | |
| 25234 </assert_contents> | |
| 25235 </output> | |
| 25236 </test> | |
| 25237 <test expect_num_outputs="2"> | |
| 25238 <conditional name="adv_opts_cond"> | |
| 25239 <param name="adv_opts_selector" value="advanced"/> | |
| 25240 <param name="legacy_traml_id" value="false"/> | |
| 25241 <param name="force" value="false"/> | |
| 25242 <param name="test" value="true"/> | |
| 25243 </conditional> | |
| 25244 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> | |
| 25245 <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25246 <param name="out_type" value="TraML"/> | |
| 25247 <section name="algorithm"> | |
| 25248 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25249 <param name="override_group_label_check" value="false"/> | |
| 25250 <param name="force_invalid_mods" value="false"/> | |
| 25251 </section> | |
| 25252 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25253 <output name="ctd_out" ftype="xml"> | |
| 25254 <assert_contents> | |
| 25255 <is_valid_xml/> | |
| 25256 </assert_contents> | |
| 25257 </output> | |
| 25258 </test> | |
| 25259 <test expect_num_outputs="2"> | |
| 25260 <conditional name="adv_opts_cond"> | |
| 25261 <param name="adv_opts_selector" value="advanced"/> | |
| 25262 <param name="legacy_traml_id" value="true"/> | |
| 25263 <param name="force" value="false"/> | |
| 25264 <param name="test" value="true"/> | |
| 25265 </conditional> | |
| 25266 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> | |
| 25267 <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25268 <param name="out_type" value="TraML"/> | |
| 25269 <section name="algorithm"> | |
| 25270 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25271 <param name="override_group_label_check" value="false"/> | |
| 25272 <param name="force_invalid_mods" value="false"/> | |
| 25273 </section> | |
| 25274 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25275 <output name="ctd_out" ftype="xml"> | |
| 25276 <assert_contents> | |
| 25277 <is_valid_xml/> | |
| 25278 </assert_contents> | |
| 25279 </output> | |
| 25280 </test> | |
| 25281 <test expect_num_outputs="2"> | |
| 25282 <conditional name="adv_opts_cond"> | |
| 25283 <param name="adv_opts_selector" value="advanced"/> | |
| 25284 <param name="legacy_traml_id" value="false"/> | |
| 25285 <param name="force" value="false"/> | |
| 25286 <param name="test" value="true"/> | |
| 25287 </conditional> | |
| 25288 <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> | |
| 25289 <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 25290 <param name="out_type" value="tsv"/> | |
| 25291 <section name="algorithm"> | |
| 25292 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25293 <param name="override_group_label_check" value="false"/> | |
| 25294 <param name="force_invalid_mods" value="false"/> | |
| 25295 </section> | |
| 25296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25297 <output name="ctd_out" ftype="xml"> | |
| 25298 <assert_contents> | |
| 25299 <is_valid_xml/> | |
| 25300 </assert_contents> | |
| 25301 </output> | |
| 25302 </test> | |
| 25303 <test expect_num_outputs="2"> | |
| 25304 <conditional name="adv_opts_cond"> | |
| 25305 <param name="adv_opts_selector" value="advanced"/> | |
| 25306 <param name="legacy_traml_id" value="false"/> | |
| 25307 <param name="force" value="false"/> | |
| 25308 <param name="test" value="true"/> | |
| 25309 </conditional> | |
| 25310 <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> | |
| 25311 <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25312 <param name="out_type" value="TraML"/> | |
| 25313 <section name="algorithm"> | |
| 25314 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25315 <param name="override_group_label_check" value="false"/> | |
| 25316 <param name="force_invalid_mods" value="false"/> | |
| 25317 </section> | |
| 25318 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25319 <output name="ctd_out" ftype="xml"> | |
| 25320 <assert_contents> | |
| 25321 <is_valid_xml/> | |
| 25322 </assert_contents> | |
| 25323 </output> | |
| 25324 </test> | |
| 25325 <test expect_num_outputs="2"> | |
| 25326 <conditional name="adv_opts_cond"> | |
| 25327 <param name="adv_opts_selector" value="advanced"/> | |
| 25328 <param name="legacy_traml_id" value="false"/> | |
| 25329 <param name="force" value="false"/> | |
| 25330 <param name="test" value="true"/> | |
| 25331 </conditional> | |
| 25332 <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> | |
| 25333 <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 25334 <param name="out_type" value="tsv"/> | |
| 25335 <section name="algorithm"> | |
| 25336 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25337 <param name="override_group_label_check" value="true"/> | |
| 25338 <param name="force_invalid_mods" value="false"/> | |
| 25339 </section> | |
| 25340 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25341 <output name="ctd_out" ftype="xml"> | |
| 25342 <assert_contents> | |
| 25343 <is_valid_xml/> | |
| 25344 </assert_contents> | |
| 25345 </output> | |
| 25346 </test> | |
| 25347 <test expect_num_outputs="2"> | |
| 25348 <conditional name="adv_opts_cond"> | |
| 25349 <param name="adv_opts_selector" value="advanced"/> | |
| 25350 <param name="legacy_traml_id" value="false"/> | |
| 25351 <param name="force" value="false"/> | |
| 25352 <param name="test" value="true"/> | |
| 25353 </conditional> | |
| 25354 <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> | |
| 25355 <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25356 <param name="out_type" value="TraML"/> | |
| 25357 <section name="algorithm"> | |
| 25358 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25359 <param name="override_group_label_check" value="true"/> | |
| 25360 <param name="force_invalid_mods" value="false"/> | |
| 25361 </section> | |
| 25362 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25363 <output name="ctd_out" ftype="xml"> | |
| 25364 <assert_contents> | |
| 25365 <is_valid_xml/> | |
| 25366 </assert_contents> | |
| 25367 </output> | |
| 25368 </test> | |
| 25369 <test expect_num_outputs="2"> | |
| 25370 <conditional name="adv_opts_cond"> | |
| 25371 <param name="adv_opts_selector" value="advanced"/> | |
| 25372 <param name="legacy_traml_id" value="false"/> | |
| 25373 <param name="force" value="false"/> | |
| 25374 <param name="test" value="true"/> | |
| 25375 </conditional> | |
| 25376 <param name="in" value="ConvertTSVToTraML_output.TraML"/> | |
| 25377 <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 25378 <param name="out_type" value="tsv"/> | |
| 25379 <section name="algorithm"> | |
| 25380 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25381 <param name="override_group_label_check" value="false"/> | |
| 25382 <param name="force_invalid_mods" value="false"/> | |
| 25383 </section> | |
| 25384 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25385 <output name="ctd_out" ftype="xml"> | |
| 25386 <assert_contents> | |
| 25387 <is_valid_xml/> | |
| 25388 </assert_contents> | |
| 25389 </output> | |
| 25390 </test> | |
| 25391 <test expect_num_outputs="2"> | |
| 25392 <conditional name="adv_opts_cond"> | |
| 25393 <param name="adv_opts_selector" value="advanced"/> | |
| 25394 <param name="legacy_traml_id" value="false"/> | |
| 25395 <param name="force" value="false"/> | |
| 25396 <param name="test" value="true"/> | |
| 25397 </conditional> | |
| 25398 <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> | |
| 25399 <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25400 <param name="out_type" value="TraML"/> | |
| 25401 <section name="algorithm"> | |
| 25402 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25403 <param name="override_group_label_check" value="true"/> | |
| 25404 <param name="force_invalid_mods" value="false"/> | |
| 25405 </section> | |
| 25406 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25407 <output name="ctd_out" ftype="xml"> | |
| 25408 <assert_contents> | |
| 25409 <is_valid_xml/> | |
| 25410 </assert_contents> | |
| 25411 </output> | |
| 25412 </test> | |
| 25413 <test expect_num_outputs="2"> | |
| 25414 <conditional name="adv_opts_cond"> | |
| 25415 <param name="adv_opts_selector" value="advanced"/> | |
| 25416 <param name="legacy_traml_id" value="false"/> | |
| 25417 <param name="force" value="false"/> | |
| 25418 <param name="test" value="true"/> | |
| 25419 </conditional> | |
| 25420 <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> | |
| 25421 <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25422 <param name="out_type" value="TraML"/> | |
| 25423 <section name="algorithm"> | |
| 25424 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25425 <param name="override_group_label_check" value="false"/> | |
| 25426 <param name="force_invalid_mods" value="false"/> | |
| 25427 </section> | |
| 25428 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25429 <output name="ctd_out" ftype="xml"> | |
| 25430 <assert_contents> | |
| 25431 <is_valid_xml/> | |
| 25432 </assert_contents> | |
| 25433 </output> | |
| 25434 </test> | |
| 25435 <test expect_num_outputs="2"> | |
| 25436 <conditional name="adv_opts_cond"> | |
| 25437 <param name="adv_opts_selector" value="advanced"/> | |
| 25438 <param name="legacy_traml_id" value="false"/> | |
| 25439 <param name="force" value="false"/> | |
| 25440 <param name="test" value="true"/> | |
| 25441 </conditional> | |
| 25442 <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> | |
| 25443 <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> | |
| 25444 <param name="out_type" value="tsv"/> | |
| 25445 <section name="algorithm"> | |
| 25446 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25447 <param name="override_group_label_check" value="false"/> | |
| 25448 <param name="force_invalid_mods" value="false"/> | |
| 25449 </section> | |
| 25450 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25451 <output name="ctd_out" ftype="xml"> | |
| 25452 <assert_contents> | |
| 25453 <is_valid_xml/> | |
| 25454 </assert_contents> | |
| 25455 </output> | |
| 25456 </test> | |
| 25457 <test expect_num_outputs="2"> | |
| 25458 <conditional name="adv_opts_cond"> | |
| 25459 <param name="adv_opts_selector" value="advanced"/> | |
| 25460 <param name="legacy_traml_id" value="false"/> | |
| 25461 <param name="force" value="false"/> | |
| 25462 <param name="test" value="true"/> | |
| 25463 </conditional> | |
| 25464 <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> | |
| 25465 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/> | |
| 25466 <param name="out_type" value="traml"/> | |
| 25467 <section name="algorithm"> | |
| 25468 <param name="retentionTimeInterpretation" value="iRT"/> | |
| 25469 <param name="override_group_label_check" value="false"/> | |
| 25470 <param name="force_invalid_mods" value="false"/> | |
| 25471 </section> | |
| 25472 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25473 <output name="ctd_out" ftype="xml"> | |
| 25474 <assert_contents> | |
| 25475 <is_valid_xml/> | |
| 25476 </assert_contents> | |
| 25477 </output> | |
| 25478 </test> | |
| 25479 </xml> | |
| 25480 <xml name="autotest_TextExporter"> | |
| 25481 <test expect_num_outputs="2"> | |
| 25482 <conditional name="adv_opts_cond"> | |
| 25483 <param name="adv_opts_selector" value="advanced"/> | |
| 25484 <param name="force" value="false"/> | |
| 25485 <param name="test" value="true"/> | |
| 25486 </conditional> | |
| 25487 <param name="in" value="TextExporter_1_input.featureXML"/> | |
| 25488 <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25489 <param name="separator" value=""/> | |
| 25490 <param name="replacement" value="_"/> | |
| 25491 <param name="quoting" value="none"/> | |
| 25492 <param name="no_ids" value="false"/> | |
| 25493 <section name="feature"> | |
| 25494 <param name="minimal" value="false"/> | |
| 25495 <param name="add_metavalues" value="-1"/> | |
| 25496 </section> | |
| 25497 <section name="id"> | |
| 25498 <param name="proteins_only" value="false"/> | |
| 25499 <param name="peptides_only" value="false"/> | |
| 25500 <param name="protein_groups" value="false"/> | |
| 25501 <param name="first_dim_rt" value="false"/> | |
| 25502 <param name="add_metavalues" value="-1"/> | |
| 25503 <param name="add_hit_metavalues" value="-1"/> | |
| 25504 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25505 </section> | |
| 25506 <section name="consensus"> | |
| 25507 <param name="sorting_method" value="none"/> | |
| 25508 <param name="sort_by_maps" value="false"/> | |
| 25509 <param name="sort_by_size" value="false"/> | |
| 25510 </section> | |
| 25511 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25512 <output name="ctd_out" ftype="xml"> | |
| 25513 <assert_contents> | |
| 25514 <is_valid_xml/> | |
| 25515 </assert_contents> | |
| 25516 </output> | |
| 25517 </test> | |
| 25518 <test expect_num_outputs="5"> | |
| 25519 <conditional name="adv_opts_cond"> | |
| 25520 <param name="adv_opts_selector" value="advanced"/> | |
| 25521 <param name="force" value="false"/> | |
| 25522 <param name="test" value="true"/> | |
| 25523 </conditional> | |
| 25524 <param name="in" value="TextExporter_2_input.consensusXML"/> | |
| 25525 <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25526 <param name="separator" value=""/> | |
| 25527 <param name="replacement" value="_"/> | |
| 25528 <param name="quoting" value="none"/> | |
| 25529 <param name="no_ids" value="true"/> | |
| 25530 <section name="feature"> | |
| 25531 <param name="minimal" value="false"/> | |
| 25532 <param name="add_metavalues" value="-1"/> | |
| 25533 </section> | |
| 25534 <section name="id"> | |
| 25535 <param name="proteins_only" value="false"/> | |
| 25536 <param name="peptides_only" value="false"/> | |
| 25537 <param name="protein_groups" value="false"/> | |
| 25538 <param name="first_dim_rt" value="false"/> | |
| 25539 <param name="add_metavalues" value="-1"/> | |
| 25540 <param name="add_hit_metavalues" value="-1"/> | |
| 25541 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25542 </section> | |
| 25543 <section name="consensus"> | |
| 25544 <param name="sorting_method" value="RT_then_MZ"/> | |
| 25545 <param name="sort_by_maps" value="true"/> | |
| 25546 <param name="sort_by_size" value="true"/> | |
| 25547 </section> | |
| 25548 <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25549 <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25550 <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25551 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> | |
| 25552 <output name="ctd_out" ftype="xml"> | |
| 25553 <assert_contents> | |
| 25554 <is_valid_xml/> | |
| 25555 </assert_contents> | |
| 25556 </output> | |
| 25557 </test> | |
| 25558 <test expect_num_outputs="2"> | |
| 25559 <conditional name="adv_opts_cond"> | |
| 25560 <param name="adv_opts_selector" value="advanced"/> | |
| 25561 <param name="force" value="false"/> | |
| 25562 <param name="test" value="true"/> | |
| 25563 </conditional> | |
| 25564 <param name="in" value="TextExporter_3_input.idXML"/> | |
| 25565 <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25566 <param name="separator" value=""/> | |
| 25567 <param name="replacement" value="_"/> | |
| 25568 <param name="quoting" value="none"/> | |
| 25569 <param name="no_ids" value="false"/> | |
| 25570 <section name="feature"> | |
| 25571 <param name="minimal" value="false"/> | |
| 25572 <param name="add_metavalues" value="-1"/> | |
| 25573 </section> | |
| 25574 <section name="id"> | |
| 25575 <param name="proteins_only" value="false"/> | |
| 25576 <param name="peptides_only" value="false"/> | |
| 25577 <param name="protein_groups" value="false"/> | |
| 25578 <param name="first_dim_rt" value="false"/> | |
| 25579 <param name="add_metavalues" value="-1"/> | |
| 25580 <param name="add_hit_metavalues" value="-1"/> | |
| 25581 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25582 </section> | |
| 25583 <section name="consensus"> | |
| 25584 <param name="sorting_method" value="none"/> | |
| 25585 <param name="sort_by_maps" value="false"/> | |
| 25586 <param name="sort_by_size" value="false"/> | |
| 25587 </section> | |
| 25588 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25589 <output name="ctd_out" ftype="xml"> | |
| 25590 <assert_contents> | |
| 25591 <is_valid_xml/> | |
| 25592 </assert_contents> | |
| 25593 </output> | |
| 25594 </test> | |
| 25595 <test expect_num_outputs="2"> | |
| 25596 <conditional name="adv_opts_cond"> | |
| 25597 <param name="adv_opts_selector" value="advanced"/> | |
| 25598 <param name="force" value="false"/> | |
| 25599 <param name="test" value="true"/> | |
| 25600 </conditional> | |
| 25601 <param name="in" value="TextExporter_3_input.idXML"/> | |
| 25602 <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25603 <param name="separator" value=""/> | |
| 25604 <param name="replacement" value="_"/> | |
| 25605 <param name="quoting" value="none"/> | |
| 25606 <param name="no_ids" value="false"/> | |
| 25607 <section name="feature"> | |
| 25608 <param name="minimal" value="false"/> | |
| 25609 <param name="add_metavalues" value="-1"/> | |
| 25610 </section> | |
| 25611 <section name="id"> | |
| 25612 <param name="proteins_only" value="true"/> | |
| 25613 <param name="peptides_only" value="false"/> | |
| 25614 <param name="protein_groups" value="false"/> | |
| 25615 <param name="first_dim_rt" value="false"/> | |
| 25616 <param name="add_metavalues" value="-1"/> | |
| 25617 <param name="add_hit_metavalues" value="-1"/> | |
| 25618 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25619 </section> | |
| 25620 <section name="consensus"> | |
| 25621 <param name="sorting_method" value="none"/> | |
| 25622 <param name="sort_by_maps" value="false"/> | |
| 25623 <param name="sort_by_size" value="false"/> | |
| 25624 </section> | |
| 25625 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25626 <output name="ctd_out" ftype="xml"> | |
| 25627 <assert_contents> | |
| 25628 <is_valid_xml/> | |
| 25629 </assert_contents> | |
| 25630 </output> | |
| 25631 </test> | |
| 25632 <test expect_num_outputs="2"> | |
| 25633 <conditional name="adv_opts_cond"> | |
| 25634 <param name="adv_opts_selector" value="advanced"/> | |
| 25635 <param name="force" value="false"/> | |
| 25636 <param name="test" value="true"/> | |
| 25637 </conditional> | |
| 25638 <param name="in" value="TextExporter_5_input.idXML"/> | |
| 25639 <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25640 <param name="separator" value=""/> | |
| 25641 <param name="replacement" value="_"/> | |
| 25642 <param name="quoting" value="none"/> | |
| 25643 <param name="no_ids" value="false"/> | |
| 25644 <section name="feature"> | |
| 25645 <param name="minimal" value="false"/> | |
| 25646 <param name="add_metavalues" value="-1"/> | |
| 25647 </section> | |
| 25648 <section name="id"> | |
| 25649 <param name="proteins_only" value="false"/> | |
| 25650 <param name="peptides_only" value="true"/> | |
| 25651 <param name="protein_groups" value="false"/> | |
| 25652 <param name="first_dim_rt" value="true"/> | |
| 25653 <param name="add_metavalues" value="-1"/> | |
| 25654 <param name="add_hit_metavalues" value="-1"/> | |
| 25655 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25656 </section> | |
| 25657 <section name="consensus"> | |
| 25658 <param name="sorting_method" value="none"/> | |
| 25659 <param name="sort_by_maps" value="false"/> | |
| 25660 <param name="sort_by_size" value="false"/> | |
| 25661 </section> | |
| 25662 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25663 <output name="ctd_out" ftype="xml"> | |
| 25664 <assert_contents> | |
| 25665 <is_valid_xml/> | |
| 25666 </assert_contents> | |
| 25667 </output> | |
| 25668 </test> | |
| 25669 <test expect_num_outputs="2"> | |
| 25670 <conditional name="adv_opts_cond"> | |
| 25671 <param name="adv_opts_selector" value="advanced"/> | |
| 25672 <param name="force" value="false"/> | |
| 25673 <param name="test" value="true"/> | |
| 25674 </conditional> | |
| 25675 <param name="in" value="TextExporter_6_input.featureXML"/> | |
| 25676 <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25677 <param name="separator" value=""/> | |
| 25678 <param name="replacement" value="_"/> | |
| 25679 <param name="quoting" value="none"/> | |
| 25680 <param name="no_ids" value="true"/> | |
| 25681 <section name="feature"> | |
| 25682 <param name="minimal" value="false"/> | |
| 25683 <param name="add_metavalues" value="-1"/> | |
| 25684 </section> | |
| 25685 <section name="id"> | |
| 25686 <param name="proteins_only" value="false"/> | |
| 25687 <param name="peptides_only" value="false"/> | |
| 25688 <param name="protein_groups" value="false"/> | |
| 25689 <param name="first_dim_rt" value="false"/> | |
| 25690 <param name="add_metavalues" value="-1"/> | |
| 25691 <param name="add_hit_metavalues" value="-1"/> | |
| 25692 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25693 </section> | |
| 25694 <section name="consensus"> | |
| 25695 <param name="sorting_method" value="none"/> | |
| 25696 <param name="sort_by_maps" value="false"/> | |
| 25697 <param name="sort_by_size" value="false"/> | |
| 25698 </section> | |
| 25699 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25700 <output name="ctd_out" ftype="xml"> | |
| 25701 <assert_contents> | |
| 25702 <is_valid_xml/> | |
| 25703 </assert_contents> | |
| 25704 </output> | |
| 25705 </test> | |
| 25706 <test expect_num_outputs="2"> | |
| 25707 <conditional name="adv_opts_cond"> | |
| 25708 <param name="adv_opts_selector" value="advanced"/> | |
| 25709 <param name="force" value="false"/> | |
| 25710 <param name="test" value="true"/> | |
| 25711 </conditional> | |
| 25712 <param name="in" value="TextExporter_7_input.consensusXML"/> | |
| 25713 <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25714 <param name="separator" value=""/> | |
| 25715 <param name="replacement" value="_"/> | |
| 25716 <param name="quoting" value="none"/> | |
| 25717 <param name="no_ids" value="false"/> | |
| 25718 <section name="feature"> | |
| 25719 <param name="minimal" value="false"/> | |
| 25720 <param name="add_metavalues" value="-1"/> | |
| 25721 </section> | |
| 25722 <section name="id"> | |
| 25723 <param name="proteins_only" value="false"/> | |
| 25724 <param name="peptides_only" value="false"/> | |
| 25725 <param name="protein_groups" value="false"/> | |
| 25726 <param name="first_dim_rt" value="false"/> | |
| 25727 <param name="add_metavalues" value="-1"/> | |
| 25728 <param name="add_hit_metavalues" value="-1"/> | |
| 25729 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25730 </section> | |
| 25731 <section name="consensus"> | |
| 25732 <param name="sorting_method" value="RT_then_MZ"/> | |
| 25733 <param name="sort_by_maps" value="true"/> | |
| 25734 <param name="sort_by_size" value="true"/> | |
| 25735 </section> | |
| 25736 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25737 <output name="ctd_out" ftype="xml"> | |
| 25738 <assert_contents> | |
| 25739 <is_valid_xml/> | |
| 25740 </assert_contents> | |
| 25741 </output> | |
| 25742 </test> | |
| 25743 <test expect_num_outputs="2"> | |
| 25744 <conditional name="adv_opts_cond"> | |
| 25745 <param name="adv_opts_selector" value="advanced"/> | |
| 25746 <param name="force" value="false"/> | |
| 25747 <param name="test" value="true"/> | |
| 25748 </conditional> | |
| 25749 <param name="in" value="TextExporter_1_input.featureXML"/> | |
| 25750 <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25751 <param name="separator" value=""/> | |
| 25752 <param name="replacement" value="_"/> | |
| 25753 <param name="quoting" value="none"/> | |
| 25754 <param name="no_ids" value="true"/> | |
| 25755 <section name="feature"> | |
| 25756 <param name="minimal" value="false"/> | |
| 25757 <param name="add_metavalues" value="-1"/> | |
| 25758 </section> | |
| 25759 <section name="id"> | |
| 25760 <param name="proteins_only" value="false"/> | |
| 25761 <param name="peptides_only" value="false"/> | |
| 25762 <param name="protein_groups" value="false"/> | |
| 25763 <param name="first_dim_rt" value="false"/> | |
| 25764 <param name="add_metavalues" value="-1"/> | |
| 25765 <param name="add_hit_metavalues" value="-1"/> | |
| 25766 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25767 </section> | |
| 25768 <section name="consensus"> | |
| 25769 <param name="sorting_method" value="none"/> | |
| 25770 <param name="sort_by_maps" value="false"/> | |
| 25771 <param name="sort_by_size" value="false"/> | |
| 25772 </section> | |
| 25773 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25774 <output name="ctd_out" ftype="xml"> | |
| 25775 <assert_contents> | |
| 25776 <is_valid_xml/> | |
| 25777 </assert_contents> | |
| 25778 </output> | |
| 25779 </test> | |
| 25780 <test expect_num_outputs="2"> | |
| 25781 <conditional name="adv_opts_cond"> | |
| 25782 <param name="adv_opts_selector" value="advanced"/> | |
| 25783 <param name="force" value="false"/> | |
| 25784 <param name="test" value="true"/> | |
| 25785 </conditional> | |
| 25786 <param name="in" value="TextExporter_9_input.idXML"/> | |
| 25787 <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> | |
| 25788 <param name="separator" value=""/> | |
| 25789 <param name="replacement" value="_"/> | |
| 25790 <param name="quoting" value="none"/> | |
| 25791 <param name="no_ids" value="false"/> | |
| 25792 <section name="feature"> | |
| 25793 <param name="minimal" value="false"/> | |
| 25794 <param name="add_metavalues" value="-1"/> | |
| 25795 </section> | |
| 25796 <section name="id"> | |
| 25797 <param name="proteins_only" value="false"/> | |
| 25798 <param name="peptides_only" value="false"/> | |
| 25799 <param name="protein_groups" value="false"/> | |
| 25800 <param name="first_dim_rt" value="false"/> | |
| 25801 <param name="add_metavalues" value="0"/> | |
| 25802 <param name="add_hit_metavalues" value="0"/> | |
| 25803 <param name="add_protein_hit_metavalues" value="-1"/> | |
| 25804 </section> | |
| 25805 <section name="consensus"> | |
| 25806 <param name="sorting_method" value="none"/> | |
| 25807 <param name="sort_by_maps" value="false"/> | |
| 25808 <param name="sort_by_size" value="false"/> | |
| 25809 </section> | |
| 25810 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 25811 <output name="ctd_out" ftype="xml"> | |
| 25812 <assert_contents> | |
| 25813 <is_valid_xml/> | |
| 25814 </assert_contents> | |
| 25815 </output> | |
| 25816 </test> | |
| 25817 </xml> | |
| 25818 <xml name="autotest_TICCalculator"> | |
| 25819 <test expect_num_outputs="1"> | |
| 25820 <conditional name="adv_opts_cond"> | |
| 25821 <param name="adv_opts_selector" value="advanced"/> | |
| 25822 <param name="force" value="false"/> | |
| 25823 <param name="test" value="true"/> | |
| 25824 </conditional> | |
| 25825 <param name="in" value="MapNormalizer_output.mzML"/> | |
| 25826 <param name="read_method" value="regular"/> | |
| 25827 <param name="loadData" value="true"/> | |
| 25828 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25829 <output name="ctd_out" ftype="xml"> | |
| 25830 <assert_contents> | |
| 25831 <is_valid_xml/> | |
| 25832 </assert_contents> | |
| 25833 </output> | |
| 25834 </test> | |
| 25835 <test expect_num_outputs="1"> | |
| 25836 <conditional name="adv_opts_cond"> | |
| 25837 <param name="adv_opts_selector" value="advanced"/> | |
| 25838 <param name="force" value="false"/> | |
| 25839 <param name="test" value="true"/> | |
| 25840 </conditional> | |
| 25841 <param name="in" value="MapNormalizer_output.mzML"/> | |
| 25842 <param name="read_method" value="streaming"/> | |
| 25843 <param name="loadData" value="true"/> | |
| 25844 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25845 <output name="ctd_out" ftype="xml"> | |
| 25846 <assert_contents> | |
| 25847 <is_valid_xml/> | |
| 25848 </assert_contents> | |
| 25849 </output> | |
| 25850 </test> | |
| 25851 <test expect_num_outputs="1"> | |
| 25852 <conditional name="adv_opts_cond"> | |
| 25853 <param name="adv_opts_selector" value="advanced"/> | |
| 25854 <param name="force" value="false"/> | |
| 25855 <param name="test" value="true"/> | |
| 25856 </conditional> | |
| 25857 <param name="in" value="MapNormalizer_output.mzML"/> | |
| 25858 <param name="read_method" value="streaming"/> | |
| 25859 <param name="loadData" value="false"/> | |
| 25860 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25861 <output name="ctd_out" ftype="xml"> | |
| 25862 <assert_contents> | |
| 25863 <is_valid_xml/> | |
| 25864 </assert_contents> | |
| 25865 </output> | |
| 25866 </test> | |
| 25867 <test expect_num_outputs="1"> | |
| 25868 <conditional name="adv_opts_cond"> | |
| 25869 <param name="adv_opts_selector" value="advanced"/> | |
| 25870 <param name="force" value="false"/> | |
| 25871 <param name="test" value="true"/> | |
| 25872 </conditional> | |
| 25873 <param name="in" value="MapNormalizer_output.mzML"/> | |
| 25874 <param name="read_method" value="indexed"/> | |
| 25875 <param name="loadData" value="true"/> | |
| 25876 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25877 <output name="ctd_out" ftype="xml"> | |
| 25878 <assert_contents> | |
| 25879 <is_valid_xml/> | |
| 25880 </assert_contents> | |
| 25881 </output> | |
| 25882 </test> | |
| 25883 <test expect_num_outputs="1"> | |
| 25884 <conditional name="adv_opts_cond"> | |
| 25885 <param name="adv_opts_selector" value="advanced"/> | |
| 25886 <param name="force" value="false"/> | |
| 25887 <param name="test" value="true"/> | |
| 25888 </conditional> | |
| 25889 <param name="in" value="MapNormalizer_output.mzML"/> | |
| 25890 <param name="read_method" value="indexed_parallel"/> | |
| 25891 <param name="loadData" value="true"/> | |
| 25892 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25893 <output name="ctd_out" ftype="xml"> | |
| 25894 <assert_contents> | |
| 25895 <is_valid_xml/> | |
| 25896 </assert_contents> | |
| 25897 </output> | |
| 25898 </test> | |
| 25899 </xml> | |
| 25900 <xml name="autotest_TOFCalibration"> | |
| 25901 <test expect_num_outputs="2"> | |
| 25902 <conditional name="adv_opts_cond"> | |
| 25903 <param name="adv_opts_selector" value="advanced"/> | |
| 25904 <param name="force" value="false"/> | |
| 25905 <param name="test" value="true"/> | |
| 25906 </conditional> | |
| 25907 <param name="in" value="TOFCalibration_1_input.mzML"/> | |
| 25908 <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 25909 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> | |
| 25910 <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/> | |
| 25911 <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/> | |
| 25912 <param name="peak_data" value="false"/> | |
| 25913 <section name="algorithm"> | |
| 25914 <section name="PeakPicker"> | |
| 25915 <param name="signal_to_noise" value="3.0"/> | |
| 25916 <param name="centroid_percentage" value="0.6"/> | |
| 25917 <param name="peak_width" value="0.15"/> | |
| 25918 <param name="estimate_peak_width" value="false"/> | |
| 25919 <param name="fwhm_lower_bound_factor" value="0.7"/> | |
| 25920 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
| 25921 <section name="optimization"> | |
| 25922 <param name="iterations" value="400"/> | |
| 25923 <section name="penalties"> | |
| 25924 <param name="position" value="0.0"/> | |
| 25925 <param name="left_width" value="1.0"/> | |
| 25926 <param name="right_width" value="1.0"/> | |
| 25927 <param name="height" value="1.0"/> | |
| 25928 </section> | |
| 25929 <section name="2d"> | |
| 25930 <param name="tolerance_mz" value="2.2"/> | |
| 25931 <param name="max_peak_distance" value="1.2"/> | |
| 25932 </section> | |
| 25933 </section> | |
| 25934 <section name="thresholds"> | |
| 25935 <param name="peak_bound" value="400.0"/> | |
| 25936 <param name="peak_bound_ms2_level" value="10.0"/> | |
| 25937 <param name="correlation" value="0.0"/> | |
| 25938 <param name="noise_level" value="0.1"/> | |
| 25939 <param name="search_radius" value="3"/> | |
| 25940 </section> | |
| 25941 <section name="wavelet_transform"> | |
| 25942 <param name="spacing" value="0.001"/> | |
| 25943 </section> | |
| 25944 <section name="deconvolution"> | |
| 25945 <param name="deconvolution" value="false"/> | |
| 25946 <param name="asym_threshold" value="0.3"/> | |
| 25947 <param name="left_width" value="2.0"/> | |
| 25948 <param name="right_width" value="2.0"/> | |
| 25949 <param name="scaling" value="0.12"/> | |
| 25950 <section name="fitting"> | |
| 25951 <param name="fwhm_threshold" value="0.7"/> | |
| 25952 <param name="eps_abs" value="9.999999747378752e-06"/> | |
| 25953 <param name="eps_rel" value="9.999999747378752e-06"/> | |
| 25954 <param name="max_iteration" value="10"/> | |
| 25955 <section name="penalties"> | |
| 25956 <param name="position" value="0.0"/> | |
| 25957 <param name="height" value="1.0"/> | |
| 25958 <param name="left_width" value="0.0"/> | |
| 25959 <param name="right_width" value="0.0"/> | |
| 25960 </section> | |
| 25961 </section> | |
| 25962 </section> | |
| 25963 <section name="SignalToNoiseEstimationParameter"> | |
| 25964 <param name="max_intensity" value="-1"/> | |
| 25965 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 25966 <param name="auto_max_percentile" value="95"/> | |
| 25967 <param name="auto_mode" value="0"/> | |
| 25968 <param name="win_len" value="200.0"/> | |
| 25969 <param name="bin_count" value="30"/> | |
| 25970 <param name="stdev_mp" value="3.0"/> | |
| 25971 <param name="min_required_elements" value="10"/> | |
| 25972 <param name="noise_for_empty_window" value="1e+20"/> | |
| 25973 </section> | |
| 25974 </section> | |
| 25975 </section> | |
| 25976 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 25977 <output name="ctd_out" ftype="xml"> | |
| 25978 <assert_contents> | |
| 25979 <is_valid_xml/> | |
| 25980 </assert_contents> | |
| 25981 </output> | |
| 25982 </test> | |
| 25983 <test expect_num_outputs="2"> | |
| 25984 <conditional name="adv_opts_cond"> | |
| 25985 <param name="adv_opts_selector" value="advanced"/> | |
| 25986 <param name="force" value="false"/> | |
| 25987 <param name="test" value="true"/> | |
| 25988 </conditional> | |
| 25989 <param name="in" value="TOFCalibration_2_input.mzML"/> | |
| 25990 <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
| 25991 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> | |
| 25992 <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/> | |
| 25993 <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/> | |
| 25994 <param name="peak_data" value="true"/> | |
| 25995 <section name="algorithm"> | |
| 25996 <section name="PeakPicker"> | |
| 25997 <param name="signal_to_noise" value="3.0"/> | |
| 25998 <param name="centroid_percentage" value="0.6"/> | |
| 25999 <param name="peak_width" value="0.15"/> | |
| 26000 <param name="estimate_peak_width" value="false"/> | |
| 26001 <param name="fwhm_lower_bound_factor" value="0.7"/> | |
| 26002 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
| 26003 <section name="optimization"> | |
| 26004 <param name="iterations" value="400"/> | |
| 26005 <section name="penalties"> | |
| 26006 <param name="position" value="0.0"/> | |
| 26007 <param name="left_width" value="1.0"/> | |
| 26008 <param name="right_width" value="1.0"/> | |
| 26009 <param name="height" value="1.0"/> | |
| 26010 </section> | |
| 26011 <section name="2d"> | |
| 26012 <param name="tolerance_mz" value="2.2"/> | |
| 26013 <param name="max_peak_distance" value="1.2"/> | |
| 26014 </section> | |
| 26015 </section> | |
| 26016 <section name="thresholds"> | |
| 26017 <param name="peak_bound" value="400.0"/> | |
| 26018 <param name="peak_bound_ms2_level" value="10.0"/> | |
| 26019 <param name="correlation" value="0.0"/> | |
| 26020 <param name="noise_level" value="0.1"/> | |
| 26021 <param name="search_radius" value="3"/> | |
| 26022 </section> | |
| 26023 <section name="wavelet_transform"> | |
| 26024 <param name="spacing" value="0.001"/> | |
| 26025 </section> | |
| 26026 <section name="deconvolution"> | |
| 26027 <param name="deconvolution" value="false"/> | |
| 26028 <param name="asym_threshold" value="0.3"/> | |
| 26029 <param name="left_width" value="2.0"/> | |
| 26030 <param name="right_width" value="2.0"/> | |
| 26031 <param name="scaling" value="0.12"/> | |
| 26032 <section name="fitting"> | |
| 26033 <param name="fwhm_threshold" value="0.7"/> | |
| 26034 <param name="eps_abs" value="9.999999747378752e-06"/> | |
| 26035 <param name="eps_rel" value="9.999999747378752e-06"/> | |
| 26036 <param name="max_iteration" value="10"/> | |
| 26037 <section name="penalties"> | |
| 26038 <param name="position" value="0.0"/> | |
| 26039 <param name="height" value="1.0"/> | |
| 26040 <param name="left_width" value="0.0"/> | |
| 26041 <param name="right_width" value="0.0"/> | |
| 26042 </section> | |
| 26043 </section> | |
| 26044 </section> | |
| 26045 <section name="SignalToNoiseEstimationParameter"> | |
| 26046 <param name="max_intensity" value="-1"/> | |
| 26047 <param name="auto_max_stdev_factor" value="3.0"/> | |
| 26048 <param name="auto_max_percentile" value="95"/> | |
| 26049 <param name="auto_mode" value="0"/> | |
| 26050 <param name="win_len" value="200.0"/> | |
| 26051 <param name="bin_count" value="30"/> | |
| 26052 <param name="stdev_mp" value="3.0"/> | |
| 26053 <param name="min_required_elements" value="10"/> | |
| 26054 <param name="noise_for_empty_window" value="1e+20"/> | |
| 26055 </section> | |
| 26056 </section> | |
| 26057 </section> | |
| 26058 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 26059 <output name="ctd_out" ftype="xml"> | |
| 26060 <assert_contents> | |
| 26061 <is_valid_xml/> | |
| 26062 </assert_contents> | |
| 26063 </output> | |
| 26064 </test> | |
| 26065 </xml> | |
| 26066 <xml name="autotest_TransformationEvaluation"> | |
| 26067 </xml> | |
| 26068 <xml name="autotest_XFDR"> | |
| 26069 <test expect_num_outputs="4"> | |
| 26070 <conditional name="adv_opts_cond"> | |
| 26071 <param name="adv_opts_selector" value="advanced"/> | |
| 26072 <param name="force" value="false"/> | |
| 26073 <param name="test" value="true"/> | |
| 26074 </conditional> | |
| 26075 <param name="in" value="XFDR_test_in1.idXML"/> | |
| 26076 <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26077 <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 26078 <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 26079 <param name="decoy_string" value="DECOY_"/> | |
| 26080 <param name="minborder" value="-50.0"/> | |
| 26081 <param name="maxborder" value="50.0"/> | |
| 26082 <param name="mindeltas" value="0.0"/> | |
| 26083 <param name="minionsmatched" value="0"/> | |
| 26084 <param name="uniquexl" value="false"/> | |
| 26085 <param name="no_qvalues" value="false"/> | |
| 26086 <param name="minscore" value="-10.0"/> | |
| 26087 <param name="binsize" value="0.1"/> | |
| 26088 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> | |
| 26089 <output name="ctd_out" ftype="xml"> | |
| 26090 <assert_contents> | |
| 26091 <is_valid_xml/> | |
| 26092 </assert_contents> | |
| 26093 </output> | |
| 26094 </test> | |
| 26095 <test expect_num_outputs="4"> | |
| 26096 <conditional name="adv_opts_cond"> | |
| 26097 <param name="adv_opts_selector" value="advanced"/> | |
| 26098 <param name="force" value="false"/> | |
| 26099 <param name="test" value="true"/> | |
| 26100 </conditional> | |
| 26101 <param name="in" value="XFDR_test_in1.idXML"/> | |
| 26102 <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26103 <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 26104 <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 26105 <param name="decoy_string" value="DECOY_"/> | |
| 26106 <param name="minborder" value="-50.0"/> | |
| 26107 <param name="maxborder" value="50.0"/> | |
| 26108 <param name="mindeltas" value="0.0"/> | |
| 26109 <param name="minionsmatched" value="0"/> | |
| 26110 <param name="uniquexl" value="true"/> | |
| 26111 <param name="no_qvalues" value="true"/> | |
| 26112 <param name="minscore" value="-10.0"/> | |
| 26113 <param name="binsize" value="0.1"/> | |
| 26114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> | |
| 26115 <output name="ctd_out" ftype="xml"> | |
| 26116 <assert_contents> | |
| 26117 <is_valid_xml/> | |
| 26118 </assert_contents> | |
| 26119 </output> | |
| 26120 </test> | |
| 26121 <test expect_num_outputs="4"> | |
| 26122 <conditional name="adv_opts_cond"> | |
| 26123 <param name="adv_opts_selector" value="advanced"/> | |
| 26124 <param name="force" value="false"/> | |
| 26125 <param name="test" value="true"/> | |
| 26126 </conditional> | |
| 26127 <param name="in" value="XFDR_test_in2.xquest.xml"/> | |
| 26128 <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26129 <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 26130 <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 26131 <param name="decoy_string" value="DECOY_"/> | |
| 26132 <param name="minborder" value="-50.0"/> | |
| 26133 <param name="maxborder" value="50.0"/> | |
| 26134 <param name="mindeltas" value="0.0"/> | |
| 26135 <param name="minionsmatched" value="0"/> | |
| 26136 <param name="uniquexl" value="false"/> | |
| 26137 <param name="no_qvalues" value="false"/> | |
| 26138 <param name="minscore" value="0.0"/> | |
| 26139 <param name="binsize" value="0.1"/> | |
| 26140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> | |
| 26141 <output name="ctd_out" ftype="xml"> | |
| 26142 <assert_contents> | |
| 26143 <is_valid_xml/> | |
| 26144 </assert_contents> | |
| 26145 </output> | |
| 26146 </test> | |
| 26147 <test expect_num_outputs="4"> | |
| 26148 <conditional name="adv_opts_cond"> | |
| 26149 <param name="adv_opts_selector" value="advanced"/> | |
| 26150 <param name="force" value="false"/> | |
| 26151 <param name="test" value="true"/> | |
| 26152 </conditional> | |
| 26153 <param name="in" value="XFDR_test_in2.xquest.xml"/> | |
| 26154 <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26155 <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 26156 <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 26157 <param name="decoy_string" value="DECOY_"/> | |
| 26158 <param name="minborder" value="-3.0"/> | |
| 26159 <param name="maxborder" value="3.0"/> | |
| 26160 <param name="mindeltas" value="0.0"/> | |
| 26161 <param name="minionsmatched" value="0"/> | |
| 26162 <param name="uniquexl" value="false"/> | |
| 26163 <param name="no_qvalues" value="false"/> | |
| 26164 <param name="minscore" value="-10.0"/> | |
| 26165 <param name="binsize" value="0.1"/> | |
| 26166 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> | |
| 26167 <output name="ctd_out" ftype="xml"> | |
| 26168 <assert_contents> | |
| 26169 <is_valid_xml/> | |
| 26170 </assert_contents> | |
| 26171 </output> | |
| 26172 </test> | |
| 26173 <test expect_num_outputs="4"> | |
| 26174 <conditional name="adv_opts_cond"> | |
| 26175 <param name="adv_opts_selector" value="advanced"/> | |
| 26176 <param name="force" value="false"/> | |
| 26177 <param name="test" value="true"/> | |
| 26178 </conditional> | |
| 26179 <param name="in" value="XFDR_test_in3.xquest.xml"/> | |
| 26180 <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26181 <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 26182 <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 26183 <param name="decoy_string" value="DECOY_"/> | |
| 26184 <param name="minborder" value="-3.0"/> | |
| 26185 <param name="maxborder" value="3.0"/> | |
| 26186 <param name="mindeltas" value="0.0"/> | |
| 26187 <param name="minionsmatched" value="0"/> | |
| 26188 <param name="uniquexl" value="false"/> | |
| 26189 <param name="no_qvalues" value="false"/> | |
| 26190 <param name="minscore" value="-10.0"/> | |
| 26191 <param name="binsize" value="0.1"/> | |
| 26192 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> | |
| 26193 <output name="ctd_out" ftype="xml"> | |
| 26194 <assert_contents> | |
| 26195 <is_valid_xml/> | |
| 26196 </assert_contents> | |
| 26197 </output> | |
| 26198 </test> | |
| 26199 <test expect_num_outputs="2"> | |
| 26200 <conditional name="adv_opts_cond"> | |
| 26201 <param name="adv_opts_selector" value="advanced"/> | |
| 26202 <param name="force" value="false"/> | |
| 26203 <param name="test" value="true"/> | |
| 26204 </conditional> | |
| 26205 <param name="in" value="XFDR_test_in4.idXML"/> | |
| 26206 <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26207 <param name="decoy_string" value="DECOY_"/> | |
| 26208 <param name="minborder" value="-50.0"/> | |
| 26209 <param name="maxborder" value="50.0"/> | |
| 26210 <param name="mindeltas" value="0.0"/> | |
| 26211 <param name="minionsmatched" value="0"/> | |
| 26212 <param name="uniquexl" value="false"/> | |
| 26213 <param name="no_qvalues" value="false"/> | |
| 26214 <param name="minscore" value="-10.0"/> | |
| 26215 <param name="binsize" value="0.1"/> | |
| 26216 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> | |
| 26217 <output name="ctd_out" ftype="xml"> | |
| 26218 <assert_contents> | |
| 26219 <is_valid_xml/> | |
| 26220 </assert_contents> | |
| 26221 </output> | |
| 26222 </test> | |
| 26223 <test expect_num_outputs="4"> | |
| 26224 <conditional name="adv_opts_cond"> | |
| 26225 <param name="adv_opts_selector" value="advanced"/> | |
| 26226 <param name="force" value="false"/> | |
| 26227 <param name="test" value="true"/> | |
| 26228 </conditional> | |
| 26229 <param name="in" value="XFDR_test_in2.xquest.xml"/> | |
| 26230 <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26231 <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> | |
| 26232 <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> | |
| 26233 <param name="decoy_string" value="DECOY_"/> | |
| 26234 <param name="minborder" value="-50.0"/> | |
| 26235 <param name="maxborder" value="50.0"/> | |
| 26236 <param name="mindeltas" value="0.0"/> | |
| 26237 <param name="minionsmatched" value="0"/> | |
| 26238 <param name="uniquexl" value="true"/> | |
| 26239 <param name="no_qvalues" value="false"/> | |
| 26240 <param name="minscore" value="0.0"/> | |
| 26241 <param name="binsize" value="0.1"/> | |
| 26242 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> | |
| 26243 <output name="ctd_out" ftype="xml"> | |
| 26244 <assert_contents> | |
| 26245 <is_valid_xml/> | |
| 26246 </assert_contents> | |
| 26247 </output> | |
| 26248 </test> | |
| 26249 </xml> | |
| 26250 <xml name="autotest_XMLValidator"> | |
| 26251 </xml> | |
| 26252 <xml name="autotest_XTandemAdapter"> | |
| 26253 <test expect_num_outputs="2"> | |
| 26254 <conditional name="adv_opts_cond"> | |
| 26255 <param name="adv_opts_selector" value="advanced"/> | |
| 26256 <param name="force" value="false"/> | |
| 26257 <param name="test" value="true"/> | |
| 26258 </conditional> | |
| 26259 <param name="in" value="spectra.mzML"/> | |
| 26260 <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26261 <param name="database" value="proteins.fasta"/> | |
| 26262 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> | |
| 26263 <param name="ignore_adapter_param" value="false"/> | |
| 26264 <param name="precursor_mass_tolerance" value="5.0"/> | |
| 26265 <param name="fragment_mass_tolerance" value="0.3"/> | |
| 26266 <param name="precursor_error_units" value="ppm"/> | |
| 26267 <param name="fragment_error_units" value="Da"/> | |
| 26268 <param name="max_precursor_charge" value="0"/> | |
| 26269 <param name="no_isotope_error" value="false"/> | |
| 26270 <param name="fixed_modifications" value=""/> | |
| 26271 <param name="variable_modifications" value="Oxidation (M)"/> | |
| 26272 <param name="minimum_fragment_mz" value="150.0"/> | |
| 26273 <param name="enzyme" value="Trypsin"/> | |
| 26274 <param name="missed_cleavages" value="1"/> | |
| 26275 <param name="semi_cleavage" value="false"/> | |
| 26276 <param name="output_results" value="all"/> | |
| 26277 <param name="max_valid_expect" value="0.1"/> | |
| 26278 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 26279 <output name="ctd_out" ftype="xml"> | |
| 26280 <assert_contents> | |
| 26281 <is_valid_xml/> | |
| 26282 </assert_contents> | |
| 26283 </output> | |
| 26284 </test> | |
| 26285 <test expect_num_outputs="2"> | |
| 26286 <conditional name="adv_opts_cond"> | |
| 26287 <param name="adv_opts_selector" value="advanced"/> | |
| 26288 <param name="force" value="false"/> | |
| 26289 <param name="test" value="true"/> | |
| 26290 </conditional> | |
| 26291 <param name="in" value="spectra.mzML"/> | |
| 26292 <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 26293 <param name="database" value="proteins.fasta"/> | |
| 26294 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> | |
| 26295 <param name="ignore_adapter_param" value="false"/> | |
| 26296 <param name="precursor_mass_tolerance" value="5.0"/> | |
| 26297 <param name="fragment_mass_tolerance" value="0.3"/> | |
| 26298 <param name="precursor_error_units" value="ppm"/> | |
| 26299 <param name="fragment_error_units" value="Da"/> | |
| 26300 <param name="max_precursor_charge" value="0"/> | |
| 26301 <param name="no_isotope_error" value="false"/> | |
| 26302 <param name="fixed_modifications" value=""/> | |
| 26303 <param name="variable_modifications" value="Oxidation (M)"/> | |
| 26304 <param name="minimum_fragment_mz" value="150.0"/> | |
| 26305 <param name="enzyme" value="Trypsin"/> | |
| 26306 <param name="missed_cleavages" value="1"/> | |
| 26307 <param name="semi_cleavage" value="false"/> | |
| 26308 <param name="output_results" value="valid"/> | |
| 26309 <param name="max_valid_expect" value="1e-14"/> | |
| 26310 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 26311 <output name="ctd_out" ftype="xml"> | |
| 26312 <assert_contents> | |
| 26313 <is_valid_xml/> | |
| 26314 </assert_contents> | |
| 26315 </output> | |
| 26316 </test> | |
| 26317 </xml> | |
| 26318 <xml name="autotest_IDDecoyProbability"/><xml name="autotest_PTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_Digestor"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_InspectAdapter"/><xml name="autotest_DigestorMotif"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/></macros> |