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comparison macros_autotest.xml @ 4:f7195ee7e18d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:16 +0000
parents 56d5a3b741f6
children
comparison
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3:56d5a3b741f6 4:f7195ee7e18d
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="auto_charge" value="false"/>
162 <param name="ion_tree" value="false"/>
163 <param name="no_recalibration" value="false"/>
164 <param name="most_intense_ms2" value="false"/>
165 </section>
166 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
167 <output name="ctd_out" ftype="xml">
168 <assert_contents>
169 <is_valid_xml/>
170 </assert_contents>
171 </output>
172 </test>
173 <test expect_num_outputs="2">
174 <conditional name="adv_opts_cond">
175 <param name="adv_opts_selector" value="advanced"/>
176 <param name="precursor_recalibration_window" value="0.1"/>
177 <param name="precursor_recalibration_window_unit" value="Da"/>
178 <param name="min_fragment_mz" value="0.0"/>
179 <param name="max_fragment_mz" value="2000.0"/>
180 <param name="force" value="false"/>
181 <param name="test" value="true"/>
182 </conditional>
183 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
184 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
185 <param name="out_type" value="tsv"/>
186 <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
187 <param name="fragment_annotation" value="none"/>
188 <param name="method" value="highest_intensity"/>
189 <param name="use_exact_mass" value="false"/>
190 <param name="exclude_ms2_precursor" value="false"/>
191 <param name="precursor_mz_distance" value="0.0001"/>
192 <param name="precursor_rt_tolerance" value="5.0"/>
193 <param name="use_known_unknowns" value="false"/>
194 <param name="min_transitions" value="1"/>
195 <param name="max_transitions" value="3"/>
196 <param name="cosine_similarity_threshold" value="0.98"/>
197 <param name="transition_threshold" value="5.0"/>
198 <param name="out_workspace_directory" value=""/>
199 <section name="deisotoping">
200 <param name="use_deisotoper" value="false"/>
201 <param name="fragment_tolerance" value="1.0"/>
202 <param name="fragment_unit" value="ppm"/>
203 <param name="min_charge" value="1"/>
204 <param name="max_charge" value="1"/>
205 <param name="min_isopeaks" value="2"/>
206 <param name="max_isopeaks" value="3"/>
207 <param name="keep_only_deisotoped" value="false"/>
208 <param name="annotate_charge" value="false"/>
209 </section>
210 <section name="preprocessing">
211 <param name="filter_by_num_masstraces" value="1"/>
212 <param name="precursor_mz_tolerance" value="0.005"/>
213 <param name="precursor_mz_tolerance_unit" value="Da"/>
214 <param name="precursor_rt_tolerance" value="5"/>
215 <param name="isotope_pattern_iterations" value="3"/>
216 <param name="feature_only" value="false"/>
217 <param name="no_masstrace_info_isotope_pattern" value="false"/>
218 </section>
219 <section name="sirius">
220 <param name="profile" value="qtof"/>
221 <param name="candidates" value="5"/>
222 <param name="database" value="all"/>
223 <param name="noise" value="0"/>
224 <param name="ppm_max" value="10"/>
225 <param name="isotope" value="both"/>
226 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
227 <param name="compound_timeout" value="10"/>
228 <param name="tree_timeout" value="0"/>
229 <param name="top_n_hits" value="10"/>
230 <param name="auto_charge" value="false"/>
231 <param name="ion_tree" value="false"/>
232 <param name="no_recalibration" value="false"/>
233 <param name="most_intense_ms2" value="false"/>
234 </section>
235 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
236 <output name="ctd_out" ftype="xml">
237 <assert_contents>
238 <is_valid_xml/>
239 </assert_contents>
240 </output>
241 </test>
242 <test expect_num_outputs="2">
243 <conditional name="adv_opts_cond">
244 <param name="adv_opts_selector" value="advanced"/>
245 <param name="precursor_recalibration_window" value="0.1"/>
246 <param name="precursor_recalibration_window_unit" value="Da"/>
247 <param name="min_fragment_mz" value="0.0"/>
248 <param name="max_fragment_mz" value="2000.0"/>
249 <param name="force" value="false"/>
250 <param name="test" value="true"/>
251 </conditional>
252 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
253 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
254 <param name="out_type" value="tsv"/>
255 <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
256 <param name="fragment_annotation" value="none"/>
257 <param name="method" value="consensus_spectrum"/>
258 <param name="use_exact_mass" value="false"/>
259 <param name="exclude_ms2_precursor" value="false"/>
260 <param name="precursor_mz_distance" value="0.0001"/>
261 <param name="precursor_rt_tolerance" value="5.0"/>
262 <param name="use_known_unknowns" value="false"/>
263 <param name="min_transitions" value="1"/>
264 <param name="max_transitions" value="3"/>
265 <param name="cosine_similarity_threshold" value="0.98"/>
266 <param name="transition_threshold" value="5.0"/>
267 <param name="out_workspace_directory" value=""/>
268 <section name="deisotoping">
269 <param name="use_deisotoper" value="false"/>
270 <param name="fragment_tolerance" value="1.0"/>
271 <param name="fragment_unit" value="ppm"/>
272 <param name="min_charge" value="1"/>
273 <param name="max_charge" value="1"/>
274 <param name="min_isopeaks" value="2"/>
275 <param name="max_isopeaks" value="3"/>
276 <param name="keep_only_deisotoped" value="false"/>
277 <param name="annotate_charge" value="false"/>
278 </section>
279 <section name="preprocessing">
280 <param name="filter_by_num_masstraces" value="1"/>
281 <param name="precursor_mz_tolerance" value="0.005"/>
282 <param name="precursor_mz_tolerance_unit" value="Da"/>
283 <param name="precursor_rt_tolerance" value="5"/>
284 <param name="isotope_pattern_iterations" value="3"/>
285 <param name="feature_only" value="false"/>
286 <param name="no_masstrace_info_isotope_pattern" value="false"/>
287 </section>
288 <section name="sirius">
289 <param name="profile" value="qtof"/>
290 <param name="candidates" value="5"/>
291 <param name="database" value="all"/>
292 <param name="noise" value="0"/>
293 <param name="ppm_max" value="10"/>
294 <param name="isotope" value="both"/>
295 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
296 <param name="compound_timeout" value="10"/>
297 <param name="tree_timeout" value="0"/>
298 <param name="top_n_hits" value="10"/>
299 <param name="auto_charge" value="false"/>
300 <param name="ion_tree" value="false"/>
301 <param name="no_recalibration" value="false"/>
302 <param name="most_intense_ms2" value="false"/>
303 </section>
304 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
305 <output name="ctd_out" ftype="xml">
306 <assert_contents>
307 <is_valid_xml/>
308 </assert_contents>
309 </output>
310 </test>
311 <test expect_num_outputs="2">
312 <conditional name="adv_opts_cond">
313 <param name="adv_opts_selector" value="advanced"/>
314 <param name="precursor_recalibration_window" value="0.1"/>
315 <param name="precursor_recalibration_window_unit" value="Da"/>
316 <param name="min_fragment_mz" value="0.0"/>
317 <param name="max_fragment_mz" value="2000.0"/>
318 <param name="force" value="false"/>
319 <param name="test" value="true"/>
320 </conditional>
321 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
322 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
323 <param name="out_type" value="tsv"/>
324 <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
325 <param name="fragment_annotation" value="none"/>
326 <param name="method" value="consensus_spectrum"/>
327 <param name="use_exact_mass" value="false"/>
328 <param name="exclude_ms2_precursor" value="false"/>
329 <param name="precursor_mz_distance" value="0.0001"/>
330 <param name="precursor_rt_tolerance" value="5.0"/>
331 <param name="use_known_unknowns" value="false"/>
332 <param name="min_transitions" value="1"/>
333 <param name="max_transitions" value="3"/>
334 <param name="cosine_similarity_threshold" value="0.98"/>
335 <param name="transition_threshold" value="5.0"/>
336 <param name="out_workspace_directory" value=""/>
337 <section name="deisotoping">
338 <param name="use_deisotoper" value="false"/>
339 <param name="fragment_tolerance" value="1.0"/>
340 <param name="fragment_unit" value="ppm"/>
341 <param name="min_charge" value="1"/>
342 <param name="max_charge" value="1"/>
343 <param name="min_isopeaks" value="2"/>
344 <param name="max_isopeaks" value="3"/>
345 <param name="keep_only_deisotoped" value="false"/>
346 <param name="annotate_charge" value="false"/>
347 </section>
348 <section name="preprocessing">
349 <param name="filter_by_num_masstraces" value="1"/>
350 <param name="precursor_mz_tolerance" value="0.005"/>
351 <param name="precursor_mz_tolerance_unit" value="Da"/>
352 <param name="precursor_rt_tolerance" value="5"/>
353 <param name="isotope_pattern_iterations" value="3"/>
354 <param name="feature_only" value="false"/>
355 <param name="no_masstrace_info_isotope_pattern" value="false"/>
356 </section>
357 <section name="sirius">
358 <param name="profile" value="qtof"/>
359 <param name="candidates" value="5"/>
360 <param name="database" value="all"/>
361 <param name="noise" value="0"/>
362 <param name="ppm_max" value="10"/>
363 <param name="isotope" value="both"/>
364 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
365 <param name="compound_timeout" value="10"/>
366 <param name="tree_timeout" value="0"/>
367 <param name="top_n_hits" value="10"/>
368 <param name="auto_charge" value="false"/>
369 <param name="ion_tree" value="false"/>
370 <param name="no_recalibration" value="false"/>
371 <param name="most_intense_ms2" value="false"/>
372 </section>
373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
374 <output name="ctd_out" ftype="xml">
375 <assert_contents>
376 <is_valid_xml/>
377 </assert_contents>
378 </output>
379 </test>
380 <test expect_num_outputs="2">
381 <conditional name="adv_opts_cond">
382 <param name="adv_opts_selector" value="advanced"/>
383 <param name="precursor_recalibration_window" value="0.1"/>
384 <param name="precursor_recalibration_window_unit" value="Da"/>
385 <param name="min_fragment_mz" value="0.0"/>
386 <param name="max_fragment_mz" value="2000.0"/>
387 <param name="force" value="false"/>
388 <param name="test" value="true"/>
389 </conditional>
390 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
391 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
392 <param name="out_type" value="tsv"/>
393 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
394 <param name="fragment_annotation" value="none"/>
395 <param name="method" value="consensus_spectrum"/>
396 <param name="use_exact_mass" value="false"/>
397 <param name="exclude_ms2_precursor" value="false"/>
398 <param name="precursor_mz_distance" value="0.0001"/>
399 <param name="precursor_rt_tolerance" value="5.0"/>
400 <param name="use_known_unknowns" value="true"/>
401 <param name="min_transitions" value="1"/>
402 <param name="max_transitions" value="3"/>
403 <param name="cosine_similarity_threshold" value="0.98"/>
404 <param name="transition_threshold" value="5.0"/>
405 <param name="out_workspace_directory" value=""/>
406 <section name="deisotoping">
407 <param name="use_deisotoper" value="false"/>
408 <param name="fragment_tolerance" value="1.0"/>
409 <param name="fragment_unit" value="ppm"/>
410 <param name="min_charge" value="1"/>
411 <param name="max_charge" value="1"/>
412 <param name="min_isopeaks" value="2"/>
413 <param name="max_isopeaks" value="3"/>
414 <param name="keep_only_deisotoped" value="false"/>
415 <param name="annotate_charge" value="false"/>
416 </section>
417 <section name="preprocessing">
418 <param name="filter_by_num_masstraces" value="1"/>
419 <param name="precursor_mz_tolerance" value="0.005"/>
420 <param name="precursor_mz_tolerance_unit" value="Da"/>
421 <param name="precursor_rt_tolerance" value="5"/>
422 <param name="isotope_pattern_iterations" value="3"/>
423 <param name="feature_only" value="false"/>
424 <param name="no_masstrace_info_isotope_pattern" value="false"/>
425 </section>
426 <section name="sirius">
427 <param name="profile" value="qtof"/>
428 <param name="candidates" value="5"/>
429 <param name="database" value="all"/>
430 <param name="noise" value="0"/>
431 <param name="ppm_max" value="10"/>
432 <param name="isotope" value="both"/>
433 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
434 <param name="compound_timeout" value="10"/>
435 <param name="tree_timeout" value="0"/>
436 <param name="top_n_hits" value="10"/>
437 <param name="auto_charge" value="false"/>
438 <param name="ion_tree" value="false"/>
439 <param name="no_recalibration" value="false"/>
440 <param name="most_intense_ms2" value="false"/>
441 </section>
442 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
443 <output name="ctd_out" ftype="xml">
444 <assert_contents>
445 <is_valid_xml/>
446 </assert_contents>
447 </output>
448 </test>
449 <test expect_num_outputs="2">
450 <conditional name="adv_opts_cond">
451 <param name="adv_opts_selector" value="advanced"/>
452 <param name="precursor_recalibration_window" value="0.1"/>
453 <param name="precursor_recalibration_window_unit" value="Da"/>
454 <param name="min_fragment_mz" value="0.0"/>
455 <param name="max_fragment_mz" value="2000.0"/>
456 <param name="force" value="false"/>
457 <param name="test" value="true"/>
458 </conditional>
459 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
460 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
461 <param name="out_type" value="tsv"/>
462 <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
463 <param name="fragment_annotation" value="sirius"/>
464 <param name="method" value="highest_intensity"/>
465 <param name="use_exact_mass" value="true"/>
466 <param name="exclude_ms2_precursor" value="false"/>
467 <param name="precursor_mz_distance" value="0.0001"/>
468 <param name="precursor_rt_tolerance" value="5.0"/>
469 <param name="use_known_unknowns" value="false"/>
470 <param name="min_transitions" value="2"/>
471 <param name="max_transitions" value="3"/>
472 <param name="cosine_similarity_threshold" value="0.98"/>
473 <param name="transition_threshold" value="3.0"/>
474 <param name="out_workspace_directory" value=""/>
475 <section name="deisotoping">
476 <param name="use_deisotoper" value="false"/>
477 <param name="fragment_tolerance" value="1.0"/>
478 <param name="fragment_unit" value="ppm"/>
479 <param name="min_charge" value="1"/>
480 <param name="max_charge" value="1"/>
481 <param name="min_isopeaks" value="2"/>
482 <param name="max_isopeaks" value="3"/>
483 <param name="keep_only_deisotoped" value="false"/>
484 <param name="annotate_charge" value="false"/>
485 </section>
486 <section name="preprocessing">
487 <param name="filter_by_num_masstraces" value="1"/>
488 <param name="precursor_mz_tolerance" value="10.0"/>
489 <param name="precursor_mz_tolerance_unit" value="ppm"/>
490 <param name="precursor_rt_tolerance" value="5"/>
491 <param name="isotope_pattern_iterations" value="3"/>
492 <param name="feature_only" value="true"/>
493 <param name="no_masstrace_info_isotope_pattern" value="false"/>
494 </section>
495 <section name="sirius">
496 <param name="profile" value="qtof"/>
497 <param name="candidates" value="5"/>
498 <param name="database" value="all"/>
499 <param name="noise" value="0"/>
500 <param name="ppm_max" value="10"/>
501 <param name="isotope" value="both"/>
502 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
503 <param name="compound_timeout" value="100"/>
504 <param name="tree_timeout" value="0"/>
505 <param name="top_n_hits" value="10"/>
506 <param name="auto_charge" value="false"/>
507 <param name="ion_tree" value="false"/>
508 <param name="no_recalibration" value="false"/>
509 <param name="most_intense_ms2" value="false"/>
510 </section>
511 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
512 <output name="ctd_out" ftype="xml">
513 <assert_contents>
514 <is_valid_xml/>
515 </assert_contents>
516 </output>
517 </test>
518 <test expect_num_outputs="2">
519 <conditional name="adv_opts_cond">
520 <param name="adv_opts_selector" value="advanced"/>
521 <param name="precursor_recalibration_window" value="0.1"/>
522 <param name="precursor_recalibration_window_unit" value="Da"/>
523 <param name="min_fragment_mz" value="0.0"/>
524 <param name="max_fragment_mz" value="2000.0"/>
525 <param name="force" value="false"/>
526 <param name="test" value="true"/>
527 </conditional>
528 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
529 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
530 <param name="out_type" value="tsv"/>
531 <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
532 <param name="fragment_annotation" value="sirius"/>
533 <param name="method" value="highest_intensity"/>
534 <param name="use_exact_mass" value="true"/>
535 <param name="exclude_ms2_precursor" value="false"/>
536 <param name="precursor_mz_distance" value="0.0001"/>
537 <param name="precursor_rt_tolerance" value="5.0"/>
538 <param name="use_known_unknowns" value="true"/>
539 <param name="min_transitions" value="2"/>
540 <param name="max_transitions" value="3"/>
541 <param name="cosine_similarity_threshold" value="0.98"/>
542 <param name="transition_threshold" value="3.0"/>
543 <param name="out_workspace_directory" value=""/>
544 <section name="deisotoping">
545 <param name="use_deisotoper" value="false"/>
546 <param name="fragment_tolerance" value="1.0"/>
547 <param name="fragment_unit" value="ppm"/>
548 <param name="min_charge" value="1"/>
549 <param name="max_charge" value="1"/>
550 <param name="min_isopeaks" value="2"/>
551 <param name="max_isopeaks" value="3"/>
552 <param name="keep_only_deisotoped" value="false"/>
553 <param name="annotate_charge" value="false"/>
554 </section>
555 <section name="preprocessing">
556 <param name="filter_by_num_masstraces" value="1"/>
557 <param name="precursor_mz_tolerance" value="10.0"/>
558 <param name="precursor_mz_tolerance_unit" value="ppm"/>
559 <param name="precursor_rt_tolerance" value="5"/>
560 <param name="isotope_pattern_iterations" value="3"/>
561 <param name="feature_only" value="true"/>
562 <param name="no_masstrace_info_isotope_pattern" value="false"/>
563 </section>
564 <section name="sirius">
565 <param name="profile" value="qtof"/>
566 <param name="candidates" value="5"/>
567 <param name="database" value="all"/>
568 <param name="noise" value="0"/>
569 <param name="ppm_max" value="10"/>
570 <param name="isotope" value="both"/>
571 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
572 <param name="compound_timeout" value="100"/>
573 <param name="tree_timeout" value="0"/>
574 <param name="top_n_hits" value="10"/>
575 <param name="auto_charge" value="false"/>
576 <param name="ion_tree" value="false"/>
577 <param name="no_recalibration" value="false"/>
578 <param name="most_intense_ms2" value="false"/>
579 </section>
580 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
581 <output name="ctd_out" ftype="xml">
582 <assert_contents>
583 <is_valid_xml/>
584 </assert_contents>
585 </output>
586 </test>
587 <test expect_num_outputs="2">
588 <conditional name="adv_opts_cond">
589 <param name="adv_opts_selector" value="advanced"/>
590 <param name="precursor_recalibration_window" value="0.1"/>
591 <param name="precursor_recalibration_window_unit" value="Da"/>
592 <param name="min_fragment_mz" value="0.0"/>
593 <param name="max_fragment_mz" value="2000.0"/>
594 <param name="force" value="false"/>
595 <param name="test" value="true"/>
596 </conditional>
597 <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
598 <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
599 <param name="out_type" value="tsv"/>
600 <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
601 <param name="fragment_annotation" value="sirius"/>
602 <param name="method" value="highest_intensity"/>
603 <param name="use_exact_mass" value="true"/>
604 <param name="exclude_ms2_precursor" value="false"/>
605 <param name="precursor_mz_distance" value="0.0001"/>
606 <param name="precursor_rt_tolerance" value="5.0"/>
607 <param name="use_known_unknowns" value="false"/>
608 <param name="min_transitions" value="2"/>
609 <param name="max_transitions" value="3"/>
610 <param name="cosine_similarity_threshold" value="0.98"/>
611 <param name="transition_threshold" value="3.0"/>
612 <param name="out_workspace_directory" value=""/>
613 <section name="deisotoping">
614 <param name="use_deisotoper" value="false"/>
615 <param name="fragment_tolerance" value="1.0"/>
616 <param name="fragment_unit" value="ppm"/>
617 <param name="min_charge" value="1"/>
618 <param name="max_charge" value="1"/>
619 <param name="min_isopeaks" value="2"/>
620 <param name="max_isopeaks" value="3"/>
621 <param name="keep_only_deisotoped" value="false"/>
622 <param name="annotate_charge" value="false"/>
623 </section>
624 <section name="preprocessing">
625 <param name="filter_by_num_masstraces" value="1"/>
626 <param name="precursor_mz_tolerance" value="10.0"/>
627 <param name="precursor_mz_tolerance_unit" value="ppm"/>
628 <param name="precursor_rt_tolerance" value="5"/>
629 <param name="isotope_pattern_iterations" value="3"/>
630 <param name="feature_only" value="true"/>
631 <param name="no_masstrace_info_isotope_pattern" value="false"/>
632 </section>
633 <section name="sirius">
634 <param name="profile" value="qtof"/>
635 <param name="candidates" value="5"/>
636 <param name="database" value="all"/>
637 <param name="noise" value="0"/>
638 <param name="ppm_max" value="10"/>
639 <param name="isotope" value="both"/>
640 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
641 <param name="compound_timeout" value="100"/>
642 <param name="tree_timeout" value="0"/>
643 <param name="top_n_hits" value="10"/>
644 <param name="auto_charge" value="false"/>
645 <param name="ion_tree" value="false"/>
646 <param name="no_recalibration" value="false"/>
647 <param name="most_intense_ms2" value="false"/>
648 </section>
649 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
650 <output name="ctd_out" ftype="xml">
651 <assert_contents>
652 <is_valid_xml/>
653 </assert_contents>
654 </output>
655 </test>
656 <test expect_num_outputs="2">
657 <conditional name="adv_opts_cond">
658 <param name="adv_opts_selector" value="advanced"/>
659 <param name="precursor_recalibration_window" value="0.1"/>
660 <param name="precursor_recalibration_window_unit" value="Da"/>
661 <param name="min_fragment_mz" value="100.0"/>
662 <param name="max_fragment_mz" value="900.0"/>
663 <param name="force" value="false"/>
664 <param name="test" value="true"/>
665 </conditional>
666 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
667 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
668 <param name="out_type" value="tsv"/>
669 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
670 <param name="fragment_annotation" value="sirius"/>
671 <param name="method" value="highest_intensity"/>
672 <param name="use_exact_mass" value="true"/>
673 <param name="exclude_ms2_precursor" value="false"/>
674 <param name="precursor_mz_distance" value="0.0001"/>
675 <param name="precursor_rt_tolerance" value="5.0"/>
676 <param name="use_known_unknowns" value="false"/>
677 <param name="min_transitions" value="2"/>
678 <param name="max_transitions" value="3"/>
679 <param name="cosine_similarity_threshold" value="0.98"/>
680 <param name="transition_threshold" value="3.0"/>
681 <param name="out_workspace_directory" value=""/>
682 <section name="deisotoping">
683 <param name="use_deisotoper" value="false"/>
684 <param name="fragment_tolerance" value="1.0"/>
685 <param name="fragment_unit" value="ppm"/>
686 <param name="min_charge" value="1"/>
687 <param name="max_charge" value="1"/>
688 <param name="min_isopeaks" value="2"/>
689 <param name="max_isopeaks" value="3"/>
690 <param name="keep_only_deisotoped" value="false"/>
691 <param name="annotate_charge" value="false"/>
692 </section>
693 <section name="preprocessing">
694 <param name="filter_by_num_masstraces" value="1"/>
695 <param name="precursor_mz_tolerance" value="10.0"/>
696 <param name="precursor_mz_tolerance_unit" value="ppm"/>
697 <param name="precursor_rt_tolerance" value="5"/>
698 <param name="isotope_pattern_iterations" value="3"/>
699 <param name="feature_only" value="true"/>
700 <param name="no_masstrace_info_isotope_pattern" value="false"/>
701 </section>
702 <section name="sirius">
703 <param name="profile" value="qtof"/>
704 <param name="candidates" value="5"/>
705 <param name="database" value="all"/>
706 <param name="noise" value="0"/>
707 <param name="ppm_max" value="10"/>
708 <param name="isotope" value="both"/>
709 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
710 <param name="compound_timeout" value="100"/>
711 <param name="tree_timeout" value="0"/>
712 <param name="top_n_hits" value="10"/>
713 <param name="auto_charge" value="false"/>
714 <param name="ion_tree" value="false"/>
715 <param name="no_recalibration" value="false"/>
716 <param name="most_intense_ms2" value="false"/>
717 </section>
718 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
719 <output name="ctd_out" ftype="xml">
720 <assert_contents>
721 <is_valid_xml/>
722 </assert_contents>
723 </output>
724 </test>
725 </xml>
726 <xml name="autotest_BaselineFilter">
727 <test expect_num_outputs="2">
728 <conditional name="adv_opts_cond">
729 <param name="adv_opts_selector" value="advanced"/>
730 <param name="force" value="false"/>
731 <param name="test" value="true"/>
732 </conditional>
733 <param name="in" value="BaselineFilter_input.mzML"/>
734 <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
735 <param name="struc_elem_length" value="1.5"/>
736 <param name="struc_elem_unit" value="Thomson"/>
737 <param name="method" value="tophat"/>
738 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
739 <output name="ctd_out" ftype="xml">
740 <assert_contents>
741 <is_valid_xml/>
742 </assert_contents>
743 </output>
744 </test>
745 </xml>
746 <xml name="autotest_ClusterMassTracesByPrecursor">
747 </xml>
748 <xml name="autotest_ClusterMassTraces">
749 </xml>
750 <xml name="autotest_CometAdapter">
751 <test expect_num_outputs="3">
752 <conditional name="adv_opts_cond">
753 <param name="adv_opts_selector" value="advanced"/>
754 <param name="use_A_ions" value="false"/>
755 <param name="use_B_ions" value="true"/>
756 <param name="use_C_ions" value="false"/>
757 <param name="use_X_ions" value="false"/>
758 <param name="use_Y_ions" value="true"/>
759 <param name="use_Z_ions" value="false"/>
760 <param name="use_NL_ions" value="false"/>
761 <param name="second_enzyme" value=""/>
762 <param name="digest_mass_range" value="600:5000"/>
763 <param name="max_precursor_charge" value="5"/>
764 <param name="spectrum_batch_size" value="1000"/>
765 <param name="mass_offsets" value="0.0"/>
766 <param name="minimum_peaks" value="10"/>
767 <param name="minimum_intensity" value="0.0"/>
768 <param name="remove_precursor_peak" value="no"/>
769 <param name="remove_precursor_tolerance" value="1.5"/>
770 <param name="clear_mz_range" value="0:0"/>
771 <param name="max_variable_mods_in_peptide" value="5"/>
772 <param name="require_variable_mod" value="false"/>
773 <param name="force" value="true"/>
774 <param name="test" value="true"/>
775 </conditional>
776 <param name="in" value="spectra_comet.mzML"/>
777 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
778 <param name="database" value="proteins.fasta"/>
779 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
780 <param name="precursor_mass_tolerance" value="3.0"/>
781 <param name="precursor_error_units" value="ppm"/>
782 <param name="isotope_error" value="off"/>
783 <param name="fragment_mass_tolerance" value="0.50025"/>
784 <param name="fragment_error_units" value="Da"/>
785 <param name="fragment_bin_offset" value="0.25"/>
786 <param name="instrument" value="high_res"/>
787 <param name="enzyme" value="Trypsin"/>
788 <param name="num_enzyme_termini" value="fully"/>
789 <param name="missed_cleavages" value="1"/>
790 <param name="min_peptide_length" value="5"/>
791 <param name="max_peptide_length" value="63"/>
792 <param name="num_hits" value="5"/>
793 <param name="precursor_charge" value="0:0"/>
794 <param name="override_charge" value="keep any known"/>
795 <param name="ms_level" value="2"/>
796 <param name="activation_method" value="ALL"/>
797 <param name="max_fragment_charge" value="3"/>
798 <param name="clip_nterm_methionine" value="false"/>
799 <param name="fixed_modifications" value=""/>
800 <param name="variable_modifications" value=""/>
801 <param name="binary_modifications" value=""/>
802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
803 <output name="ctd_out" ftype="xml">
804 <assert_contents>
805 <is_valid_xml/>
806 </assert_contents>
807 </output>
808 </test>
809 <test expect_num_outputs="3">
810 <conditional name="adv_opts_cond">
811 <param name="adv_opts_selector" value="advanced"/>
812 <param name="use_A_ions" value="false"/>
813 <param name="use_B_ions" value="true"/>
814 <param name="use_C_ions" value="false"/>
815 <param name="use_X_ions" value="false"/>
816 <param name="use_Y_ions" value="true"/>
817 <param name="use_Z_ions" value="false"/>
818 <param name="use_NL_ions" value="false"/>
819 <param name="second_enzyme" value=""/>
820 <param name="digest_mass_range" value="600:5000"/>
821 <param name="max_precursor_charge" value="5"/>
822 <param name="spectrum_batch_size" value="1000"/>
823 <param name="mass_offsets" value="0.0"/>
824 <param name="minimum_peaks" value="10"/>
825 <param name="minimum_intensity" value="0.0"/>
826 <param name="remove_precursor_peak" value="no"/>
827 <param name="remove_precursor_tolerance" value="1.5"/>
828 <param name="clear_mz_range" value="0:0"/>
829 <param name="max_variable_mods_in_peptide" value="5"/>
830 <param name="require_variable_mod" value="false"/>
831 <param name="force" value="true"/>
832 <param name="test" value="true"/>
833 </conditional>
834 <param name="in" value="CometAdapter_2_prepared.mzML"/>
835 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
836 <param name="database" value="CometAdapter_2_in.fasta"/>
837 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
838 <param name="precursor_mass_tolerance" value="3.0"/>
839 <param name="precursor_error_units" value="Da"/>
840 <param name="isotope_error" value="off"/>
841 <param name="fragment_mass_tolerance" value="0.50025"/>
842 <param name="fragment_error_units" value="Da"/>
843 <param name="fragment_bin_offset" value="0.25"/>
844 <param name="instrument" value="high_res"/>
845 <param name="enzyme" value="Trypsin"/>
846 <param name="num_enzyme_termini" value="fully"/>
847 <param name="missed_cleavages" value="1"/>
848 <param name="min_peptide_length" value="5"/>
849 <param name="max_peptide_length" value="63"/>
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="binary_modifications" value=""/>
860 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
861 <output name="ctd_out" ftype="xml">
862 <assert_contents>
863 <is_valid_xml/>
864 </assert_contents>
865 </output>
866 </test>
867 <test expect_num_outputs="3">
868 <conditional name="adv_opts_cond">
869 <param name="adv_opts_selector" value="advanced"/>
870 <param name="use_A_ions" value="false"/>
871 <param name="use_B_ions" value="true"/>
872 <param name="use_C_ions" value="false"/>
873 <param name="use_X_ions" value="false"/>
874 <param name="use_Y_ions" value="true"/>
875 <param name="use_Z_ions" value="false"/>
876 <param name="use_NL_ions" value="false"/>
877 <param name="second_enzyme" value=""/>
878 <param name="digest_mass_range" value="600:5000"/>
879 <param name="max_precursor_charge" value="5"/>
880 <param name="spectrum_batch_size" value="20000"/>
881 <param name="mass_offsets" value="0.0"/>
882 <param name="minimum_peaks" value="10"/>
883 <param name="minimum_intensity" value="0.0"/>
884 <param name="remove_precursor_peak" value="no"/>
885 <param name="remove_precursor_tolerance" value="1.5"/>
886 <param name="clear_mz_range" value="0:0"/>
887 <param name="max_variable_mods_in_peptide" value="3"/>
888 <param name="require_variable_mod" value="false"/>
889 <param name="force" value="false"/>
890 <param name="test" value="true"/>
891 </conditional>
892 <param name="in" value="CometAdapter_3.mzML"/>
893 <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
894 <param name="database" value="CometAdapter_3.fasta"/>
895 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
896 <param name="precursor_mass_tolerance" value="5.0"/>
897 <param name="precursor_error_units" value="ppm"/>
898 <param name="isotope_error" value="off"/>
899 <param name="fragment_mass_tolerance" value="0.01"/>
900 <param name="fragment_error_units" value="Da"/>
901 <param name="fragment_bin_offset" value="0.0"/>
902 <param name="instrument" value="high_res"/>
903 <param name="enzyme" value="Trypsin"/>
904 <param name="num_enzyme_termini" value="fully"/>
905 <param name="missed_cleavages" value="3"/>
906 <param name="min_peptide_length" value="5"/>
907 <param name="max_peptide_length" value="63"/>
908 <param name="num_hits" value="5"/>
909 <param name="precursor_charge" value="0:0"/>
910 <param name="override_charge" value="keep known search unknown"/>
911 <param name="ms_level" value="2"/>
912 <param name="activation_method" value="ALL"/>
913 <param name="max_fragment_charge" value="3"/>
914 <param name="clip_nterm_methionine" value="false"/>
915 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
916 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
917 <param name="binary_modifications" value=""/>
918 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
919 <output name="ctd_out" ftype="xml">
920 <assert_contents>
921 <is_valid_xml/>
922 </assert_contents>
923 </output>
924 </test>
925 <test expect_num_outputs="2">
926 <conditional name="adv_opts_cond">
927 <param name="adv_opts_selector" value="advanced"/>
928 <param name="use_A_ions" value="false"/>
929 <param name="use_B_ions" value="true"/>
930 <param name="use_C_ions" value="false"/>
931 <param name="use_X_ions" value="false"/>
932 <param name="use_Y_ions" value="true"/>
933 <param name="use_Z_ions" value="false"/>
934 <param name="use_NL_ions" value="false"/>
935 <param name="second_enzyme" value=""/>
936 <param name="digest_mass_range" value="600:1200"/>
937 <param name="max_precursor_charge" value="5"/>
938 <param name="spectrum_batch_size" value="20000"/>
939 <param name="mass_offsets" value="0.0"/>
940 <param name="minimum_peaks" value="10"/>
941 <param name="minimum_intensity" value="0.0"/>
942 <param name="remove_precursor_peak" value="no"/>
943 <param name="remove_precursor_tolerance" value="1.5"/>
944 <param name="clear_mz_range" value="0:0"/>
945 <param name="max_variable_mods_in_peptide" value="3"/>
946 <param name="require_variable_mod" value="false"/>
947 <param name="force" value="false"/>
948 <param name="test" value="true"/>
949 </conditional>
950 <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
951 <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
952 <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
953 <param name="precursor_mass_tolerance" value="5.0"/>
954 <param name="precursor_error_units" value="ppm"/>
955 <param name="isotope_error" value="off"/>
956 <param name="fragment_mass_tolerance" value="0.01"/>
957 <param name="fragment_error_units" value="Da"/>
958 <param name="fragment_bin_offset" value="0.0"/>
959 <param name="instrument" value="high_res"/>
960 <param name="enzyme" value="Trypsin"/>
961 <param name="num_enzyme_termini" value="fully"/>
962 <param name="missed_cleavages" value="3"/>
963 <param name="min_peptide_length" value="5"/>
964 <param name="max_peptide_length" value="63"/>
965 <param name="num_hits" value="5"/>
966 <param name="precursor_charge" value="0:0"/>
967 <param name="override_charge" value="keep known search unknown"/>
968 <param name="ms_level" value="2"/>
969 <param name="activation_method" value="ALL"/>
970 <param name="max_fragment_charge" value="3"/>
971 <param name="clip_nterm_methionine" value="false"/>
972 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
973 <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
974 <param name="binary_modifications" value=""/>
975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
976 <output name="ctd_out" ftype="xml">
977 <assert_contents>
978 <is_valid_xml/>
979 </assert_contents>
980 </output>
981 </test>
982 </xml>
983 <xml name="autotest_CompNovoCID">
984 <test expect_num_outputs="2">
985 <conditional name="adv_opts_cond">
986 <param name="adv_opts_selector" value="advanced"/>
987 <param name="force" value="false"/>
988 <param name="test" value="true"/>
989 </conditional>
990 <param name="in" value="CompNovoCID_1_input.mzML"/>
991 <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
992 <section name="algorithm">
993 <param name="max_number_aa_per_decomp" value="4"/>
994 <param name="tryptic_only" value="true"/>
995 <param name="precursor_mass_tolerance" value="0.3"/>
996 <param name="fragment_mass_tolerance" value="0.3"/>
997 <param name="max_number_pivot" value="9"/>
998 <param name="max_subscore_number" value="40"/>
999 <param name="decomp_weights_precision" value="0.01"/>
1000 <param name="double_charged_iso_threshold" value="0.6"/>
1001 <param name="max_mz" value="2000.0"/>
1002 <param name="min_mz" value="200.0"/>
1003 <param name="max_isotope_to_score" value="3"/>
1004 <param name="max_decomp_weight" value="450.0"/>
1005 <param name="max_isotope" value="3"/>
1006 <param name="missed_cleavages" value="1"/>
1007 <param name="number_of_hits" value="1"/>
1008 <param name="estimate_precursor_mz" value="true"/>
1009 <param name="number_of_prescoring_hits" value="250"/>
1010 <param name="fixed_modifications" value=""/>
1011 <param name="variable_modifications" value=""/>
1012 <param name="residue_set" value="Natural19WithoutI"/>
1013 </section>
1014 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1015 <output name="ctd_out" ftype="xml">
1016 <assert_contents>
1017 <is_valid_xml/>
1018 </assert_contents>
1019 </output>
1020 </test>
1021 </xml>
1022 <xml name="autotest_CompNovo">
1023 <test expect_num_outputs="2">
1024 <conditional name="adv_opts_cond">
1025 <param name="adv_opts_selector" value="advanced"/>
1026 <param name="force" value="false"/>
1027 <param name="test" value="true"/>
1028 </conditional>
1029 <param name="in" value="CompNovo_1_input.mzML"/>
1030 <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1031 <section name="algorithm">
1032 <param name="max_number_aa_per_decomp" value="4"/>
1033 <param name="tryptic_only" value="true"/>
1034 <param name="precursor_mass_tolerance" value="0.3"/>
1035 <param name="fragment_mass_tolerance" value="0.3"/>
1036 <param name="max_number_pivot" value="9"/>
1037 <param name="max_subscore_number" value="40"/>
1038 <param name="decomp_weights_precision" value="0.01"/>
1039 <param name="double_charged_iso_threshold" value="0.6"/>
1040 <param name="max_mz" value="2000.0"/>
1041 <param name="min_mz" value="200.0"/>
1042 <param name="max_isotope_to_score" value="3"/>
1043 <param name="max_decomp_weight" value="450.0"/>
1044 <param name="max_isotope" value="3"/>
1045 <param name="missed_cleavages" value="1"/>
1046 <param name="number_of_hits" value="1"/>
1047 <param name="estimate_precursor_mz" value="true"/>
1048 <param name="number_of_prescoring_hits" value="250"/>
1049 <param name="fixed_modifications" value=""/>
1050 <param name="variable_modifications" value=""/>
1051 <param name="residue_set" value="Natural19WithoutI"/>
1052 </section>
1053 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1054 <output name="ctd_out" ftype="xml">
1055 <assert_contents>
1056 <is_valid_xml/>
1057 </assert_contents>
1058 </output>
1059 </test>
1060 </xml>
1061 <xml name="autotest_ConsensusID">
1062 <test expect_num_outputs="2">
1063 <conditional name="adv_opts_cond">
1064 <param name="adv_opts_selector" value="advanced"/>
1065 <param name="force" value="false"/>
1066 <param name="test" value="true"/>
1067 </conditional>
1068 <param name="in" value="ConsensusID_1_input.idXML"/>
1069 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1070 <param name="rt_delta" value="0.1"/>
1071 <param name="mz_delta" value="0.1"/>
1072 <param name="per_spectrum" value="false"/>
1073 <param name="algorithm" value="PEPMatrix"/>
1074 <section name="filter">
1075 <param name="considered_hits" value="0"/>
1076 <param name="min_support" value="0.0"/>
1077 <param name="count_empty" value="false"/>
1078 <param name="keep_old_scores" value="false"/>
1079 </section>
1080 <section name="PEPIons">
1081 <param name="mass_tolerance" value="0.5"/>
1082 <param name="min_shared" value="2"/>
1083 </section>
1084 <section name="PEPMatrix">
1085 <param name="matrix" value="PAM30MS"/>
1086 <param name="penalty" value="5"/>
1087 </section>
1088 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1089 <output name="ctd_out" ftype="xml">
1090 <assert_contents>
1091 <is_valid_xml/>
1092 </assert_contents>
1093 </output>
1094 </test>
1095 <test expect_num_outputs="2">
1096 <conditional name="adv_opts_cond">
1097 <param name="adv_opts_selector" value="advanced"/>
1098 <param name="force" value="false"/>
1099 <param name="test" value="true"/>
1100 </conditional>
1101 <param name="in" value="ConsensusID_2_input.featureXML"/>
1102 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
1103 <param name="rt_delta" value="0.1"/>
1104 <param name="mz_delta" value="0.1"/>
1105 <param name="per_spectrum" value="false"/>
1106 <param name="algorithm" value="average"/>
1107 <section name="filter">
1108 <param name="considered_hits" value="0"/>
1109 <param name="min_support" value="0.0"/>
1110 <param name="count_empty" value="false"/>
1111 <param name="keep_old_scores" value="false"/>
1112 </section>
1113 <section name="PEPIons">
1114 <param name="mass_tolerance" value="0.5"/>
1115 <param name="min_shared" value="2"/>
1116 </section>
1117 <section name="PEPMatrix">
1118 <param name="matrix" value="identity"/>
1119 <param name="penalty" value="5"/>
1120 </section>
1121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1122 <output name="ctd_out" ftype="xml">
1123 <assert_contents>
1124 <is_valid_xml/>
1125 </assert_contents>
1126 </output>
1127 </test>
1128 <test expect_num_outputs="2">
1129 <conditional name="adv_opts_cond">
1130 <param name="adv_opts_selector" value="advanced"/>
1131 <param name="force" value="false"/>
1132 <param name="test" value="true"/>
1133 </conditional>
1134 <param name="in" value="ConsensusID_3_input.consensusXML"/>
1135 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1136 <param name="rt_delta" value="0.1"/>
1137 <param name="mz_delta" value="0.1"/>
1138 <param name="per_spectrum" value="false"/>
1139 <param name="algorithm" value="best"/>
1140 <section name="filter">
1141 <param name="considered_hits" value="0"/>
1142 <param name="min_support" value="0.0"/>
1143 <param name="count_empty" value="false"/>
1144 <param name="keep_old_scores" value="false"/>
1145 </section>
1146 <section name="PEPIons">
1147 <param name="mass_tolerance" value="0.5"/>
1148 <param name="min_shared" value="2"/>
1149 </section>
1150 <section name="PEPMatrix">
1151 <param name="matrix" value="identity"/>
1152 <param name="penalty" value="5"/>
1153 </section>
1154 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1155 <output name="ctd_out" ftype="xml">
1156 <assert_contents>
1157 <is_valid_xml/>
1158 </assert_contents>
1159 </output>
1160 </test>
1161 <test expect_num_outputs="2">
1162 <conditional name="adv_opts_cond">
1163 <param name="adv_opts_selector" value="advanced"/>
1164 <param name="force" value="false"/>
1165 <param name="test" value="true"/>
1166 </conditional>
1167 <param name="in" value="ConsensusID_1_input.idXML"/>
1168 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1169 <param name="rt_delta" value="0.1"/>
1170 <param name="mz_delta" value="0.1"/>
1171 <param name="per_spectrum" value="false"/>
1172 <param name="algorithm" value="PEPMatrix"/>
1173 <section name="filter">
1174 <param name="considered_hits" value="6"/>
1175 <param name="min_support" value="0.0"/>
1176 <param name="count_empty" value="false"/>
1177 <param name="keep_old_scores" value="false"/>
1178 </section>
1179 <section name="PEPIons">
1180 <param name="mass_tolerance" value="0.5"/>
1181 <param name="min_shared" value="2"/>
1182 </section>
1183 <section name="PEPMatrix">
1184 <param name="matrix" value="identity"/>
1185 <param name="penalty" value="5"/>
1186 </section>
1187 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1188 <output name="ctd_out" ftype="xml">
1189 <assert_contents>
1190 <is_valid_xml/>
1191 </assert_contents>
1192 </output>
1193 </test>
1194 <test expect_num_outputs="2">
1195 <conditional name="adv_opts_cond">
1196 <param name="adv_opts_selector" value="advanced"/>
1197 <param name="force" value="false"/>
1198 <param name="test" value="true"/>
1199 </conditional>
1200 <param name="in" value="ConsensusID_1_input.idXML"/>
1201 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1202 <param name="rt_delta" value="0.1"/>
1203 <param name="mz_delta" value="0.1"/>
1204 <param name="per_spectrum" value="false"/>
1205 <param name="algorithm" value="PEPIons"/>
1206 <section name="filter">
1207 <param name="considered_hits" value="0"/>
1208 <param name="min_support" value="0.0"/>
1209 <param name="count_empty" value="false"/>
1210 <param name="keep_old_scores" value="false"/>
1211 </section>
1212 <section name="PEPIons">
1213 <param name="mass_tolerance" value="0.5"/>
1214 <param name="min_shared" value="2"/>
1215 </section>
1216 <section name="PEPMatrix">
1217 <param name="matrix" value="identity"/>
1218 <param name="penalty" value="5"/>
1219 </section>
1220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1221 <output name="ctd_out" ftype="xml">
1222 <assert_contents>
1223 <is_valid_xml/>
1224 </assert_contents>
1225 </output>
1226 </test>
1227 <test expect_num_outputs="2">
1228 <conditional name="adv_opts_cond">
1229 <param name="adv_opts_selector" value="advanced"/>
1230 <param name="force" value="false"/>
1231 <param name="test" value="true"/>
1232 </conditional>
1233 <param name="in" value="ConsensusID_1_input.idXML"/>
1234 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1235 <param name="rt_delta" value="0.1"/>
1236 <param name="mz_delta" value="0.1"/>
1237 <param name="per_spectrum" value="false"/>
1238 <param name="algorithm" value="best"/>
1239 <section name="filter">
1240 <param name="considered_hits" value="0"/>
1241 <param name="min_support" value="0.5"/>
1242 <param name="count_empty" value="false"/>
1243 <param name="keep_old_scores" value="false"/>
1244 </section>
1245 <section name="PEPIons">
1246 <param name="mass_tolerance" value="0.5"/>
1247 <param name="min_shared" value="2"/>
1248 </section>
1249 <section name="PEPMatrix">
1250 <param name="matrix" value="identity"/>
1251 <param name="penalty" value="5"/>
1252 </section>
1253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1254 <output name="ctd_out" ftype="xml">
1255 <assert_contents>
1256 <is_valid_xml/>
1257 </assert_contents>
1258 </output>
1259 </test>
1260 <test expect_num_outputs="2">
1261 <conditional name="adv_opts_cond">
1262 <param name="adv_opts_selector" value="advanced"/>
1263 <param name="force" value="false"/>
1264 <param name="test" value="true"/>
1265 </conditional>
1266 <param name="in" value="ConsensusID_6_input.idXML"/>
1267 <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1268 <param name="rt_delta" value="0.1"/>
1269 <param name="mz_delta" value="0.1"/>
1270 <param name="per_spectrum" value="true"/>
1271 <param name="algorithm" value="best"/>
1272 <section name="filter">
1273 <param name="considered_hits" value="0"/>
1274 <param name="min_support" value="0.0"/>
1275 <param name="count_empty" value="false"/>
1276 <param name="keep_old_scores" value="true"/>
1277 </section>
1278 <section name="PEPIons">
1279 <param name="mass_tolerance" value="0.5"/>
1280 <param name="min_shared" value="2"/>
1281 </section>
1282 <section name="PEPMatrix">
1283 <param name="matrix" value="identity"/>
1284 <param name="penalty" value="5"/>
1285 </section>
1286 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1287 <output name="ctd_out" ftype="xml">
1288 <assert_contents>
1289 <is_valid_xml/>
1290 </assert_contents>
1291 </output>
1292 </test>
1293 <test expect_num_outputs="2">
1294 <conditional name="adv_opts_cond">
1295 <param name="adv_opts_selector" value="advanced"/>
1296 <param name="force" value="false"/>
1297 <param name="test" value="true"/>
1298 </conditional>
1299 <param name="in" value="ConsensusID_8_input.idXML"/>
1300 <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1301 <param name="rt_delta" value="0.1"/>
1302 <param name="mz_delta" value="0.1"/>
1303 <param name="per_spectrum" value="true"/>
1304 <param name="algorithm" value="best"/>
1305 <section name="filter">
1306 <param name="considered_hits" value="0"/>
1307 <param name="min_support" value="0.0"/>
1308 <param name="count_empty" value="false"/>
1309 <param name="keep_old_scores" value="true"/>
1310 </section>
1311 <section name="PEPIons">
1312 <param name="mass_tolerance" value="0.5"/>
1313 <param name="min_shared" value="2"/>
1314 </section>
1315 <section name="PEPMatrix">
1316 <param name="matrix" value="identity"/>
1317 <param name="penalty" value="5"/>
1318 </section>
1319 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1320 <output name="ctd_out" ftype="xml">
1321 <assert_contents>
1322 <is_valid_xml/>
1323 </assert_contents>
1324 </output>
1325 </test>
1326 </xml>
1327 <xml name="autotest_ConsensusMapNormalizer">
1328 <test expect_num_outputs="2">
1329 <conditional name="adv_opts_cond">
1330 <param name="adv_opts_selector" value="advanced"/>
1331 <param name="accession_filter" value=""/>
1332 <param name="description_filter" value=""/>
1333 <param name="force" value="false"/>
1334 <param name="test" value="true"/>
1335 </conditional>
1336 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
1337 <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1338 <param name="algorithm_type" value="robust_regression"/>
1339 <param name="ratio_threshold" value="0.67"/>
1340 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1341 <output name="ctd_out" ftype="xml">
1342 <assert_contents>
1343 <is_valid_xml/>
1344 </assert_contents>
1345 </output>
1346 </test>
1347 </xml>
1348 <xml name="autotest_CruxAdapter">
1349 <test expect_num_outputs="2">
1350 <conditional name="adv_opts_cond">
1351 <param name="adv_opts_selector" value="advanced"/>
1352 <param name="custom_enzyme" value=""/>
1353 <param name="decoy_prefix" value="decoy_"/>
1354 <param name="deisotope" value="false"/>
1355 <param name="report_decoys" value="false"/>
1356 <param name="force" value="false"/>
1357 <param name="test" value="true"/>
1358 </conditional>
1359 <param name="in" value="spectra_comet.mzML"/>
1360 <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1361 <param name="database" value="proteins.fasta"/>
1362 <param name="extra_index_args" value=""/>
1363 <param name="extra_search_args" value=""/>
1364 <param name="extra_percolator_args" value=""/>
1365 <param name="precursor_mass_tolerance" value="10.0"/>
1366 <param name="precursor_mass_units" value="ppm"/>
1367 <param name="fragment_bin_offset" value="0.0"/>
1368 <param name="fragment_bin_width" value="0.02"/>
1369 <param name="isotope_error" value=""/>
1370 <param name="run_percolator" value="false"/>
1371 <param name="enzyme" value="trypsin"/>
1372 <param name="digestion" value="full-digest"/>
1373 <param name="allowed_missed_cleavages" value="0"/>
1374 <param name="decoy_format" value="peptide-reverse"/>
1375 <param name="keep_terminal_aminos" value="NC"/>
1376 <param name="cterm_modifications" value=""/>
1377 <param name="nterm_modifications" value=""/>
1378 <param name="modifications" value=""/>
1379 <param name="test_fdr" value="0.01"/>
1380 <param name="train_fdr" value="0.01"/>
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 </xml>
1389 <xml name="autotest_CVInspector">
1390 </xml>
1391 <xml name="autotest_DatabaseFilter">
1392 <test expect_num_outputs="2">
1393 <conditional name="adv_opts_cond">
1394 <param name="adv_opts_selector" value="advanced"/>
1395 <param name="force" value="false"/>
1396 <param name="test" value="true"/>
1397 </conditional>
1398 <param name="in" value="DatabaseFilter_1.fasta"/>
1399 <param name="id" value="DatabaseFilter_1.idXML"/>
1400 <param name="method" value="whitelist"/>
1401 <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1402 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1403 <output name="ctd_out" ftype="xml">
1404 <assert_contents>
1405 <is_valid_xml/>
1406 </assert_contents>
1407 </output>
1408 </test>
1409 <test expect_num_outputs="2">
1410 <conditional name="adv_opts_cond">
1411 <param name="adv_opts_selector" value="advanced"/>
1412 <param name="force" value="false"/>
1413 <param name="test" value="true"/>
1414 </conditional>
1415 <param name="in" value="DatabaseFilter_1.fasta"/>
1416 <param name="id" value="DatabaseFilter_1.idXML"/>
1417 <param name="method" value="blacklist"/>
1418 <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1419 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1420 <output name="ctd_out" ftype="xml">
1421 <assert_contents>
1422 <is_valid_xml/>
1423 </assert_contents>
1424 </output>
1425 </test>
1426 <test expect_num_outputs="2">
1427 <conditional name="adv_opts_cond">
1428 <param name="adv_opts_selector" value="advanced"/>
1429 <param name="force" value="false"/>
1430 <param name="test" value="true"/>
1431 </conditional>
1432 <param name="in" value="DatabaseFilter_3.fasta"/>
1433 <param name="id" value="DatabaseFilter_3.mzid"/>
1434 <param name="method" value="whitelist"/>
1435 <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1437 <output name="ctd_out" ftype="xml">
1438 <assert_contents>
1439 <is_valid_xml/>
1440 </assert_contents>
1441 </output>
1442 </test>
1443 <test expect_num_outputs="2">
1444 <conditional name="adv_opts_cond">
1445 <param name="adv_opts_selector" value="advanced"/>
1446 <param name="force" value="false"/>
1447 <param name="test" value="true"/>
1448 </conditional>
1449 <param name="in" value="DatabaseFilter_3.fasta"/>
1450 <param name="id" value="DatabaseFilter_3.mzid"/>
1451 <param name="method" value="blacklist"/>
1452 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1453 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1454 <output name="ctd_out" ftype="xml">
1455 <assert_contents>
1456 <is_valid_xml/>
1457 </assert_contents>
1458 </output>
1459 </test>
1460 </xml>
1461 <xml name="autotest_DatabaseSuitability">
1462 <test expect_num_outputs="2">
1463 <conditional name="adv_opts_cond">
1464 <param name="adv_opts_selector" value="advanced"/>
1465 <param name="force" value="false"/>
1466 <param name="test" value="true"/>
1467 </conditional>
1468 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1469 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1470 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1471 <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1472 <section name="algorithm">
1473 <param name="no_rerank" value="false"/>
1474 <param name="reranking_cutoff_percentile" value="0.01"/>
1475 <param name="FDR" value="0.8"/>
1476 </section>
1477 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1478 <output name="ctd_out" ftype="xml">
1479 <assert_contents>
1480 <is_valid_xml/>
1481 </assert_contents>
1482 </output>
1483 </test>
1484 <test expect_num_outputs="2">
1485 <conditional name="adv_opts_cond">
1486 <param name="adv_opts_selector" value="advanced"/>
1487 <param name="force" value="false"/>
1488 <param name="test" value="true"/>
1489 </conditional>
1490 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1491 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1492 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1493 <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1494 <section name="algorithm">
1495 <param name="no_rerank" value="false"/>
1496 <param name="reranking_cutoff_percentile" value="0.9"/>
1497 <param name="FDR" value="1.0"/>
1498 </section>
1499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1500 <output name="ctd_out" ftype="xml">
1501 <assert_contents>
1502 <is_valid_xml/>
1503 </assert_contents>
1504 </output>
1505 </test>
1506 <test expect_num_outputs="2">
1507 <conditional name="adv_opts_cond">
1508 <param name="adv_opts_selector" value="advanced"/>
1509 <param name="force" value="false"/>
1510 <param name="test" value="true"/>
1511 </conditional>
1512 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1513 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1514 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1515 <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1516 <section name="algorithm">
1517 <param name="no_rerank" value="true"/>
1518 <param name="reranking_cutoff_percentile" value="0.01"/>
1519 <param name="FDR" value="0.9"/>
1520 </section>
1521 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1522 <output name="ctd_out" ftype="xml">
1523 <assert_contents>
1524 <is_valid_xml/>
1525 </assert_contents>
1526 </output>
1527 </test>
1528 </xml>
1529 <xml name="autotest_Decharger">
1530 <test expect_num_outputs="4">
1531 <conditional name="adv_opts_cond">
1532 <param name="adv_opts_selector" value="advanced"/>
1533 <param name="force" value="false"/>
1534 <param name="test" value="true"/>
1535 </conditional>
1536 <param name="in" value="Decharger_input.featureXML"/>
1537 <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1538 <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
1539 <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/>
1540 <section name="algorithm">
1541 <section name="FeatureDeconvolution">
1542 <param name="charge_min" value="1"/>
1543 <param name="charge_max" value="10"/>
1544 <param name="charge_span_max" value="4"/>
1545 <param name="q_try" value="feature"/>
1546 <param name="retention_max_diff" value="1.0"/>
1547 <param name="retention_max_diff_local" value="1.0"/>
1548 <param name="mass_max_diff" value="0.1"/>
1549 <param name="potential_adducts" value="&quot;H:+:0.7&quot; &quot;Na:+:0.1&quot; &quot;(2)H4H-4:0:0.1:-2:heavy&quot;"/>
1550 <param name="max_neutrals" value="0"/>
1551 <param name="max_minority_bound" value="2"/>
1552 <param name="min_rt_overlap" value="0.66"/>
1553 <param name="intensity_filter" value="false"/>
1554 <param name="negative_mode" value="false"/>
1555 <param name="default_map_label" value="decharged features"/>
1556 <param name="verbose_level" value="0"/>
1557 </section>
1558 </section>
1559 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/>
1560 <output name="ctd_out" ftype="xml">
1561 <assert_contents>
1562 <is_valid_xml/>
1563 </assert_contents>
1564 </output>
1565 </test>
1566 </xml>
1567 <xml name="autotest_DecoyDatabase">
1568 <test expect_num_outputs="2">
1569 <conditional name="adv_opts_cond">
1570 <param name="adv_opts_selector" value="advanced"/>
1571 <param name="shuffle_max_attempts" value="30"/>
1572 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1573 <param name="seed" value="1"/>
1574 <param name="force" value="false"/>
1575 <param name="test" value="true"/>
1576 </conditional>
1577 <param name="in" value="DecoyDatabase_1.fasta"/>
1578 <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1579 <param name="decoy_string" value="DECOY_"/>
1580 <param name="decoy_string_position" value="prefix"/>
1581 <param name="only_decoy" value="true"/>
1582 <param name="type" value="protein"/>
1583 <param name="method" value="reverse"/>
1584 <param name="enzyme" value="Trypsin"/>
1585 <section name="Decoy">
1586 <param name="non_shuffle_pattern" value=""/>
1587 <param name="keepPeptideNTerm" value="true"/>
1588 <param name="keepPeptideCTerm" value="true"/>
1589 </section>
1590 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1591 <output name="ctd_out" ftype="xml">
1592 <assert_contents>
1593 <is_valid_xml/>
1594 </assert_contents>
1595 </output>
1596 </test>
1597 <test expect_num_outputs="2">
1598 <conditional name="adv_opts_cond">
1599 <param name="adv_opts_selector" value="advanced"/>
1600 <param name="shuffle_max_attempts" value="30"/>
1601 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1602 <param name="seed" value="42"/>
1603 <param name="force" value="false"/>
1604 <param name="test" value="true"/>
1605 </conditional>
1606 <param name="in" value="DecoyDatabase_1.fasta"/>
1607 <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1608 <param name="decoy_string" value="blabla"/>
1609 <param name="decoy_string_position" value="prefix"/>
1610 <param name="only_decoy" value="false"/>
1611 <param name="type" value="protein"/>
1612 <param name="method" value="shuffle"/>
1613 <param name="enzyme" value="Trypsin"/>
1614 <section name="Decoy">
1615 <param name="non_shuffle_pattern" value="KRP"/>
1616 <param name="keepPeptideNTerm" value="true"/>
1617 <param name="keepPeptideCTerm" value="true"/>
1618 </section>
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 <test expect_num_outputs="2">
1627 <conditional name="adv_opts_cond">
1628 <param name="adv_opts_selector" value="advanced"/>
1629 <param name="shuffle_max_attempts" value="30"/>
1630 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1631 <param name="seed" value="42"/>
1632 <param name="force" value="false"/>
1633 <param name="test" value="true"/>
1634 </conditional>
1635 <param name="in" value="DecoyDatabase_1.fasta"/>
1636 <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1637 <param name="decoy_string" value="blabla"/>
1638 <param name="decoy_string_position" value="prefix"/>
1639 <param name="only_decoy" value="false"/>
1640 <param name="type" value="protein"/>
1641 <param name="method" value="shuffle"/>
1642 <param name="enzyme" value="Chymotrypsin"/>
1643 <section name="Decoy">
1644 <param name="non_shuffle_pattern" value="KR"/>
1645 <param name="keepPeptideNTerm" value="true"/>
1646 <param name="keepPeptideCTerm" value="true"/>
1647 </section>
1648 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1649 <output name="ctd_out" ftype="xml">
1650 <assert_contents>
1651 <is_valid_xml/>
1652 </assert_contents>
1653 </output>
1654 </test>
1655 <test expect_num_outputs="2">
1656 <conditional name="adv_opts_cond">
1657 <param name="adv_opts_selector" value="advanced"/>
1658 <param name="shuffle_max_attempts" value="30"/>
1659 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1660 <param name="seed" value="42"/>
1661 <param name="force" value="false"/>
1662 <param name="test" value="true"/>
1663 </conditional>
1664 <param name="in" value="DecoyDatabase_4.fasta"/>
1665 <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1666 <param name="decoy_string" value="blabla"/>
1667 <param name="decoy_string_position" value="prefix"/>
1668 <param name="only_decoy" value="false"/>
1669 <param name="type" value="RNA"/>
1670 <param name="method" value="reverse"/>
1671 <param name="enzyme" value="Trypsin"/>
1672 <section name="Decoy">
1673 <param name="non_shuffle_pattern" value=""/>
1674 <param name="keepPeptideNTerm" value="true"/>
1675 <param name="keepPeptideCTerm" value="true"/>
1676 </section>
1677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1678 <output name="ctd_out" ftype="xml">
1679 <assert_contents>
1680 <is_valid_xml/>
1681 </assert_contents>
1682 </output>
1683 </test>
1684 </xml>
1685 <xml name="autotest_DeMeanderize">
1686 </xml>
1687 <xml name="autotest_DigestorMotif">
1688 </xml>
1689 <xml name="autotest_Digestor">
1690 </xml>
1691 <xml name="autotest_DTAExtractor">
1692 <test expect_num_outputs="1">
1693 <conditional name="adv_opts_cond">
1694 <param name="adv_opts_selector" value="advanced"/>
1695 <param name="force" value="false"/>
1696 <param name="test" value="true"/>
1697 </conditional>
1698 <param name="in" value="DTAExtractor_1_input.mzML"/>
1699 <param name="out" value="DTAExtractor"/>
1700 <param name="mz" value=":"/>
1701 <param name="rt" value=":61"/>
1702 <param name="level" value="1,2,3"/>
1703 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1704 <output name="ctd_out" ftype="xml">
1705 <assert_contents>
1706 <is_valid_xml/>
1707 </assert_contents>
1708 </output>
1709 </test>
1710 <test expect_num_outputs="1">
1711 <conditional name="adv_opts_cond">
1712 <param name="adv_opts_selector" value="advanced"/>
1713 <param name="force" value="false"/>
1714 <param name="test" value="true"/>
1715 </conditional>
1716 <param name="in" value="DTAExtractor_1_input.mzML"/>
1717 <param name="out" value="DTAExtractor"/>
1718 <param name="mz" value=":"/>
1719 <param name="rt" value=":"/>
1720 <param name="level" value="1"/>
1721 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1722 <output name="ctd_out" ftype="xml">
1723 <assert_contents>
1724 <is_valid_xml/>
1725 </assert_contents>
1726 </output>
1727 </test>
1728 <test expect_num_outputs="1">
1729 <conditional name="adv_opts_cond">
1730 <param name="adv_opts_selector" value="advanced"/>
1731 <param name="force" value="false"/>
1732 <param name="test" value="true"/>
1733 </conditional>
1734 <param name="in" value="DTAExtractor_1_input.mzML"/>
1735 <param name="out" value="DTAExtractor"/>
1736 <param name="mz" value=":1000"/>
1737 <param name="rt" value=":"/>
1738 <param name="level" value="2"/>
1739 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1740 <output name="ctd_out" ftype="xml">
1741 <assert_contents>
1742 <is_valid_xml/>
1743 </assert_contents>
1744 </output>
1745 </test>
1746 </xml>
1747 <xml name="autotest_EICExtractor">
1748 </xml>
1749 <xml name="autotest_Epifany">
1750 <test expect_num_outputs="2">
1751 <conditional name="adv_opts_cond">
1752 <param name="adv_opts_selector" value="advanced"/>
1753 <param name="conservative_fdr" value="true"/>
1754 <param name="min_psms_extreme_probability" value="0.0"/>
1755 <param name="force" value="false"/>
1756 <param name="test" value="true"/>
1757 </conditional>
1758 <param name="in" value="FidoAdapter_1_input.idXML"/>
1759 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1760 <param name="out_type" value="idxml"/>
1761 <param name="protein_fdr" value="false"/>
1762 <param name="greedy_group_resolution" value="none"/>
1763 <param name="max_psms_extreme_probability" value="1.0"/>
1764 <section name="algorithm">
1765 <param name="psm_probability_cutoff" value="0.001"/>
1766 <param name="top_PSMs" value="1"/>
1767 <param name="keep_best_PSM_only" value="true"/>
1768 <param name="update_PSM_probabilities" value="true"/>
1769 <param name="user_defined_priors" value="false"/>
1770 <param name="annotate_group_probabilities" value="true"/>
1771 <param name="use_ids_outside_features" value="false"/>
1772 <section name="model_parameters">
1773 <param name="prot_prior" value="0.7"/>
1774 <param name="pep_emission" value="0.1"/>
1775 <param name="pep_spurious_emission" value="0.001"/>
1776 <param name="pep_prior" value="0.1"/>
1777 <param name="regularize" value="false"/>
1778 <param name="extended_model" value="false"/>
1779 </section>
1780 <section name="loopy_belief_propagation">
1781 <param name="scheduling_type" value="priority"/>
1782 <param name="convergence_threshold" value="1e-05"/>
1783 <param name="dampening_lambda" value="0.001"/>
1784 <param name="max_nr_iterations" value="2147483647"/>
1785 <param name="p_norm_inference" value="1.0"/>
1786 </section>
1787 <section name="param_optimize">
1788 <param name="aucweight" value="0.3"/>
1789 <param name="conservative_fdr" value="true"/>
1790 <param name="regularized_fdr" value="true"/>
1791 </section>
1792 </section>
1793 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1794 <output name="ctd_out" ftype="xml">
1795 <assert_contents>
1796 <is_valid_xml/>
1797 </assert_contents>
1798 </output>
1799 </test>
1800 <test expect_num_outputs="2">
1801 <conditional name="adv_opts_cond">
1802 <param name="adv_opts_selector" value="advanced"/>
1803 <param name="conservative_fdr" value="true"/>
1804 <param name="min_psms_extreme_probability" value="0.0"/>
1805 <param name="force" value="false"/>
1806 <param name="test" value="true"/>
1807 </conditional>
1808 <param name="in" value="Epifany_2_input.consensusXML"/>
1809 <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1810 <param name="out_type" value="consensusXML"/>
1811 <param name="protein_fdr" value="false"/>
1812 <param name="greedy_group_resolution" value="none"/>
1813 <param name="max_psms_extreme_probability" value="1.0"/>
1814 <section name="algorithm">
1815 <param name="psm_probability_cutoff" value="0.001"/>
1816 <param name="top_PSMs" value="1"/>
1817 <param name="keep_best_PSM_only" value="true"/>
1818 <param name="update_PSM_probabilities" value="true"/>
1819 <param name="user_defined_priors" value="false"/>
1820 <param name="annotate_group_probabilities" value="true"/>
1821 <param name="use_ids_outside_features" value="false"/>
1822 <section name="model_parameters">
1823 <param name="prot_prior" value="0.7"/>
1824 <param name="pep_emission" value="0.1"/>
1825 <param name="pep_spurious_emission" value="0.001"/>
1826 <param name="pep_prior" value="0.1"/>
1827 <param name="regularize" value="false"/>
1828 <param name="extended_model" value="false"/>
1829 </section>
1830 <section name="loopy_belief_propagation">
1831 <param name="scheduling_type" value="priority"/>
1832 <param name="convergence_threshold" value="1e-05"/>
1833 <param name="dampening_lambda" value="0.001"/>
1834 <param name="max_nr_iterations" value="2147483647"/>
1835 <param name="p_norm_inference" value="1.0"/>
1836 </section>
1837 <section name="param_optimize">
1838 <param name="aucweight" value="0.3"/>
1839 <param name="conservative_fdr" value="true"/>
1840 <param name="regularized_fdr" value="true"/>
1841 </section>
1842 </section>
1843 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1844 <output name="ctd_out" ftype="xml">
1845 <assert_contents>
1846 <is_valid_xml/>
1847 </assert_contents>
1848 </output>
1849 </test>
1850 <test expect_num_outputs="2">
1851 <conditional name="adv_opts_cond">
1852 <param name="adv_opts_selector" value="advanced"/>
1853 <param name="conservative_fdr" value="true"/>
1854 <param name="min_psms_extreme_probability" value="0.0"/>
1855 <param name="force" value="false"/>
1856 <param name="test" value="true"/>
1857 </conditional>
1858 <param name="in" value="Epifany_2_input.consensusXML"/>
1859 <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1860 <param name="out_type" value="consensusXML"/>
1861 <param name="protein_fdr" value="false"/>
1862 <param name="greedy_group_resolution" value="none"/>
1863 <param name="max_psms_extreme_probability" value="1.0"/>
1864 <section name="algorithm">
1865 <param name="psm_probability_cutoff" value="0.001"/>
1866 <param name="top_PSMs" value="1"/>
1867 <param name="keep_best_PSM_only" value="false"/>
1868 <param name="update_PSM_probabilities" value="true"/>
1869 <param name="user_defined_priors" value="false"/>
1870 <param name="annotate_group_probabilities" value="true"/>
1871 <param name="use_ids_outside_features" value="false"/>
1872 <section name="model_parameters">
1873 <param name="prot_prior" value="0.7"/>
1874 <param name="pep_emission" value="0.1"/>
1875 <param name="pep_spurious_emission" value="0.001"/>
1876 <param name="pep_prior" value="0.1"/>
1877 <param name="regularize" value="false"/>
1878 <param name="extended_model" value="false"/>
1879 </section>
1880 <section name="loopy_belief_propagation">
1881 <param name="scheduling_type" value="priority"/>
1882 <param name="convergence_threshold" value="1e-05"/>
1883 <param name="dampening_lambda" value="0.001"/>
1884 <param name="max_nr_iterations" value="2147483647"/>
1885 <param name="p_norm_inference" value="1.0"/>
1886 </section>
1887 <section name="param_optimize">
1888 <param name="aucweight" value="0.3"/>
1889 <param name="conservative_fdr" value="true"/>
1890 <param name="regularized_fdr" value="true"/>
1891 </section>
1892 </section>
1893 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1894 <output name="ctd_out" ftype="xml">
1895 <assert_contents>
1896 <is_valid_xml/>
1897 </assert_contents>
1898 </output>
1899 </test>
1900 </xml>
1901 <xml name="autotest_ERPairFinder">
1902 </xml>
1903 <xml name="autotest_ExternalCalibration">
1904 <test expect_num_outputs="2">
1905 <conditional name="adv_opts_cond">
1906 <param name="adv_opts_selector" value="advanced"/>
1907 <param name="force" value="false"/>
1908 <param name="test" value="true"/>
1909 </conditional>
1910 <param name="in" value="ExternalCalibration_1_input.mzML"/>
1911 <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1912 <param name="offset" value="-5.5"/>
1913 <param name="slope" value="0.0001"/>
1914 <param name="power" value="0.0"/>
1915 <param name="ms_level" value="1"/>
1916 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1917 <output name="ctd_out" ftype="xml">
1918 <assert_contents>
1919 <is_valid_xml/>
1920 </assert_contents>
1921 </output>
1922 </test>
1923 <test expect_num_outputs="2">
1924 <conditional name="adv_opts_cond">
1925 <param name="adv_opts_selector" value="advanced"/>
1926 <param name="force" value="false"/>
1927 <param name="test" value="true"/>
1928 </conditional>
1929 <param name="in" value="ExternalCalibration_1_input.mzML"/>
1930 <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1931 <param name="offset" value="-5.5"/>
1932 <param name="slope" value="0.0001"/>
1933 <param name="power" value="0.0"/>
1934 <param name="ms_level" value="2"/>
1935 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1936 <output name="ctd_out" ftype="xml">
1937 <assert_contents>
1938 <is_valid_xml/>
1939 </assert_contents>
1940 </output>
1941 </test>
1942 </xml>
1943 <xml name="autotest_FalseDiscoveryRate">
1944 <test expect_num_outputs="2">
1945 <conditional name="adv_opts_cond">
1946 <param name="adv_opts_selector" value="advanced"/>
1947 <param name="force" value="false"/>
1948 <param name="test" value="true"/>
1949 </conditional>
1950 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
1951 <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1952 <param name="PSM" value="true"/>
1953 <param name="protein" value="false"/>
1954 <section name="FDR">
1955 <param name="PSM" value="1.0"/>
1956 <param name="protein" value="1.0"/>
1957 <section name="cleanup">
1958 <param name="remove_proteins_without_psms" value="true"/>
1959 <param name="remove_psms_without_proteins" value="true"/>
1960 <param name="remove_spectra_without_psms" value="true"/>
1961 </section>
1962 </section>
1963 <section name="algorithm">
1964 <param name="no_qvalues" value="false"/>
1965 <param name="use_all_hits" value="false"/>
1966 <param name="split_charge_variants" value="false"/>
1967 <param name="treat_runs_separately" value="false"/>
1968 <param name="add_decoy_peptides" value="false"/>
1969 <param name="add_decoy_proteins" value="false"/>
1970 <param name="conservative" value="true"/>
1971 </section>
1972 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1973 <output name="ctd_out" ftype="xml">
1974 <assert_contents>
1975 <is_valid_xml/>
1976 </assert_contents>
1977 </output>
1978 </test>
1979 <test expect_num_outputs="2">
1980 <conditional name="adv_opts_cond">
1981 <param name="adv_opts_selector" value="advanced"/>
1982 <param name="force" value="false"/>
1983 <param name="test" value="true"/>
1984 </conditional>
1985 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
1986 <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1987 <param name="PSM" value="true"/>
1988 <param name="protein" value="false"/>
1989 <section name="FDR">
1990 <param name="PSM" value="1.0"/>
1991 <param name="protein" value="1.0"/>
1992 <section name="cleanup">
1993 <param name="remove_proteins_without_psms" value="true"/>
1994 <param name="remove_psms_without_proteins" value="true"/>
1995 <param name="remove_spectra_without_psms" value="true"/>
1996 </section>
1997 </section>
1998 <section name="algorithm">
1999 <param name="no_qvalues" value="false"/>
2000 <param name="use_all_hits" value="false"/>
2001 <param name="split_charge_variants" value="false"/>
2002 <param name="treat_runs_separately" value="true"/>
2003 <param name="add_decoy_peptides" value="false"/>
2004 <param name="add_decoy_proteins" value="false"/>
2005 <param name="conservative" value="true"/>
2006 </section>
2007 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2008 <output name="ctd_out" ftype="xml">
2009 <assert_contents>
2010 <is_valid_xml/>
2011 </assert_contents>
2012 </output>
2013 </test>
2014 <test expect_num_outputs="2">
2015 <conditional name="adv_opts_cond">
2016 <param name="adv_opts_selector" value="advanced"/>
2017 <param name="force" value="false"/>
2018 <param name="test" value="true"/>
2019 </conditional>
2020 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
2021 <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2022 <param name="PSM" value="true"/>
2023 <param name="protein" value="false"/>
2024 <section name="FDR">
2025 <param name="PSM" value="1.0"/>
2026 <param name="protein" value="1.0"/>
2027 <section name="cleanup">
2028 <param name="remove_proteins_without_psms" value="true"/>
2029 <param name="remove_psms_without_proteins" value="true"/>
2030 <param name="remove_spectra_without_psms" value="true"/>
2031 </section>
2032 </section>
2033 <section name="algorithm">
2034 <param name="no_qvalues" value="false"/>
2035 <param name="use_all_hits" value="false"/>
2036 <param name="split_charge_variants" value="true"/>
2037 <param name="treat_runs_separately" value="false"/>
2038 <param name="add_decoy_peptides" value="false"/>
2039 <param name="add_decoy_proteins" value="false"/>
2040 <param name="conservative" value="true"/>
2041 </section>
2042 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2043 <output name="ctd_out" ftype="xml">
2044 <assert_contents>
2045 <is_valid_xml/>
2046 </assert_contents>
2047 </output>
2048 </test>
2049 <test expect_num_outputs="2">
2050 <conditional name="adv_opts_cond">
2051 <param name="adv_opts_selector" value="advanced"/>
2052 <param name="force" value="false"/>
2053 <param name="test" value="true"/>
2054 </conditional>
2055 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
2056 <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2057 <param name="PSM" value="true"/>
2058 <param name="protein" value="false"/>
2059 <section name="FDR">
2060 <param name="PSM" value="1.0"/>
2061 <param name="protein" value="1.0"/>
2062 <section name="cleanup">
2063 <param name="remove_proteins_without_psms" value="true"/>
2064 <param name="remove_psms_without_proteins" value="true"/>
2065 <param name="remove_spectra_without_psms" value="true"/>
2066 </section>
2067 </section>
2068 <section name="algorithm">
2069 <param name="no_qvalues" value="false"/>
2070 <param name="use_all_hits" value="false"/>
2071 <param name="split_charge_variants" value="true"/>
2072 <param name="treat_runs_separately" value="false"/>
2073 <param name="add_decoy_peptides" value="false"/>
2074 <param name="add_decoy_proteins" value="false"/>
2075 <param name="conservative" value="true"/>
2076 </section>
2077 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2078 <output name="ctd_out" ftype="xml">
2079 <assert_contents>
2080 <is_valid_xml/>
2081 </assert_contents>
2082 </output>
2083 </test>
2084 <test expect_num_outputs="2">
2085 <conditional name="adv_opts_cond">
2086 <param name="adv_opts_selector" value="advanced"/>
2087 <param name="force" value="true"/>
2088 <param name="test" value="true"/>
2089 </conditional>
2090 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
2091 <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2092 <param name="PSM" value="false"/>
2093 <param name="protein" value="true"/>
2094 <section name="FDR">
2095 <param name="PSM" value="1.0"/>
2096 <param name="protein" value="1.0"/>
2097 <section name="cleanup">
2098 <param name="remove_proteins_without_psms" value="true"/>
2099 <param name="remove_psms_without_proteins" value="true"/>
2100 <param name="remove_spectra_without_psms" value="true"/>
2101 </section>
2102 </section>
2103 <section name="algorithm">
2104 <param name="no_qvalues" value="false"/>
2105 <param name="use_all_hits" value="false"/>
2106 <param name="split_charge_variants" value="false"/>
2107 <param name="treat_runs_separately" value="false"/>
2108 <param name="add_decoy_peptides" value="false"/>
2109 <param name="add_decoy_proteins" value="true"/>
2110 <param name="conservative" value="true"/>
2111 </section>
2112 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2113 <output name="ctd_out" ftype="xml">
2114 <assert_contents>
2115 <is_valid_xml/>
2116 </assert_contents>
2117 </output>
2118 </test>
2119 <test expect_num_outputs="2">
2120 <conditional name="adv_opts_cond">
2121 <param name="adv_opts_selector" value="advanced"/>
2122 <param name="force" value="false"/>
2123 <param name="test" value="true"/>
2124 </conditional>
2125 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
2126 <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2127 <param name="PSM" value="true"/>
2128 <param name="protein" value="false"/>
2129 <section name="FDR">
2130 <param name="PSM" value="0.05"/>
2131 <param name="protein" value="1.0"/>
2132 <section name="cleanup">
2133 <param name="remove_proteins_without_psms" value="true"/>
2134 <param name="remove_psms_without_proteins" value="true"/>
2135 <param name="remove_spectra_without_psms" value="true"/>
2136 </section>
2137 </section>
2138 <section name="algorithm">
2139 <param name="no_qvalues" value="false"/>
2140 <param name="use_all_hits" value="false"/>
2141 <param name="split_charge_variants" value="false"/>
2142 <param name="treat_runs_separately" value="false"/>
2143 <param name="add_decoy_peptides" value="false"/>
2144 <param name="add_decoy_proteins" value="false"/>
2145 <param name="conservative" value="true"/>
2146 </section>
2147 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2148 <output name="ctd_out" ftype="xml">
2149 <assert_contents>
2150 <is_valid_xml/>
2151 </assert_contents>
2152 </output>
2153 </test>
2154 <test expect_num_outputs="2">
2155 <conditional name="adv_opts_cond">
2156 <param name="adv_opts_selector" value="advanced"/>
2157 <param name="force" value="true"/>
2158 <param name="test" value="true"/>
2159 </conditional>
2160 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
2161 <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2162 <param name="PSM" value="false"/>
2163 <param name="protein" value="true"/>
2164 <section name="FDR">
2165 <param name="PSM" value="1.0"/>
2166 <param name="protein" value="0.3"/>
2167 <section name="cleanup">
2168 <param name="remove_proteins_without_psms" value="true"/>
2169 <param name="remove_psms_without_proteins" value="true"/>
2170 <param name="remove_spectra_without_psms" value="true"/>
2171 </section>
2172 </section>
2173 <section name="algorithm">
2174 <param name="no_qvalues" value="false"/>
2175 <param name="use_all_hits" value="false"/>
2176 <param name="split_charge_variants" value="false"/>
2177 <param name="treat_runs_separately" value="false"/>
2178 <param name="add_decoy_peptides" value="false"/>
2179 <param name="add_decoy_proteins" value="false"/>
2180 <param name="conservative" value="true"/>
2181 </section>
2182 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2183 <output name="ctd_out" ftype="xml">
2184 <assert_contents>
2185 <is_valid_xml/>
2186 </assert_contents>
2187 </output>
2188 </test>
2189 </xml>
2190 <xml name="autotest_FeatureFinderCentroided">
2191 <test expect_num_outputs="2">
2192 <conditional name="adv_opts_cond">
2193 <param name="adv_opts_selector" value="advanced"/>
2194 <param name="force" value="false"/>
2195 <param name="test" value="true"/>
2196 <param name="pseudo_rt_shift" value="500.0"/>
2197 </conditional>
2198 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
2199 <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2200 <section name="algorithm">
2201 <section name="intensity">
2202 <param name="bins" value="1"/>
2203 </section>
2204 <section name="mass_trace">
2205 <param name="mz_tolerance" value="0.02"/>
2206 <param name="min_spectra" value="14"/>
2207 <param name="max_missing" value="1"/>
2208 <param name="slope_bound" value="0.1"/>
2209 </section>
2210 <section name="isotopic_pattern">
2211 <param name="charge_low" value="2"/>
2212 <param name="charge_high" value="2"/>
2213 <param name="mz_tolerance" value="0.02"/>
2214 <param name="intensity_percentage" value="10.0"/>
2215 <param name="intensity_percentage_optional" value="0.1"/>
2216 <param name="optional_fit_improvement" value="2.0"/>
2217 <param name="mass_window_width" value="100.0"/>
2218 <param name="abundance_12C" value="98.93"/>
2219 <param name="abundance_14N" value="99.632"/>
2220 </section>
2221 <section name="seed">
2222 <param name="min_score" value="0.8"/>
2223 </section>
2224 <section name="fit">
2225 <param name="max_iterations" value="500"/>
2226 </section>
2227 <section name="feature">
2228 <param name="min_score" value="0.7"/>
2229 <param name="min_isotope_fit" value="0.8"/>
2230 <param name="min_trace_score" value="0.5"/>
2231 <param name="min_rt_span" value="0.333"/>
2232 <param name="max_rt_span" value="2.5"/>
2233 <param name="rt_shape" value="symmetric"/>
2234 <param name="max_intersection" value="0.35"/>
2235 <param name="reported_mz" value="monoisotopic"/>
2236 </section>
2237 <section name="user-seed">
2238 <param name="rt_tolerance" value="5.0"/>
2239 <param name="mz_tolerance" value="1.1"/>
2240 <param name="min_score" value="0.5"/>
2241 </section>
2242 </section>
2243 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2244 <output name="ctd_out" ftype="xml">
2245 <assert_contents>
2246 <is_valid_xml/>
2247 </assert_contents>
2248 </output>
2249 </test>
2250 </xml>
2251 <xml name="autotest_FeatureFinderIdentification">
2252 <test expect_num_outputs="2">
2253 <conditional name="adv_opts_cond">
2254 <param name="adv_opts_selector" value="advanced"/>
2255 <param name="force" value="false"/>
2256 <param name="test" value="true"/>
2257 </conditional>
2258 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
2259 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
2260 <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2261 <section name="extract">
2262 <param name="batch_size" value="1000"/>
2263 <param name="mz_window" value="0.1"/>
2264 <param name="n_isotopes" value="2"/>
2265 <param name="isotope_pmin" value="0.0"/>
2266 <param name="rt_quantile" value="0.95"/>
2267 <param name="rt_window" value="0.0"/>
2268 </section>
2269 <section name="detect">
2270 <param name="peak_width" value="60.0"/>
2271 <param name="min_peak_width" value="0.2"/>
2272 <param name="signal_to_noise" value="0.8"/>
2273 <param name="mapping_tolerance" value="0.0"/>
2274 </section>
2275 <section name="svm">
2276 <param name="samples" value="0"/>
2277 <param name="no_selection" value="false"/>
2278 <param name="kernel" value="RBF"/>
2279 <param name="xval" value="5"/>
2280 <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"/>
2281 <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"/>
2282 <param name="epsilon" value="0.001"/>
2283 <param name="cache_size" value="100.0"/>
2284 <param name="no_shrinking" value="false"/>
2285 <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"/>
2286 <param name="min_prob" value="0.0"/>
2287 </section>
2288 <section name="model">
2289 <param name="type" value="none"/>
2290 <param name="add_zeros" value="0.2"/>
2291 <param name="unweighted_fit" value="false"/>
2292 <param name="no_imputation" value="false"/>
2293 <param name="each_trace" value="false"/>
2294 <section name="check">
2295 <param name="min_area" value="1.0"/>
2296 <param name="boundaries" value="0.5"/>
2297 <param name="width" value="10.0"/>
2298 <param name="asymmetry" value="10.0"/>
2299 </section>
2300 </section>
2301 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2302 <output name="ctd_out" ftype="xml">
2303 <assert_contents>
2304 <is_valid_xml/>
2305 </assert_contents>
2306 </output>
2307 </test>
2308 <test expect_num_outputs="2">
2309 <conditional name="adv_opts_cond">
2310 <param name="adv_opts_selector" value="advanced"/>
2311 <param name="force" value="false"/>
2312 <param name="test" value="true"/>
2313 </conditional>
2314 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
2315 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
2316 <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2317 <section name="extract">
2318 <param name="batch_size" value="1000"/>
2319 <param name="mz_window" value="0.1"/>
2320 <param name="n_isotopes" value="2"/>
2321 <param name="isotope_pmin" value="0.0"/>
2322 <param name="rt_quantile" value="0.95"/>
2323 <param name="rt_window" value="0.0"/>
2324 </section>
2325 <section name="detect">
2326 <param name="peak_width" value="60.0"/>
2327 <param name="min_peak_width" value="0.2"/>
2328 <param name="signal_to_noise" value="0.8"/>
2329 <param name="mapping_tolerance" value="0.0"/>
2330 </section>
2331 <section name="svm">
2332 <param name="samples" value="0"/>
2333 <param name="no_selection" value="false"/>
2334 <param name="kernel" value="RBF"/>
2335 <param name="xval" value="5"/>
2336 <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"/>
2337 <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"/>
2338 <param name="epsilon" value="0.001"/>
2339 <param name="cache_size" value="100.0"/>
2340 <param name="no_shrinking" value="false"/>
2341 <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"/>
2342 <param name="min_prob" value="0.0"/>
2343 </section>
2344 <section name="model">
2345 <param name="type" value="symmetric"/>
2346 <param name="add_zeros" value="0.2"/>
2347 <param name="unweighted_fit" value="false"/>
2348 <param name="no_imputation" value="false"/>
2349 <param name="each_trace" value="false"/>
2350 <section name="check">
2351 <param name="min_area" value="1.0"/>
2352 <param name="boundaries" value="0.5"/>
2353 <param name="width" value="10.0"/>
2354 <param name="asymmetry" value="10.0"/>
2355 </section>
2356 </section>
2357 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2358 <output name="ctd_out" ftype="xml">
2359 <assert_contents>
2360 <is_valid_xml/>
2361 </assert_contents>
2362 </output>
2363 </test>
2364 </xml>
2365 <xml name="autotest_FeatureFinderIsotopeWavelet">
2366 </xml>
2367 <xml name="autotest_FeatureFinderMetaboIdent">
2368 <test expect_num_outputs="2">
2369 <conditional name="adv_opts_cond">
2370 <param name="adv_opts_selector" value="advanced"/>
2371 <param name="force" value="false"/>
2372 <param name="test" value="true"/>
2373 </conditional>
2374 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
2375 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
2376 <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2377 <section name="extract">
2378 <param name="mz_window" value="5.0"/>
2379 <param name="n_isotopes" value="2"/>
2380 <param name="isotope_pmin" value="0.0"/>
2381 <param name="rt_window" value="20.0"/>
2382 </section>
2383 <section name="detect">
2384 <param name="peak_width" value="3.0"/>
2385 <param name="min_peak_width" value="0.2"/>
2386 <param name="signal_to_noise" value="0.8"/>
2387 </section>
2388 <section name="model">
2389 <param name="type" value="symmetric"/>
2390 <param name="add_zeros" value="0.2"/>
2391 <param name="unweighted_fit" value="false"/>
2392 <param name="no_imputation" value="false"/>
2393 <param name="each_trace" value="false"/>
2394 <section name="check">
2395 <param name="min_area" value="1.0"/>
2396 <param name="boundaries" value="0.5"/>
2397 <param name="width" value="10.0"/>
2398 <param name="asymmetry" value="10.0"/>
2399 </section>
2400 </section>
2401 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2402 <output name="ctd_out" ftype="xml">
2403 <assert_contents>
2404 <is_valid_xml/>
2405 </assert_contents>
2406 </output>
2407 </test>
2408 </xml>
2409 <xml name="autotest_FeatureFinderMetabo">
2410 <test expect_num_outputs="2">
2411 <conditional name="adv_opts_cond">
2412 <param name="adv_opts_selector" value="advanced"/>
2413 <param name="force" value="false"/>
2414 <param name="test" value="true"/>
2415 </conditional>
2416 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
2417 <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2418 <section name="algorithm">
2419 <section name="common">
2420 <param name="noise_threshold_int" value="10.0"/>
2421 <param name="chrom_peak_snr" value="3.0"/>
2422 <param name="chrom_fwhm" value="5.0"/>
2423 </section>
2424 <section name="mtd">
2425 <param name="mass_error_ppm" value="20.0"/>
2426 <param name="reestimate_mt_sd" value="true"/>
2427 <param name="quant_method" value="area"/>
2428 <param name="trace_termination_criterion" value="outlier"/>
2429 <param name="trace_termination_outliers" value="5"/>
2430 <param name="min_sample_rate" value="0.5"/>
2431 <param name="min_trace_length" value="5.0"/>
2432 <param name="max_trace_length" value="300.0"/>
2433 </section>
2434 <section name="epd">
2435 <param name="enabled" value="true"/>
2436 <param name="width_filtering" value="off"/>
2437 <param name="min_fwhm" value="3.0"/>
2438 <param name="max_fwhm" value="60.0"/>
2439 <param name="masstrace_snr_filtering" value="false"/>
2440 </section>
2441 <section name="ffm">
2442 <param name="local_rt_range" value="10.0"/>
2443 <param name="local_mz_range" value="6.5"/>
2444 <param name="charge_lower_bound" value="1"/>
2445 <param name="charge_upper_bound" value="3"/>
2446 <param name="report_summed_ints" value="false"/>
2447 <param name="enable_RT_filtering" value="true"/>
2448 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
2449 <param name="mz_scoring_13C" value="true"/>
2450 <param name="use_smoothed_intensities" value="true"/>
2451 <param name="report_convex_hulls" value="false"/>
2452 <param name="remove_single_traces" value="false"/>
2453 <param name="mz_scoring_by_elements" value="false"/>
2454 <param name="elements" value="CHNOPS"/>
2455 </section>
2456 </section>
2457 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2458 <output name="ctd_out" ftype="xml">
2459 <assert_contents>
2460 <is_valid_xml/>
2461 </assert_contents>
2462 </output>
2463 </test>
2464 <test expect_num_outputs="2">
2465 <conditional name="adv_opts_cond">
2466 <param name="adv_opts_selector" value="advanced"/>
2467 <param name="force" value="false"/>
2468 <param name="test" value="true"/>
2469 </conditional>
2470 <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
2471 <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2472 <section name="algorithm">
2473 <section name="common">
2474 <param name="noise_threshold_int" value="100.0"/>
2475 <param name="chrom_peak_snr" value="0.0"/>
2476 <param name="chrom_fwhm" value="100.0"/>
2477 </section>
2478 <section name="mtd">
2479 <param name="mass_error_ppm" value="5.0"/>
2480 <param name="reestimate_mt_sd" value="true"/>
2481 <param name="quant_method" value="median"/>
2482 <param name="trace_termination_criterion" value="sample_rate"/>
2483 <param name="trace_termination_outliers" value="2"/>
2484 <param name="min_sample_rate" value="0.01"/>
2485 <param name="min_trace_length" value="30.0"/>
2486 <param name="max_trace_length" value="3000.0"/>
2487 </section>
2488 <section name="epd">
2489 <param name="enabled" value="false"/>
2490 <param name="width_filtering" value="off"/>
2491 <param name="min_fwhm" value="10.0"/>
2492 <param name="max_fwhm" value="80.0"/>
2493 <param name="masstrace_snr_filtering" value="false"/>
2494 </section>
2495 <section name="ffm">
2496 <param name="local_rt_range" value="10.0"/>
2497 <param name="local_mz_range" value="4.5"/>
2498 <param name="charge_lower_bound" value="1"/>
2499 <param name="charge_upper_bound" value="3"/>
2500 <param name="report_summed_ints" value="false"/>
2501 <param name="enable_RT_filtering" value="false"/>
2502 <param name="isotope_filtering_model" value="none"/>
2503 <param name="mz_scoring_13C" value="false"/>
2504 <param name="use_smoothed_intensities" value="false"/>
2505 <param name="report_convex_hulls" value="true"/>
2506 <param name="remove_single_traces" value="false"/>
2507 <param name="mz_scoring_by_elements" value="false"/>
2508 <param name="elements" value="CHNOPS"/>
2509 </section>
2510 </section>
2511 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2512 <output name="ctd_out" ftype="xml">
2513 <assert_contents>
2514 <is_valid_xml/>
2515 </assert_contents>
2516 </output>
2517 </test>
2518 <test expect_num_outputs="3">
2519 <conditional name="adv_opts_cond">
2520 <param name="adv_opts_selector" value="advanced"/>
2521 <param name="force" value="false"/>
2522 <param name="test" value="true"/>
2523 </conditional>
2524 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
2525 <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
2526 <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
2527 <section name="algorithm">
2528 <section name="common">
2529 <param name="noise_threshold_int" value="10.0"/>
2530 <param name="chrom_peak_snr" value="3.0"/>
2531 <param name="chrom_fwhm" value="5.0"/>
2532 </section>
2533 <section name="mtd">
2534 <param name="mass_error_ppm" value="5.0"/>
2535 <param name="reestimate_mt_sd" value="true"/>
2536 <param name="quant_method" value="area"/>
2537 <param name="trace_termination_criterion" value="outlier"/>
2538 <param name="trace_termination_outliers" value="5"/>
2539 <param name="min_sample_rate" value="0.5"/>
2540 <param name="min_trace_length" value="5.0"/>
2541 <param name="max_trace_length" value="-1.0"/>
2542 </section>
2543 <section name="epd">
2544 <param name="enabled" value="true"/>
2545 <param name="width_filtering" value="fixed"/>
2546 <param name="min_fwhm" value="3.0"/>
2547 <param name="max_fwhm" value="60.0"/>
2548 <param name="masstrace_snr_filtering" value="false"/>
2549 </section>
2550 <section name="ffm">
2551 <param name="local_rt_range" value="10.0"/>
2552 <param name="local_mz_range" value="6.5"/>
2553 <param name="charge_lower_bound" value="1"/>
2554 <param name="charge_upper_bound" value="3"/>
2555 <param name="report_summed_ints" value="false"/>
2556 <param name="enable_RT_filtering" value="true"/>
2557 <param name="isotope_filtering_model" value="none"/>
2558 <param name="mz_scoring_13C" value="true"/>
2559 <param name="use_smoothed_intensities" value="true"/>
2560 <param name="report_convex_hulls" value="true"/>
2561 <param name="remove_single_traces" value="false"/>
2562 <param name="mz_scoring_by_elements" value="false"/>
2563 <param name="elements" value="CHNOPS"/>
2564 </section>
2565 </section>
2566 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
2567 <output name="ctd_out" ftype="xml">
2568 <assert_contents>
2569 <is_valid_xml/>
2570 </assert_contents>
2571 </output>
2572 </test>
2573 <test expect_num_outputs="3">
2574 <conditional name="adv_opts_cond">
2575 <param name="adv_opts_selector" value="advanced"/>
2576 <param name="force" value="false"/>
2577 <param name="test" value="true"/>
2578 </conditional>
2579 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
2580 <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2581 <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
2582 <section name="algorithm">
2583 <section name="common">
2584 <param name="noise_threshold_int" value="10.0"/>
2585 <param name="chrom_peak_snr" value="3.0"/>
2586 <param name="chrom_fwhm" value="5.0"/>
2587 </section>
2588 <section name="mtd">
2589 <param name="mass_error_ppm" value="5.0"/>
2590 <param name="reestimate_mt_sd" value="true"/>
2591 <param name="quant_method" value="area"/>
2592 <param name="trace_termination_criterion" value="outlier"/>
2593 <param name="trace_termination_outliers" value="5"/>
2594 <param name="min_sample_rate" value="0.5"/>
2595 <param name="min_trace_length" value="5.0"/>
2596 <param name="max_trace_length" value="-1.0"/>
2597 </section>
2598 <section name="epd">
2599 <param name="enabled" value="true"/>
2600 <param name="width_filtering" value="fixed"/>
2601 <param name="min_fwhm" value="3.0"/>
2602 <param name="max_fwhm" value="60.0"/>
2603 <param name="masstrace_snr_filtering" value="false"/>
2604 </section>
2605 <section name="ffm">
2606 <param name="local_rt_range" value="10.0"/>
2607 <param name="local_mz_range" value="6.5"/>
2608 <param name="charge_lower_bound" value="1"/>
2609 <param name="charge_upper_bound" value="3"/>
2610 <param name="report_summed_ints" value="false"/>
2611 <param name="enable_RT_filtering" value="true"/>
2612 <param name="isotope_filtering_model" value="none"/>
2613 <param name="mz_scoring_13C" value="true"/>
2614 <param name="use_smoothed_intensities" value="true"/>
2615 <param name="report_convex_hulls" value="true"/>
2616 <param name="remove_single_traces" value="true"/>
2617 <param name="mz_scoring_by_elements" value="false"/>
2618 <param name="elements" value="CHNOPS"/>
2619 </section>
2620 </section>
2621 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
2622 <output name="ctd_out" ftype="xml">
2623 <assert_contents>
2624 <is_valid_xml/>
2625 </assert_contents>
2626 </output>
2627 </test>
2628 <test expect_num_outputs="2">
2629 <conditional name="adv_opts_cond">
2630 <param name="adv_opts_selector" value="advanced"/>
2631 <param name="force" value="false"/>
2632 <param name="test" value="true"/>
2633 </conditional>
2634 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
2635 <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2636 <section name="algorithm">
2637 <section name="common">
2638 <param name="noise_threshold_int" value="10.0"/>
2639 <param name="chrom_peak_snr" value="3.0"/>
2640 <param name="chrom_fwhm" value="5.0"/>
2641 </section>
2642 <section name="mtd">
2643 <param name="mass_error_ppm" value="20.0"/>
2644 <param name="reestimate_mt_sd" value="true"/>
2645 <param name="quant_method" value="max_height"/>
2646 <param name="trace_termination_criterion" value="outlier"/>
2647 <param name="trace_termination_outliers" value="5"/>
2648 <param name="min_sample_rate" value="0.5"/>
2649 <param name="min_trace_length" value="5.0"/>
2650 <param name="max_trace_length" value="300.0"/>
2651 </section>
2652 <section name="epd">
2653 <param name="enabled" value="true"/>
2654 <param name="width_filtering" value="off"/>
2655 <param name="min_fwhm" value="3.0"/>
2656 <param name="max_fwhm" value="60.0"/>
2657 <param name="masstrace_snr_filtering" value="false"/>
2658 </section>
2659 <section name="ffm">
2660 <param name="local_rt_range" value="10.0"/>
2661 <param name="local_mz_range" value="6.5"/>
2662 <param name="charge_lower_bound" value="1"/>
2663 <param name="charge_upper_bound" value="3"/>
2664 <param name="report_summed_ints" value="false"/>
2665 <param name="enable_RT_filtering" value="true"/>
2666 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
2667 <param name="mz_scoring_13C" value="true"/>
2668 <param name="use_smoothed_intensities" value="true"/>
2669 <param name="report_convex_hulls" value="false"/>
2670 <param name="remove_single_traces" value="false"/>
2671 <param name="mz_scoring_by_elements" value="false"/>
2672 <param name="elements" value="CHNOPS"/>
2673 </section>
2674 </section>
2675 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2676 <output name="ctd_out" ftype="xml">
2677 <assert_contents>
2678 <is_valid_xml/>
2679 </assert_contents>
2680 </output>
2681 </test>
2682 </xml>
2683 <xml name="autotest_FeatureFinderMRM">
2684 <test expect_num_outputs="2">
2685 <conditional name="adv_opts_cond">
2686 <param name="adv_opts_selector" value="advanced"/>
2687 <param name="force" value="false"/>
2688 <param name="test" value="true"/>
2689 </conditional>
2690 <param name="in" value="FeatureFinderMRM_1_input.mzML"/>
2691 <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2692 <section name="algorithm">
2693 <param name="min_rt_distance" value="10.0"/>
2694 <param name="min_num_peaks_per_feature" value="5"/>
2695 <param name="min_signal_to_noise_ratio" value="2.0"/>
2696 <param name="write_debug_files" value="false"/>
2697 <param name="resample_traces" value="false"/>
2698 <param name="write_debuginfo" value="false"/>
2699 </section>
2700 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2701 <output name="ctd_out" ftype="xml">
2702 <assert_contents>
2703 <is_valid_xml/>
2704 </assert_contents>
2705 </output>
2706 </test>
2707 </xml>
2708 <xml name="autotest_FeatureFinderMultiplex">
2709 <test expect_num_outputs="3">
2710 <conditional name="adv_opts_cond">
2711 <param name="adv_opts_selector" value="advanced"/>
2712 <param name="force" value="false"/>
2713 <param name="test" value="true"/>
2714 </conditional>
2715 <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
2716 <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2717 <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2718 <section name="algorithm">
2719 <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
2720 <param name="charge" value="1:4"/>
2721 <param name="isotopes_per_peptide" value="3:6"/>
2722 <param name="rt_typical" value="90.0"/>
2723 <param name="rt_band" value="10.0"/>
2724 <param name="rt_min" value="5.0"/>
2725 <param name="mz_tolerance" value="40.0"/>
2726 <param name="mz_unit" value="ppm"/>
2727 <param name="intensity_cutoff" value="10.0"/>
2728 <param name="peptide_similarity" value="0.8"/>
2729 <param name="averagine_similarity" value="0.75"/>
2730 <param name="averagine_similarity_scaling" value="0.75"/>
2731 <param name="missed_cleavages" value="1"/>
2732 <param name="spectrum_type" value="automatic"/>
2733 <param name="averagine_type" value="peptide"/>
2734 <param name="knock_out" value="false"/>
2735 </section>
2736 <section name="labels">
2737 <param name="Arg6" value="6.0201290268"/>
2738 <param name="Arg10" value="10.0082686"/>
2739 <param name="Lys4" value="4.0251069836"/>
2740 <param name="Lys6" value="6.0201290268"/>
2741 <param name="Lys8" value="8.0141988132"/>
2742 <param name="Leu3" value="3.01883"/>
2743 <param name="Dimethyl0" value="28.0313"/>
2744 <param name="Dimethyl4" value="32.056407"/>
2745 <param name="Dimethyl6" value="34.063117"/>
2746 <param name="Dimethyl8" value="36.07567"/>
2747 <param name="ICPL0" value="105.021464"/>
2748 <param name="ICPL4" value="109.046571"/>
2749 <param name="ICPL6" value="111.041593"/>
2750 <param name="ICPL10" value="115.0667"/>
2751 </section>
2752 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2753 <output name="ctd_out" ftype="xml">
2754 <assert_contents>
2755 <is_valid_xml/>
2756 </assert_contents>
2757 </output>
2758 </test>
2759 <test expect_num_outputs="3">
2760 <conditional name="adv_opts_cond">
2761 <param name="adv_opts_selector" value="advanced"/>
2762 <param name="force" value="false"/>
2763 <param name="test" value="true"/>
2764 </conditional>
2765 <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
2766 <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2767 <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2768 <section name="algorithm">
2769 <param name="labels" value="[][Lys8,Arg10]"/>
2770 <param name="charge" value="1:4"/>
2771 <param name="isotopes_per_peptide" value="3:6"/>
2772 <param name="rt_typical" value="40.0"/>
2773 <param name="rt_band" value="5.0"/>
2774 <param name="rt_min" value="2.0"/>
2775 <param name="mz_tolerance" value="6.0"/>
2776 <param name="mz_unit" value="ppm"/>
2777 <param name="intensity_cutoff" value="1000.0"/>
2778 <param name="peptide_similarity" value="0.5"/>
2779 <param name="averagine_similarity" value="0.4"/>
2780 <param name="averagine_similarity_scaling" value="0.75"/>
2781 <param name="missed_cleavages" value="0"/>
2782 <param name="spectrum_type" value="automatic"/>
2783 <param name="averagine_type" value="peptide"/>
2784 <param name="knock_out" value="false"/>
2785 </section>
2786 <section name="labels">
2787 <param name="Arg6" value="6.0201290268"/>
2788 <param name="Arg10" value="10.0082686"/>
2789 <param name="Lys4" value="4.0251069836"/>
2790 <param name="Lys6" value="6.0201290268"/>
2791 <param name="Lys8" value="8.0141988132"/>
2792 <param name="Leu3" value="3.01883"/>
2793 <param name="Dimethyl0" value="28.0313"/>
2794 <param name="Dimethyl4" value="32.056407"/>
2795 <param name="Dimethyl6" value="34.063117"/>
2796 <param name="Dimethyl8" value="36.07567"/>
2797 <param name="ICPL0" value="105.021464"/>
2798 <param name="ICPL4" value="109.046571"/>
2799 <param name="ICPL6" value="111.041593"/>
2800 <param name="ICPL10" value="115.0667"/>
2801 </section>
2802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2803 <output name="ctd_out" ftype="xml">
2804 <assert_contents>
2805 <is_valid_xml/>
2806 </assert_contents>
2807 </output>
2808 </test>
2809 <test expect_num_outputs="3">
2810 <conditional name="adv_opts_cond">
2811 <param name="adv_opts_selector" value="advanced"/>
2812 <param name="force" value="false"/>
2813 <param name="test" value="true"/>
2814 </conditional>
2815 <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
2816 <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2817 <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2818 <section name="algorithm">
2819 <param name="labels" value="[]"/>
2820 <param name="charge" value="5:15"/>
2821 <param name="isotopes_per_peptide" value="5:10"/>
2822 <param name="rt_typical" value="45.0"/>
2823 <param name="rt_band" value="5.0"/>
2824 <param name="rt_min" value="2.0"/>
2825 <param name="mz_tolerance" value="6.0"/>
2826 <param name="mz_unit" value="ppm"/>
2827 <param name="intensity_cutoff" value="200.0"/>
2828 <param name="peptide_similarity" value="0.5"/>
2829 <param name="averagine_similarity" value="0.4"/>
2830 <param name="averagine_similarity_scaling" value="0.75"/>
2831 <param name="missed_cleavages" value="0"/>
2832 <param name="spectrum_type" value="automatic"/>
2833 <param name="averagine_type" value="RNA"/>
2834 <param name="knock_out" value="false"/>
2835 </section>
2836 <section name="labels">
2837 <param name="Arg6" value="6.0201290268"/>
2838 <param name="Arg10" value="10.0082686"/>
2839 <param name="Lys4" value="4.0251069836"/>
2840 <param name="Lys6" value="6.0201290268"/>
2841 <param name="Lys8" value="8.0141988132"/>
2842 <param name="Leu3" value="3.01883"/>
2843 <param name="Dimethyl0" value="28.0313"/>
2844 <param name="Dimethyl4" value="32.056407"/>
2845 <param name="Dimethyl6" value="34.063117"/>
2846 <param name="Dimethyl8" value="36.07567"/>
2847 <param name="ICPL0" value="105.021464"/>
2848 <param name="ICPL4" value="109.046571"/>
2849 <param name="ICPL6" value="111.041593"/>
2850 <param name="ICPL10" value="115.0667"/>
2851 </section>
2852 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2853 <output name="ctd_out" ftype="xml">
2854 <assert_contents>
2855 <is_valid_xml/>
2856 </assert_contents>
2857 </output>
2858 </test>
2859 <test expect_num_outputs="3">
2860 <conditional name="adv_opts_cond">
2861 <param name="adv_opts_selector" value="advanced"/>
2862 <param name="force" value="false"/>
2863 <param name="test" value="true"/>
2864 </conditional>
2865 <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
2866 <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2867 <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2868 <section name="algorithm">
2869 <param name="labels" value="[]"/>
2870 <param name="charge" value="5:15"/>
2871 <param name="isotopes_per_peptide" value="5:10"/>
2872 <param name="rt_typical" value="45.0"/>
2873 <param name="rt_band" value="5.0"/>
2874 <param name="rt_min" value="2.0"/>
2875 <param name="mz_tolerance" value="6.0"/>
2876 <param name="mz_unit" value="ppm"/>
2877 <param name="intensity_cutoff" value="200.0"/>
2878 <param name="peptide_similarity" value="0.5"/>
2879 <param name="averagine_similarity" value="0.4"/>
2880 <param name="averagine_similarity_scaling" value="0.75"/>
2881 <param name="missed_cleavages" value="0"/>
2882 <param name="spectrum_type" value="automatic"/>
2883 <param name="averagine_type" value="DNA"/>
2884 <param name="knock_out" value="false"/>
2885 </section>
2886 <section name="labels">
2887 <param name="Arg6" value="6.0201290268"/>
2888 <param name="Arg10" value="10.0082686"/>
2889 <param name="Lys4" value="4.0251069836"/>
2890 <param name="Lys6" value="6.0201290268"/>
2891 <param name="Lys8" value="8.0141988132"/>
2892 <param name="Leu3" value="3.01883"/>
2893 <param name="Dimethyl0" value="28.0313"/>
2894 <param name="Dimethyl4" value="32.056407"/>
2895 <param name="Dimethyl6" value="34.063117"/>
2896 <param name="Dimethyl8" value="36.07567"/>
2897 <param name="ICPL0" value="105.021464"/>
2898 <param name="ICPL4" value="109.046571"/>
2899 <param name="ICPL6" value="111.041593"/>
2900 <param name="ICPL10" value="115.0667"/>
2901 </section>
2902 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2903 <output name="ctd_out" ftype="xml">
2904 <assert_contents>
2905 <is_valid_xml/>
2906 </assert_contents>
2907 </output>
2908 </test>
2909 <test expect_num_outputs="3">
2910 <conditional name="adv_opts_cond">
2911 <param name="adv_opts_selector" value="advanced"/>
2912 <param name="force" value="false"/>
2913 <param name="test" value="true"/>
2914 </conditional>
2915 <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
2916 <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2917 <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2918 <section name="algorithm">
2919 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
2920 <param name="charge" value="1:5"/>
2921 <param name="isotopes_per_peptide" value="3:6"/>
2922 <param name="rt_typical" value="50.0"/>
2923 <param name="rt_band" value="3.0"/>
2924 <param name="rt_min" value="8.0"/>
2925 <param name="mz_tolerance" value="10.0"/>
2926 <param name="mz_unit" value="ppm"/>
2927 <param name="intensity_cutoff" value="10000000.0"/>
2928 <param name="peptide_similarity" value="0.95"/>
2929 <param name="averagine_similarity" value="0.8"/>
2930 <param name="averagine_similarity_scaling" value="0.95"/>
2931 <param name="missed_cleavages" value="3"/>
2932 <param name="spectrum_type" value="profile"/>
2933 <param name="averagine_type" value="peptide"/>
2934 <param name="knock_out" value="false"/>
2935 </section>
2936 <section name="labels">
2937 <param name="Arg6" value="6.0201290268"/>
2938 <param name="Arg10" value="10.0082686"/>
2939 <param name="Lys4" value="4.0251069836"/>
2940 <param name="Lys6" value="6.0201290268"/>
2941 <param name="Lys8" value="8.0141988132"/>
2942 <param name="Leu3" value="3.01883"/>
2943 <param name="Dimethyl0" value="28.0313"/>
2944 <param name="Dimethyl4" value="32.056407"/>
2945 <param name="Dimethyl6" value="34.063117"/>
2946 <param name="Dimethyl8" value="36.07567"/>
2947 <param name="ICPL0" value="105.021464"/>
2948 <param name="ICPL4" value="109.046571"/>
2949 <param name="ICPL6" value="111.041593"/>
2950 <param name="ICPL10" value="115.0667"/>
2951 </section>
2952 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2953 <output name="ctd_out" ftype="xml">
2954 <assert_contents>
2955 <is_valid_xml/>
2956 </assert_contents>
2957 </output>
2958 </test>
2959 <test expect_num_outputs="3">
2960 <conditional name="adv_opts_cond">
2961 <param name="adv_opts_selector" value="advanced"/>
2962 <param name="force" value="false"/>
2963 <param name="test" value="true"/>
2964 </conditional>
2965 <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
2966 <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2967 <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2968 <section name="algorithm">
2969 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
2970 <param name="charge" value="1:5"/>
2971 <param name="isotopes_per_peptide" value="3:6"/>
2972 <param name="rt_typical" value="50.0"/>
2973 <param name="rt_band" value="3.0"/>
2974 <param name="rt_min" value="8.0"/>
2975 <param name="mz_tolerance" value="10.0"/>
2976 <param name="mz_unit" value="ppm"/>
2977 <param name="intensity_cutoff" value="10000000.0"/>
2978 <param name="peptide_similarity" value="0.95"/>
2979 <param name="averagine_similarity" value="0.8"/>
2980 <param name="averagine_similarity_scaling" value="1.0"/>
2981 <param name="missed_cleavages" value="3"/>
2982 <param name="spectrum_type" value="profile"/>
2983 <param name="averagine_type" value="peptide"/>
2984 <param name="knock_out" value="false"/>
2985 </section>
2986 <section name="labels">
2987 <param name="Arg6" value="6.0201290268"/>
2988 <param name="Arg10" value="10.0082686"/>
2989 <param name="Lys4" value="4.0251069836"/>
2990 <param name="Lys6" value="6.0201290268"/>
2991 <param name="Lys8" value="8.0141988132"/>
2992 <param name="Leu3" value="3.01883"/>
2993 <param name="Dimethyl0" value="28.0313"/>
2994 <param name="Dimethyl4" value="32.056407"/>
2995 <param name="Dimethyl6" value="34.063117"/>
2996 <param name="Dimethyl8" value="36.07567"/>
2997 <param name="ICPL0" value="105.021464"/>
2998 <param name="ICPL4" value="109.046571"/>
2999 <param name="ICPL6" value="111.041593"/>
3000 <param name="ICPL10" value="115.0667"/>
3001 </section>
3002 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3003 <output name="ctd_out" ftype="xml">
3004 <assert_contents>
3005 <is_valid_xml/>
3006 </assert_contents>
3007 </output>
3008 </test>
3009 <test expect_num_outputs="3">
3010 <conditional name="adv_opts_cond">
3011 <param name="adv_opts_selector" value="advanced"/>
3012 <param name="force" value="false"/>
3013 <param name="test" value="true"/>
3014 </conditional>
3015 <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
3016 <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3017 <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3018 <section name="algorithm">
3019 <param name="labels" value="[][Dimethyl4]"/>
3020 <param name="charge" value="1:4"/>
3021 <param name="isotopes_per_peptide" value="3:6"/>
3022 <param name="rt_typical" value="40.0"/>
3023 <param name="rt_band" value="5.0"/>
3024 <param name="rt_min" value="2.0"/>
3025 <param name="mz_tolerance" value="6.0"/>
3026 <param name="mz_unit" value="ppm"/>
3027 <param name="intensity_cutoff" value="1000.0"/>
3028 <param name="peptide_similarity" value="0.5"/>
3029 <param name="averagine_similarity" value="0.4"/>
3030 <param name="averagine_similarity_scaling" value="0.75"/>
3031 <param name="missed_cleavages" value="0"/>
3032 <param name="spectrum_type" value="automatic"/>
3033 <param name="averagine_type" value="peptide"/>
3034 <param name="knock_out" value="false"/>
3035 </section>
3036 <section name="labels">
3037 <param name="Arg6" value="6.0201290268"/>
3038 <param name="Arg10" value="10.0082686"/>
3039 <param name="Lys4" value="4.0251069836"/>
3040 <param name="Lys6" value="6.0201290268"/>
3041 <param name="Lys8" value="8.0141988132"/>
3042 <param name="Leu3" value="3.01883"/>
3043 <param name="Dimethyl0" value="28.0313"/>
3044 <param name="Dimethyl4" value="31.0094"/>
3045 <param name="Dimethyl6" value="34.063117"/>
3046 <param name="Dimethyl8" value="36.07567"/>
3047 <param name="ICPL0" value="105.021464"/>
3048 <param name="ICPL4" value="109.046571"/>
3049 <param name="ICPL6" value="111.041593"/>
3050 <param name="ICPL10" value="115.0667"/>
3051 </section>
3052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3053 <output name="ctd_out" ftype="xml">
3054 <assert_contents>
3055 <is_valid_xml/>
3056 </assert_contents>
3057 </output>
3058 </test>
3059 <test expect_num_outputs="3">
3060 <conditional name="adv_opts_cond">
3061 <param name="adv_opts_selector" value="advanced"/>
3062 <param name="force" value="false"/>
3063 <param name="test" value="true"/>
3064 </conditional>
3065 <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
3066 <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3067 <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3068 <section name="algorithm">
3069 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
3070 <param name="charge" value="1:7"/>
3071 <param name="isotopes_per_peptide" value="3:8"/>
3072 <param name="rt_typical" value="50.0"/>
3073 <param name="rt_band" value="3.0"/>
3074 <param name="rt_min" value="8.0"/>
3075 <param name="mz_tolerance" value="10.0"/>
3076 <param name="mz_unit" value="ppm"/>
3077 <param name="intensity_cutoff" value="10.0"/>
3078 <param name="peptide_similarity" value="0.2"/>
3079 <param name="averagine_similarity" value="0.25"/>
3080 <param name="averagine_similarity_scaling" value="0.95"/>
3081 <param name="missed_cleavages" value="4"/>
3082 <param name="spectrum_type" value="automatic"/>
3083 <param name="averagine_type" value="peptide"/>
3084 <param name="knock_out" value="true"/>
3085 </section>
3086 <section name="labels">
3087 <param name="Arg6" value="6.0201290268"/>
3088 <param name="Arg10" value="10.0082686"/>
3089 <param name="Lys4" value="4.0251069836"/>
3090 <param name="Lys6" value="6.0201290268"/>
3091 <param name="Lys8" value="8.0141988132"/>
3092 <param name="Leu3" value="3.01883"/>
3093 <param name="Dimethyl0" value="28.0313"/>
3094 <param name="Dimethyl4" value="32.056407"/>
3095 <param name="Dimethyl6" value="34.063117"/>
3096 <param name="Dimethyl8" value="36.07567"/>
3097 <param name="ICPL0" value="105.021464"/>
3098 <param name="ICPL4" value="109.046571"/>
3099 <param name="ICPL6" value="111.041593"/>
3100 <param name="ICPL10" value="115.0667"/>
3101 </section>
3102 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3103 <output name="ctd_out" ftype="xml">
3104 <assert_contents>
3105 <is_valid_xml/>
3106 </assert_contents>
3107 </output>
3108 </test>
3109 <test expect_num_outputs="3">
3110 <conditional name="adv_opts_cond">
3111 <param name="adv_opts_selector" value="advanced"/>
3112 <param name="force" value="false"/>
3113 <param name="test" value="true"/>
3114 </conditional>
3115 <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
3116 <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3117 <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3118 <section name="algorithm">
3119 <param name="labels" value="[0][6.03705]"/>
3120 <param name="charge" value="2:8"/>
3121 <param name="isotopes_per_peptide" value="3:8"/>
3122 <param name="rt_typical" value="40.0"/>
3123 <param name="rt_band" value="0.0"/>
3124 <param name="rt_min" value="4.0"/>
3125 <param name="mz_tolerance" value="10.0"/>
3126 <param name="mz_unit" value="ppm"/>
3127 <param name="intensity_cutoff" value="1000.0"/>
3128 <param name="peptide_similarity" value="0.5"/>
3129 <param name="averagine_similarity" value="0.4"/>
3130 <param name="averagine_similarity_scaling" value="0.95"/>
3131 <param name="missed_cleavages" value="0"/>
3132 <param name="spectrum_type" value="centroid"/>
3133 <param name="averagine_type" value="peptide"/>
3134 <param name="knock_out" value="false"/>
3135 </section>
3136 <section name="labels">
3137 <param name="Arg6" value="6.0201290268"/>
3138 <param name="Arg10" value="10.0082686"/>
3139 <param name="Lys4" value="4.0251069836"/>
3140 <param name="Lys6" value="6.0201290268"/>
3141 <param name="Lys8" value="8.0141988132"/>
3142 <param name="Leu3" value="3.01883"/>
3143 <param name="Dimethyl0" value="28.0313"/>
3144 <param name="Dimethyl4" value="32.056407"/>
3145 <param name="Dimethyl6" value="34.063117"/>
3146 <param name="Dimethyl8" value="36.07567"/>
3147 <param name="ICPL0" value="105.021464"/>
3148 <param name="ICPL4" value="109.046571"/>
3149 <param name="ICPL6" value="111.041593"/>
3150 <param name="ICPL10" value="115.0667"/>
3151 </section>
3152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3153 <output name="ctd_out" ftype="xml">
3154 <assert_contents>
3155 <is_valid_xml/>
3156 </assert_contents>
3157 </output>
3158 </test>
3159 <test expect_num_outputs="3">
3160 <conditional name="adv_opts_cond">
3161 <param name="adv_opts_selector" value="advanced"/>
3162 <param name="force" value="false"/>
3163 <param name="test" value="true"/>
3164 </conditional>
3165 <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
3166 <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3167 <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3168 <section name="algorithm">
3169 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
3170 <param name="charge" value="1:7"/>
3171 <param name="isotopes_per_peptide" value="3:6"/>
3172 <param name="rt_typical" value="50.0"/>
3173 <param name="rt_band" value="5.0"/>
3174 <param name="rt_min" value="8.0"/>
3175 <param name="mz_tolerance" value="6.0"/>
3176 <param name="mz_unit" value="ppm"/>
3177 <param name="intensity_cutoff" value="10.0"/>
3178 <param name="peptide_similarity" value="0.4"/>
3179 <param name="averagine_similarity" value="0.5"/>
3180 <param name="averagine_similarity_scaling" value="0.95"/>
3181 <param name="missed_cleavages" value="3"/>
3182 <param name="spectrum_type" value="profile"/>
3183 <param name="averagine_type" value="peptide"/>
3184 <param name="knock_out" value="true"/>
3185 </section>
3186 <section name="labels">
3187 <param name="Arg6" value="6.0201290268"/>
3188 <param name="Arg10" value="10.0082686"/>
3189 <param name="Lys4" value="4.0251069836"/>
3190 <param name="Lys6" value="6.0201290268"/>
3191 <param name="Lys8" value="8.0141988132"/>
3192 <param name="Leu3" value="3.01883"/>
3193 <param name="Dimethyl0" value="28.0313"/>
3194 <param name="Dimethyl4" value="32.056407"/>
3195 <param name="Dimethyl6" value="34.063117"/>
3196 <param name="Dimethyl8" value="36.07567"/>
3197 <param name="ICPL0" value="105.021464"/>
3198 <param name="ICPL4" value="109.046571"/>
3199 <param name="ICPL6" value="111.041593"/>
3200 <param name="ICPL10" value="115.0667"/>
3201 </section>
3202 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3203 <output name="ctd_out" ftype="xml">
3204 <assert_contents>
3205 <is_valid_xml/>
3206 </assert_contents>
3207 </output>
3208 </test>
3209 <test expect_num_outputs="2">
3210 <conditional name="adv_opts_cond">
3211 <param name="adv_opts_selector" value="advanced"/>
3212 <param name="force" value="false"/>
3213 <param name="test" value="true"/>
3214 </conditional>
3215 <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
3216 <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3217 <section name="algorithm">
3218 <param name="labels" value="[]"/>
3219 <param name="charge" value="1:4"/>
3220 <param name="isotopes_per_peptide" value="3:6"/>
3221 <param name="rt_typical" value="1e-05"/>
3222 <param name="rt_band" value="0.0"/>
3223 <param name="rt_min" value="0.0"/>
3224 <param name="mz_tolerance" value="10.0"/>
3225 <param name="mz_unit" value="ppm"/>
3226 <param name="intensity_cutoff" value="1000.0"/>
3227 <param name="peptide_similarity" value="0.5"/>
3228 <param name="averagine_similarity" value="0.7"/>
3229 <param name="averagine_similarity_scaling" value="0.95"/>
3230 <param name="missed_cleavages" value="0"/>
3231 <param name="spectrum_type" value="automatic"/>
3232 <param name="averagine_type" value="peptide"/>
3233 <param name="knock_out" value="false"/>
3234 </section>
3235 <section name="labels">
3236 <param name="Arg6" value="6.0201290268"/>
3237 <param name="Arg10" value="10.0082686"/>
3238 <param name="Lys4" value="4.0251069836"/>
3239 <param name="Lys6" value="6.0201290268"/>
3240 <param name="Lys8" value="8.0141988132"/>
3241 <param name="Leu3" value="3.01883"/>
3242 <param name="Dimethyl0" value="28.0313"/>
3243 <param name="Dimethyl4" value="32.056407"/>
3244 <param name="Dimethyl6" value="34.063117"/>
3245 <param name="Dimethyl8" value="36.07567"/>
3246 <param name="ICPL0" value="105.021464"/>
3247 <param name="ICPL4" value="109.046571"/>
3248 <param name="ICPL6" value="111.041593"/>
3249 <param name="ICPL10" value="115.0667"/>
3250 </section>
3251 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
3252 <output name="ctd_out" ftype="xml">
3253 <assert_contents>
3254 <is_valid_xml/>
3255 </assert_contents>
3256 </output>
3257 </test>
3258 </xml>
3259 <xml name="autotest_FeatureFinderSuperHirn">
3260 <test expect_num_outputs="2">
3261 <conditional name="adv_opts_cond">
3262 <param name="adv_opts_selector" value="advanced"/>
3263 <param name="force" value="false"/>
3264 <param name="test" value="true"/>
3265 </conditional>
3266 <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/>
3267 <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3268 <section name="algorithm">
3269 <section name="centroiding">
3270 <param name="active" value="false"/>
3271 <param name="window_width" value="5"/>
3272 <param name="absolute_isotope_mass_precision" value="0.01"/>
3273 <param name="relative_isotope_mass_precision" value="10.0"/>
3274 <param name="minimal_peak_height" value="0.0"/>
3275 <param name="min_ms_signal_intensity" value="50.0"/>
3276 </section>
3277 <section name="ms1">
3278 <param name="precursor_detection_scan_levels" value="1"/>
3279 <param name="max_inter_scan_distance" value="0"/>
3280 <param name="tr_resolution" value="0.01"/>
3281 <param name="intensity_threshold" value="1000.0"/>
3282 <param name="max_inter_scan_rt_distance" value="0.1"/>
3283 <param name="min_nb_cluster_members" value="4"/>
3284 <param name="detectable_isotope_factor" value="0.05"/>
3285 <param name="intensity_cv" value="0.9"/>
3286 <param name="retention_time_tolerance" value="0.5"/>
3287 <param name="mz_tolerance" value="0.0"/>
3288 </section>
3289 <section name="ms1_feature_merger">
3290 <param name="active" value="true"/>
3291 <param name="tr_resolution" value="0.01"/>
3292 <param name="initial_apex_tr_tolerance" value="5.0"/>
3293 <param name="feature_merging_tr_tolerance" value="1.0"/>
3294 <param name="intensity_variation_percentage" value="25.0"/>
3295 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
3296 </section>
3297 <section name="ms1_feature_selection_options">
3298 <param name="start_elution_window" value="0.0"/>
3299 <param name="end_elution_window" value="180.0"/>
3300 <param name="mz_range_min" value="0.0"/>
3301 <param name="mz_range_max" value="2000.0"/>
3302 <param name="chrg_range_min" value="1"/>
3303 <param name="chrg_range_max" value="5"/>
3304 </section>
3305 </section>
3306 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3307 <output name="ctd_out" ftype="xml">
3308 <assert_contents>
3309 <is_valid_xml/>
3310 </assert_contents>
3311 </output>
3312 </test>
3313 <test expect_num_outputs="2">
3314 <conditional name="adv_opts_cond">
3315 <param name="adv_opts_selector" value="advanced"/>
3316 <param name="force" value="false"/>
3317 <param name="test" value="true"/>
3318 </conditional>
3319 <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/>
3320 <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3321 <section name="algorithm">
3322 <section name="centroiding">
3323 <param name="active" value="true"/>
3324 <param name="window_width" value="5"/>
3325 <param name="absolute_isotope_mass_precision" value="0.01"/>
3326 <param name="relative_isotope_mass_precision" value="10.0"/>
3327 <param name="minimal_peak_height" value="0.0"/>
3328 <param name="min_ms_signal_intensity" value="50.0"/>
3329 </section>
3330 <section name="ms1">
3331 <param name="precursor_detection_scan_levels" value="1"/>
3332 <param name="max_inter_scan_distance" value="0"/>
3333 <param name="tr_resolution" value="0.01"/>
3334 <param name="intensity_threshold" value="1000.0"/>
3335 <param name="max_inter_scan_rt_distance" value="0.1"/>
3336 <param name="min_nb_cluster_members" value="4"/>
3337 <param name="detectable_isotope_factor" value="0.05"/>
3338 <param name="intensity_cv" value="0.9"/>
3339 <param name="retention_time_tolerance" value="0.5"/>
3340 <param name="mz_tolerance" value="0.0"/>
3341 </section>
3342 <section name="ms1_feature_merger">
3343 <param name="active" value="true"/>
3344 <param name="tr_resolution" value="0.01"/>
3345 <param name="initial_apex_tr_tolerance" value="5.0"/>
3346 <param name="feature_merging_tr_tolerance" value="1.0"/>
3347 <param name="intensity_variation_percentage" value="25.0"/>
3348 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
3349 </section>
3350 <section name="ms1_feature_selection_options">
3351 <param name="start_elution_window" value="0.0"/>
3352 <param name="end_elution_window" value="180.0"/>
3353 <param name="mz_range_min" value="0.0"/>
3354 <param name="mz_range_max" value="2000.0"/>
3355 <param name="chrg_range_min" value="1"/>
3356 <param name="chrg_range_max" value="5"/>
3357 </section>
3358 </section>
3359 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3360 <output name="ctd_out" ftype="xml">
3361 <assert_contents>
3362 <is_valid_xml/>
3363 </assert_contents>
3364 </output>
3365 </test>
3366 </xml>
3367 <xml name="autotest_FeatureLinkerLabeled">
3368 <test expect_num_outputs="2">
3369 <conditional name="adv_opts_cond">
3370 <param name="adv_opts_selector" value="advanced"/>
3371 <param name="force" value="false"/>
3372 <param name="test" value="true"/>
3373 </conditional>
3374 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
3375 <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3376 <section name="algorithm">
3377 <param name="rt_estimate" value="false"/>
3378 <param name="rt_pair_dist" value="-1.0"/>
3379 <param name="rt_dev_low" value="0.4"/>
3380 <param name="rt_dev_high" value="0.4"/>
3381 <param name="mz_pair_dists" value="8.0"/>
3382 <param name="mz_dev" value="0.1"/>
3383 <param name="mrm" value="false"/>
3384 </section>
3385 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3386 <output name="ctd_out" ftype="xml">
3387 <assert_contents>
3388 <is_valid_xml/>
3389 </assert_contents>
3390 </output>
3391 </test>
3392 <test expect_num_outputs="2">
3393 <conditional name="adv_opts_cond">
3394 <param name="adv_opts_selector" value="advanced"/>
3395 <param name="force" value="false"/>
3396 <param name="test" value="true"/>
3397 </conditional>
3398 <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
3399 <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3400 <section name="algorithm">
3401 <param name="rt_estimate" value="true"/>
3402 <param name="rt_pair_dist" value="-121.0382"/>
3403 <param name="rt_dev_low" value="123.3965"/>
3404 <param name="rt_dev_high" value="123.3965"/>
3405 <param name="mz_pair_dists" value="4.0"/>
3406 <param name="mz_dev" value="0.1"/>
3407 <param name="mrm" value="false"/>
3408 </section>
3409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3410 <output name="ctd_out" ftype="xml">
3411 <assert_contents>
3412 <is_valid_xml/>
3413 </assert_contents>
3414 </output>
3415 </test>
3416 </xml>
3417 <xml name="autotest_FeatureLinkerUnlabeledKD">
3418 <test expect_num_outputs="2">
3419 <conditional name="adv_opts_cond">
3420 <param name="adv_opts_selector" value="advanced"/>
3421 <param name="force" value="false"/>
3422 <param name="test" value="true"/>
3423 </conditional>
3424 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3425 <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3426 <param name="keep_subelements" value="false"/>
3427 <section name="algorithm">
3428 <param name="mz_unit" value="Da"/>
3429 <param name="nr_partitions" value="1"/>
3430 <section name="warp">
3431 <param name="enabled" value="false"/>
3432 <param name="rt_tol" value="100.0"/>
3433 <param name="mz_tol" value="0.3"/>
3434 <param name="max_pairwise_log_fc" value="0.5"/>
3435 <param name="min_rel_cc_size" value="0.5"/>
3436 <param name="max_nr_conflicts" value="0"/>
3437 </section>
3438 <section name="link">
3439 <param name="rt_tol" value="100.0"/>
3440 <param name="mz_tol" value="0.3"/>
3441 <param name="charge_merging" value="With_charge_zero"/>
3442 <param name="adduct_merging" value="Any"/>
3443 </section>
3444 <section name="distance_RT">
3445 <param name="exponent" value="1.0"/>
3446 <param name="weight" value="1.0"/>
3447 </section>
3448 <section name="distance_MZ">
3449 <param name="exponent" value="2.0"/>
3450 <param name="weight" value="1.0"/>
3451 </section>
3452 <section name="distance_intensity">
3453 <param name="exponent" value="1.0"/>
3454 <param name="weight" value="1.0"/>
3455 <param name="log_transform" value="enabled"/>
3456 </section>
3457 <section name="LOWESS">
3458 <param name="span" value="0.666666666666667"/>
3459 <param name="num_iterations" value="3"/>
3460 <param name="delta" value="-1.0"/>
3461 <param name="interpolation_type" value="cspline"/>
3462 <param name="extrapolation_type" value="four-point-linear"/>
3463 </section>
3464 </section>
3465 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3466 <output name="ctd_out" ftype="xml">
3467 <assert_contents>
3468 <is_valid_xml/>
3469 </assert_contents>
3470 </output>
3471 </test>
3472 <test expect_num_outputs="2">
3473 <conditional name="adv_opts_cond">
3474 <param name="adv_opts_selector" value="advanced"/>
3475 <param name="force" value="false"/>
3476 <param name="test" value="true"/>
3477 </conditional>
3478 <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
3479 <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3480 <param name="keep_subelements" value="true"/>
3481 <section name="algorithm">
3482 <param name="mz_unit" value="Da"/>
3483 <param name="nr_partitions" value="99999"/>
3484 <section name="warp">
3485 <param name="enabled" value="false"/>
3486 <param name="rt_tol" value="100.0"/>
3487 <param name="mz_tol" value="0.3"/>
3488 <param name="max_pairwise_log_fc" value="0.5"/>
3489 <param name="min_rel_cc_size" value="0.5"/>
3490 <param name="max_nr_conflicts" value="0"/>
3491 </section>
3492 <section name="link">
3493 <param name="rt_tol" value="100.0"/>
3494 <param name="mz_tol" value="0.3"/>
3495 <param name="charge_merging" value="With_charge_zero"/>
3496 <param name="adduct_merging" value="Any"/>
3497 </section>
3498 <section name="distance_RT">
3499 <param name="exponent" value="1.0"/>
3500 <param name="weight" value="1.0"/>
3501 </section>
3502 <section name="distance_MZ">
3503 <param name="exponent" value="2.0"/>
3504 <param name="weight" value="1.0"/>
3505 </section>
3506 <section name="distance_intensity">
3507 <param name="exponent" value="1.0"/>
3508 <param name="weight" value="1.0"/>
3509 <param name="log_transform" value="enabled"/>
3510 </section>
3511 <section name="LOWESS">
3512 <param name="span" value="0.666666666666667"/>
3513 <param name="num_iterations" value="3"/>
3514 <param name="delta" value="-1.0"/>
3515 <param name="interpolation_type" value="cspline"/>
3516 <param name="extrapolation_type" value="four-point-linear"/>
3517 </section>
3518 </section>
3519 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3520 <output name="ctd_out" ftype="xml">
3521 <assert_contents>
3522 <is_valid_xml/>
3523 </assert_contents>
3524 </output>
3525 </test>
3526 <test expect_num_outputs="2">
3527 <conditional name="adv_opts_cond">
3528 <param name="adv_opts_selector" value="advanced"/>
3529 <param name="force" value="false"/>
3530 <param name="test" value="true"/>
3531 </conditional>
3532 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
3533 <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3534 <param name="keep_subelements" value="false"/>
3535 <section name="algorithm">
3536 <param name="mz_unit" value="Da"/>
3537 <param name="nr_partitions" value="100"/>
3538 <section name="warp">
3539 <param name="enabled" value="false"/>
3540 <param name="rt_tol" value="100.0"/>
3541 <param name="mz_tol" value="0.3"/>
3542 <param name="max_pairwise_log_fc" value="0.5"/>
3543 <param name="min_rel_cc_size" value="0.5"/>
3544 <param name="max_nr_conflicts" value="0"/>
3545 </section>
3546 <section name="link">
3547 <param name="rt_tol" value="100.0"/>
3548 <param name="mz_tol" value="0.3"/>
3549 <param name="charge_merging" value="With_charge_zero"/>
3550 <param name="adduct_merging" value="Any"/>
3551 </section>
3552 <section name="distance_RT">
3553 <param name="exponent" value="1.0"/>
3554 <param name="weight" value="1.0"/>
3555 </section>
3556 <section name="distance_MZ">
3557 <param name="exponent" value="2.0"/>
3558 <param name="weight" value="1.0"/>
3559 </section>
3560 <section name="distance_intensity">
3561 <param name="exponent" value="1.0"/>
3562 <param name="weight" value="1.0"/>
3563 <param name="log_transform" value="enabled"/>
3564 </section>
3565 <section name="LOWESS">
3566 <param name="span" value="0.666666666666667"/>
3567 <param name="num_iterations" value="3"/>
3568 <param name="delta" value="-1.0"/>
3569 <param name="interpolation_type" value="cspline"/>
3570 <param name="extrapolation_type" value="four-point-linear"/>
3571 </section>
3572 </section>
3573 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3574 <output name="ctd_out" ftype="xml">
3575 <assert_contents>
3576 <is_valid_xml/>
3577 </assert_contents>
3578 </output>
3579 </test>
3580 <test expect_num_outputs="2">
3581 <conditional name="adv_opts_cond">
3582 <param name="adv_opts_selector" value="advanced"/>
3583 <param name="force" value="false"/>
3584 <param name="test" value="true"/>
3585 </conditional>
3586 <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"/>
3587 <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3588 <param name="keep_subelements" value="false"/>
3589 <section name="algorithm">
3590 <param name="mz_unit" value="ppm"/>
3591 <param name="nr_partitions" value="100"/>
3592 <section name="warp">
3593 <param name="enabled" value="true"/>
3594 <param name="rt_tol" value="100.0"/>
3595 <param name="mz_tol" value="5.0"/>
3596 <param name="max_pairwise_log_fc" value="0.5"/>
3597 <param name="min_rel_cc_size" value="0.5"/>
3598 <param name="max_nr_conflicts" value="0"/>
3599 </section>
3600 <section name="link">
3601 <param name="rt_tol" value="30.0"/>
3602 <param name="mz_tol" value="10.0"/>
3603 <param name="charge_merging" value="Identical"/>
3604 <param name="adduct_merging" value="Any"/>
3605 </section>
3606 <section name="distance_RT">
3607 <param name="exponent" value="1.0"/>
3608 <param name="weight" value="1.0"/>
3609 </section>
3610 <section name="distance_MZ">
3611 <param name="exponent" value="2.0"/>
3612 <param name="weight" value="1.0"/>
3613 </section>
3614 <section name="distance_intensity">
3615 <param name="exponent" value="1.0"/>
3616 <param name="weight" value="1.0"/>
3617 <param name="log_transform" value="enabled"/>
3618 </section>
3619 <section name="LOWESS">
3620 <param name="span" value="0.666666666666667"/>
3621 <param name="num_iterations" value="3"/>
3622 <param name="delta" value="-1.0"/>
3623 <param name="interpolation_type" value="cspline"/>
3624 <param name="extrapolation_type" value="four-point-linear"/>
3625 </section>
3626 </section>
3627 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3628 <output name="ctd_out" ftype="xml">
3629 <assert_contents>
3630 <is_valid_xml/>
3631 </assert_contents>
3632 </output>
3633 </test>
3634 <test expect_num_outputs="2">
3635 <conditional name="adv_opts_cond">
3636 <param name="adv_opts_selector" value="advanced"/>
3637 <param name="force" value="false"/>
3638 <param name="test" value="true"/>
3639 </conditional>
3640 <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"/>
3641 <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3642 <param name="keep_subelements" value="false"/>
3643 <section name="algorithm">
3644 <param name="mz_unit" value="ppm"/>
3645 <param name="nr_partitions" value="100"/>
3646 <section name="warp">
3647 <param name="enabled" value="true"/>
3648 <param name="rt_tol" value="100.0"/>
3649 <param name="mz_tol" value="5.0"/>
3650 <param name="max_pairwise_log_fc" value="0.5"/>
3651 <param name="min_rel_cc_size" value="0.5"/>
3652 <param name="max_nr_conflicts" value="0"/>
3653 </section>
3654 <section name="link">
3655 <param name="rt_tol" value="30.0"/>
3656 <param name="mz_tol" value="10.0"/>
3657 <param name="charge_merging" value="With_charge_zero"/>
3658 <param name="adduct_merging" value="Any"/>
3659 </section>
3660 <section name="distance_RT">
3661 <param name="exponent" value="1.0"/>
3662 <param name="weight" value="1.0"/>
3663 </section>
3664 <section name="distance_MZ">
3665 <param name="exponent" value="2.0"/>
3666 <param name="weight" value="1.0"/>
3667 </section>
3668 <section name="distance_intensity">
3669 <param name="exponent" value="1.0"/>
3670 <param name="weight" value="1.0"/>
3671 <param name="log_transform" value="enabled"/>
3672 </section>
3673 <section name="LOWESS">
3674 <param name="span" value="0.666666666666667"/>
3675 <param name="num_iterations" value="3"/>
3676 <param name="delta" value="-1.0"/>
3677 <param name="interpolation_type" value="cspline"/>
3678 <param name="extrapolation_type" value="four-point-linear"/>
3679 </section>
3680 </section>
3681 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3682 <output name="ctd_out" ftype="xml">
3683 <assert_contents>
3684 <is_valid_xml/>
3685 </assert_contents>
3686 </output>
3687 </test>
3688 <test expect_num_outputs="2">
3689 <conditional name="adv_opts_cond">
3690 <param name="adv_opts_selector" value="advanced"/>
3691 <param name="force" value="false"/>
3692 <param name="test" value="true"/>
3693 </conditional>
3694 <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"/>
3695 <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3696 <param name="keep_subelements" value="false"/>
3697 <section name="algorithm">
3698 <param name="mz_unit" value="ppm"/>
3699 <param name="nr_partitions" value="100"/>
3700 <section name="warp">
3701 <param name="enabled" value="true"/>
3702 <param name="rt_tol" value="100.0"/>
3703 <param name="mz_tol" value="5.0"/>
3704 <param name="max_pairwise_log_fc" value="0.5"/>
3705 <param name="min_rel_cc_size" value="0.5"/>
3706 <param name="max_nr_conflicts" value="0"/>
3707 </section>
3708 <section name="link">
3709 <param name="rt_tol" value="30.0"/>
3710 <param name="mz_tol" value="10.0"/>
3711 <param name="charge_merging" value="Any"/>
3712 <param name="adduct_merging" value="With_unknown_adducts"/>
3713 </section>
3714 <section name="distance_RT">
3715 <param name="exponent" value="1.0"/>
3716 <param name="weight" value="1.0"/>
3717 </section>
3718 <section name="distance_MZ">
3719 <param name="exponent" value="2.0"/>
3720 <param name="weight" value="1.0"/>
3721 </section>
3722 <section name="distance_intensity">
3723 <param name="exponent" value="1.0"/>
3724 <param name="weight" value="1.0"/>
3725 <param name="log_transform" value="enabled"/>
3726 </section>
3727 <section name="LOWESS">
3728 <param name="span" value="0.666666666666667"/>
3729 <param name="num_iterations" value="3"/>
3730 <param name="delta" value="-1.0"/>
3731 <param name="interpolation_type" value="cspline"/>
3732 <param name="extrapolation_type" value="four-point-linear"/>
3733 </section>
3734 </section>
3735 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3736 <output name="ctd_out" ftype="xml">
3737 <assert_contents>
3738 <is_valid_xml/>
3739 </assert_contents>
3740 </output>
3741 </test>
3742 <test expect_num_outputs="2">
3743 <conditional name="adv_opts_cond">
3744 <param name="adv_opts_selector" value="advanced"/>
3745 <param name="force" value="false"/>
3746 <param name="test" value="true"/>
3747 </conditional>
3748 <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"/>
3749 <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3750 <param name="keep_subelements" value="false"/>
3751 <section name="algorithm">
3752 <param name="mz_unit" value="ppm"/>
3753 <param name="nr_partitions" value="100"/>
3754 <section name="warp">
3755 <param name="enabled" value="true"/>
3756 <param name="rt_tol" value="100.0"/>
3757 <param name="mz_tol" value="5.0"/>
3758 <param name="max_pairwise_log_fc" value="0.5"/>
3759 <param name="min_rel_cc_size" value="0.5"/>
3760 <param name="max_nr_conflicts" value="0"/>
3761 </section>
3762 <section name="link">
3763 <param name="rt_tol" value="30.0"/>
3764 <param name="mz_tol" value="10.0"/>
3765 <param name="charge_merging" value="Any"/>
3766 <param name="adduct_merging" value="Identical"/>
3767 </section>
3768 <section name="distance_RT">
3769 <param name="exponent" value="1.0"/>
3770 <param name="weight" value="1.0"/>
3771 </section>
3772 <section name="distance_MZ">
3773 <param name="exponent" value="2.0"/>
3774 <param name="weight" value="1.0"/>
3775 </section>
3776 <section name="distance_intensity">
3777 <param name="exponent" value="1.0"/>
3778 <param name="weight" value="1.0"/>
3779 <param name="log_transform" value="enabled"/>
3780 </section>
3781 <section name="LOWESS">
3782 <param name="span" value="0.666666666666667"/>
3783 <param name="num_iterations" value="3"/>
3784 <param name="delta" value="-1.0"/>
3785 <param name="interpolation_type" value="cspline"/>
3786 <param name="extrapolation_type" value="four-point-linear"/>
3787 </section>
3788 </section>
3789 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3790 <output name="ctd_out" ftype="xml">
3791 <assert_contents>
3792 <is_valid_xml/>
3793 </assert_contents>
3794 </output>
3795 </test>
3796 </xml>
3797 <xml name="autotest_FeatureLinkerUnlabeledQT">
3798 <test expect_num_outputs="2">
3799 <conditional name="adv_opts_cond">
3800 <param name="adv_opts_selector" value="advanced"/>
3801 <param name="force" value="false"/>
3802 <param name="test" value="true"/>
3803 </conditional>
3804 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3805 <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3806 <param name="keep_subelements" value="false"/>
3807 <section name="algorithm">
3808 <param name="use_identifications" value="false"/>
3809 <param name="nr_partitions" value="100"/>
3810 <param name="ignore_charge" value="false"/>
3811 <param name="ignore_adduct" value="true"/>
3812 <section name="distance_RT">
3813 <param name="max_difference" value="100.0"/>
3814 <param name="exponent" value="1.0"/>
3815 <param name="weight" value="1.0"/>
3816 </section>
3817 <section name="distance_MZ">
3818 <param name="max_difference" value="0.3"/>
3819 <param name="unit" value="Da"/>
3820 <param name="exponent" value="2.0"/>
3821 <param name="weight" value="1.0"/>
3822 </section>
3823 <section name="distance_intensity">
3824 <param name="exponent" value="1.0"/>
3825 <param name="weight" value="0.0"/>
3826 <param name="log_transform" value="disabled"/>
3827 </section>
3828 </section>
3829 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3830 <output name="ctd_out" ftype="xml">
3831 <assert_contents>
3832 <is_valid_xml/>
3833 </assert_contents>
3834 </output>
3835 </test>
3836 <test expect_num_outputs="2">
3837 <conditional name="adv_opts_cond">
3838 <param name="adv_opts_selector" value="advanced"/>
3839 <param name="force" value="false"/>
3840 <param name="test" value="true"/>
3841 </conditional>
3842 <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
3843 <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3844 <param name="keep_subelements" value="true"/>
3845 <section name="algorithm">
3846 <param name="use_identifications" value="false"/>
3847 <param name="nr_partitions" value="100"/>
3848 <param name="ignore_charge" value="false"/>
3849 <param name="ignore_adduct" value="true"/>
3850 <section name="distance_RT">
3851 <param name="max_difference" value="100.0"/>
3852 <param name="exponent" value="1.0"/>
3853 <param name="weight" value="1.0"/>
3854 </section>
3855 <section name="distance_MZ">
3856 <param name="max_difference" value="0.3"/>
3857 <param name="unit" value="Da"/>
3858 <param name="exponent" value="2.0"/>
3859 <param name="weight" value="1.0"/>
3860 </section>
3861 <section name="distance_intensity">
3862 <param name="exponent" value="1.0"/>
3863 <param name="weight" value="0.0"/>
3864 <param name="log_transform" value="disabled"/>
3865 </section>
3866 </section>
3867 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3868 <output name="ctd_out" ftype="xml">
3869 <assert_contents>
3870 <is_valid_xml/>
3871 </assert_contents>
3872 </output>
3873 </test>
3874 <test expect_num_outputs="2">
3875 <conditional name="adv_opts_cond">
3876 <param name="adv_opts_selector" value="advanced"/>
3877 <param name="force" value="false"/>
3878 <param name="test" value="true"/>
3879 </conditional>
3880 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
3881 <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3882 <param name="keep_subelements" value="false"/>
3883 <section name="algorithm">
3884 <param name="use_identifications" value="false"/>
3885 <param name="nr_partitions" value="99999"/>
3886 <param name="ignore_charge" value="false"/>
3887 <param name="ignore_adduct" value="true"/>
3888 <section name="distance_RT">
3889 <param name="max_difference" value="100.0"/>
3890 <param name="exponent" value="1.0"/>
3891 <param name="weight" value="1.0"/>
3892 </section>
3893 <section name="distance_MZ">
3894 <param name="max_difference" value="0.3"/>
3895 <param name="unit" value="Da"/>
3896 <param name="exponent" value="2.0"/>
3897 <param name="weight" value="1.0"/>
3898 </section>
3899 <section name="distance_intensity">
3900 <param name="exponent" value="1.0"/>
3901 <param name="weight" value="0.0"/>
3902 <param name="log_transform" value="disabled"/>
3903 </section>
3904 </section>
3905 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3906 <output name="ctd_out" ftype="xml">
3907 <assert_contents>
3908 <is_valid_xml/>
3909 </assert_contents>
3910 </output>
3911 </test>
3912 <test expect_num_outputs="2">
3913 <conditional name="adv_opts_cond">
3914 <param name="adv_opts_selector" value="advanced"/>
3915 <param name="force" value="false"/>
3916 <param name="test" value="true"/>
3917 </conditional>
3918 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3919 <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3920 <param name="keep_subelements" value="false"/>
3921 <section name="algorithm">
3922 <param name="use_identifications" value="true"/>
3923 <param name="nr_partitions" value="100"/>
3924 <param name="ignore_charge" value="false"/>
3925 <param name="ignore_adduct" value="true"/>
3926 <section name="distance_RT">
3927 <param name="max_difference" value="100.0"/>
3928 <param name="exponent" value="1.0"/>
3929 <param name="weight" value="1.0"/>
3930 </section>
3931 <section name="distance_MZ">
3932 <param name="max_difference" value="0.3"/>
3933 <param name="unit" value="Da"/>
3934 <param name="exponent" value="2.0"/>
3935 <param name="weight" value="1.0"/>
3936 </section>
3937 <section name="distance_intensity">
3938 <param name="exponent" value="1.0"/>
3939 <param name="weight" value="0.0"/>
3940 <param name="log_transform" value="disabled"/>
3941 </section>
3942 </section>
3943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3944 <output name="ctd_out" ftype="xml">
3945 <assert_contents>
3946 <is_valid_xml/>
3947 </assert_contents>
3948 </output>
3949 </test>
3950 <test expect_num_outputs="2">
3951 <conditional name="adv_opts_cond">
3952 <param name="adv_opts_selector" value="advanced"/>
3953 <param name="force" value="false"/>
3954 <param name="test" value="true"/>
3955 </conditional>
3956 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
3957 <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3958 <param name="keep_subelements" value="false"/>
3959 <section name="algorithm">
3960 <param name="use_identifications" value="false"/>
3961 <param name="nr_partitions" value="100"/>
3962 <param name="ignore_charge" value="false"/>
3963 <param name="ignore_adduct" value="true"/>
3964 <section name="distance_RT">
3965 <param name="max_difference" value="200.0"/>
3966 <param name="exponent" value="1.0"/>
3967 <param name="weight" value="1.0"/>
3968 </section>
3969 <section name="distance_MZ">
3970 <param name="max_difference" value="0.3"/>
3971 <param name="unit" value="Da"/>
3972 <param name="exponent" value="2.0"/>
3973 <param name="weight" value="1.0"/>
3974 </section>
3975 <section name="distance_intensity">
3976 <param name="exponent" value="1.0"/>
3977 <param name="weight" value="0.0"/>
3978 <param name="log_transform" value="disabled"/>
3979 </section>
3980 </section>
3981 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3982 <output name="ctd_out" ftype="xml">
3983 <assert_contents>
3984 <is_valid_xml/>
3985 </assert_contents>
3986 </output>
3987 </test>
3988 <test expect_num_outputs="2">
3989 <conditional name="adv_opts_cond">
3990 <param name="adv_opts_selector" value="advanced"/>
3991 <param name="force" value="false"/>
3992 <param name="test" value="true"/>
3993 </conditional>
3994 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
3995 <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3996 <param name="keep_subelements" value="false"/>
3997 <section name="algorithm">
3998 <param name="use_identifications" value="true"/>
3999 <param name="nr_partitions" value="100"/>
4000 <param name="ignore_charge" value="false"/>
4001 <param name="ignore_adduct" value="true"/>
4002 <section name="distance_RT">
4003 <param name="max_difference" value="200.0"/>
4004 <param name="exponent" value="1.0"/>
4005 <param name="weight" value="1.0"/>
4006 </section>
4007 <section name="distance_MZ">
4008 <param name="max_difference" value="0.3"/>
4009 <param name="unit" value="Da"/>
4010 <param name="exponent" value="2.0"/>
4011 <param name="weight" value="1.0"/>
4012 </section>
4013 <section name="distance_intensity">
4014 <param name="exponent" value="1.0"/>
4015 <param name="weight" value="0.0"/>
4016 <param name="log_transform" value="disabled"/>
4017 </section>
4018 </section>
4019 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4020 <output name="ctd_out" ftype="xml">
4021 <assert_contents>
4022 <is_valid_xml/>
4023 </assert_contents>
4024 </output>
4025 </test>
4026 </xml>
4027 <xml name="autotest_FeatureLinkerUnlabeled">
4028 <test expect_num_outputs="2">
4029 <conditional name="adv_opts_cond">
4030 <param name="adv_opts_selector" value="advanced"/>
4031 <param name="force" value="false"/>
4032 <param name="test" value="true"/>
4033 </conditional>
4034 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
4035 <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4036 <param name="keep_subelements" value="false"/>
4037 <section name="algorithm">
4038 <param name="second_nearest_gap" value="2.0"/>
4039 <param name="use_identifications" value="false"/>
4040 <param name="ignore_charge" value="true"/>
4041 <param name="ignore_adduct" value="true"/>
4042 <section name="distance_RT">
4043 <param name="max_difference" value="200.0"/>
4044 <param name="exponent" value="1.0"/>
4045 <param name="weight" value="1.0"/>
4046 </section>
4047 <section name="distance_MZ">
4048 <param name="max_difference" value="0.5"/>
4049 <param name="unit" value="Da"/>
4050 <param name="exponent" value="1.0"/>
4051 <param name="weight" value="1.0"/>
4052 </section>
4053 <section name="distance_intensity">
4054 <param name="exponent" value="1.0"/>
4055 <param name="weight" value="0.0"/>
4056 <param name="log_transform" value="disabled"/>
4057 </section>
4058 </section>
4059 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4060 <output name="ctd_out" ftype="xml">
4061 <assert_contents>
4062 <is_valid_xml/>
4063 </assert_contents>
4064 </output>
4065 </test>
4066 <test expect_num_outputs="2">
4067 <conditional name="adv_opts_cond">
4068 <param name="adv_opts_selector" value="advanced"/>
4069 <param name="force" value="false"/>
4070 <param name="test" value="true"/>
4071 </conditional>
4072 <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
4073 <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4074 <param name="keep_subelements" value="false"/>
4075 <section name="algorithm">
4076 <param name="second_nearest_gap" value="2.0"/>
4077 <param name="use_identifications" value="false"/>
4078 <param name="ignore_charge" value="false"/>
4079 <param name="ignore_adduct" value="true"/>
4080 <section name="distance_RT">
4081 <param name="max_difference" value="100.0"/>
4082 <param name="exponent" value="1.0"/>
4083 <param name="weight" value="1.0"/>
4084 </section>
4085 <section name="distance_MZ">
4086 <param name="max_difference" value="0.3"/>
4087 <param name="unit" value="Da"/>
4088 <param name="exponent" value="2.0"/>
4089 <param name="weight" value="1.0"/>
4090 </section>
4091 <section name="distance_intensity">
4092 <param name="exponent" value="1.0"/>
4093 <param name="weight" value="0.5"/>
4094 <param name="log_transform" value="disabled"/>
4095 </section>
4096 </section>
4097 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4098 <output name="ctd_out" ftype="xml">
4099 <assert_contents>
4100 <is_valid_xml/>
4101 </assert_contents>
4102 </output>
4103 </test>
4104 <test expect_num_outputs="2">
4105 <conditional name="adv_opts_cond">
4106 <param name="adv_opts_selector" value="advanced"/>
4107 <param name="force" value="false"/>
4108 <param name="test" value="true"/>
4109 </conditional>
4110 <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
4111 <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4112 <param name="keep_subelements" value="false"/>
4113 <section name="algorithm">
4114 <param name="second_nearest_gap" value="1.5"/>
4115 <param name="use_identifications" value="false"/>
4116 <param name="ignore_charge" value="true"/>
4117 <param name="ignore_adduct" value="true"/>
4118 <section name="distance_RT">
4119 <param name="max_difference" value="30.0"/>
4120 <param name="exponent" value="1.0"/>
4121 <param name="weight" value="1.0"/>
4122 </section>
4123 <section name="distance_MZ">
4124 <param name="max_difference" value="0.3"/>
4125 <param name="unit" value="Da"/>
4126 <param name="exponent" value="2.0"/>
4127 <param name="weight" value="1.0"/>
4128 </section>
4129 <section name="distance_intensity">
4130 <param name="exponent" value="1.0"/>
4131 <param name="weight" value="0.0"/>
4132 <param name="log_transform" value="disabled"/>
4133 </section>
4134 </section>
4135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4136 <output name="ctd_out" ftype="xml">
4137 <assert_contents>
4138 <is_valid_xml/>
4139 </assert_contents>
4140 </output>
4141 </test>
4142 <test expect_num_outputs="2">
4143 <conditional name="adv_opts_cond">
4144 <param name="adv_opts_selector" value="advanced"/>
4145 <param name="force" value="false"/>
4146 <param name="test" value="true"/>
4147 </conditional>
4148 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
4149 <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4150 <param name="keep_subelements" value="false"/>
4151 <section name="algorithm">
4152 <param name="second_nearest_gap" value="2.0"/>
4153 <param name="use_identifications" value="true"/>
4154 <param name="ignore_charge" value="true"/>
4155 <param name="ignore_adduct" value="true"/>
4156 <section name="distance_RT">
4157 <param name="max_difference" value="200.0"/>
4158 <param name="exponent" value="2.0"/>
4159 <param name="weight" value="1.0"/>
4160 </section>
4161 <section name="distance_MZ">
4162 <param name="max_difference" value="0.5"/>
4163 <param name="unit" value="Da"/>
4164 <param name="exponent" value="2.0"/>
4165 <param name="weight" value="1.0"/>
4166 </section>
4167 <section name="distance_intensity">
4168 <param name="exponent" value="1.0"/>
4169 <param name="weight" value="0.0"/>
4170 <param name="log_transform" value="disabled"/>
4171 </section>
4172 </section>
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 </xml>
4181 <xml name="autotest_FFEval">
4182 </xml>
4183 <xml name="autotest_FidoAdapter">
4184 <test expect_num_outputs="2">
4185 <conditional name="adv_opts_cond">
4186 <param name="adv_opts_selector" value="advanced"/>
4187 <param name="keep_zero_group" value="false"/>
4188 <param name="accuracy" value=""/>
4189 <param name="log2_states_precalc" value="0"/>
4190 <param name="force" value="false"/>
4191 <param name="test" value="true"/>
4192 </conditional>
4193 <param name="in" value="FidoAdapter_1_input.idXML"/>
4194 <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4195 <param name="separate_runs" value="false"/>
4196 <param name="greedy_group_resolution" value="false"/>
4197 <param name="no_cleanup" value="false"/>
4198 <param name="all_PSMs" value="false"/>
4199 <param name="group_level" value="false"/>
4200 <param name="log2_states" value="0"/>
4201 <section name="prob">
4202 <param name="protein" value="0.0"/>
4203 <param name="peptide" value="0.0"/>
4204 <param name="spurious" value="0.0"/>
4205 </section>
4206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4207 <output name="ctd_out" ftype="xml">
4208 <assert_contents>
4209 <is_valid_xml/>
4210 </assert_contents>
4211 </output>
4212 </test>
4213 <test expect_num_outputs="2">
4214 <conditional name="adv_opts_cond">
4215 <param name="adv_opts_selector" value="advanced"/>
4216 <param name="keep_zero_group" value="false"/>
4217 <param name="accuracy" value=""/>
4218 <param name="log2_states_precalc" value="0"/>
4219 <param name="force" value="false"/>
4220 <param name="test" value="true"/>
4221 </conditional>
4222 <param name="in" value="FidoAdapter_1_input.idXML"/>
4223 <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4224 <param name="separate_runs" value="true"/>
4225 <param name="greedy_group_resolution" value="false"/>
4226 <param name="no_cleanup" value="false"/>
4227 <param name="all_PSMs" value="false"/>
4228 <param name="group_level" value="false"/>
4229 <param name="log2_states" value="0"/>
4230 <section name="prob">
4231 <param name="protein" value="0.0"/>
4232 <param name="peptide" value="0.0"/>
4233 <param name="spurious" value="0.0"/>
4234 </section>
4235 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4236 <output name="ctd_out" ftype="xml">
4237 <assert_contents>
4238 <is_valid_xml/>
4239 </assert_contents>
4240 </output>
4241 </test>
4242 <test expect_num_outputs="2">
4243 <conditional name="adv_opts_cond">
4244 <param name="adv_opts_selector" value="advanced"/>
4245 <param name="keep_zero_group" value="false"/>
4246 <param name="accuracy" value=""/>
4247 <param name="log2_states_precalc" value="0"/>
4248 <param name="force" value="false"/>
4249 <param name="test" value="true"/>
4250 </conditional>
4251 <param name="in" value="FidoAdapter_1_input.idXML"/>
4252 <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4253 <param name="separate_runs" value="false"/>
4254 <param name="greedy_group_resolution" value="false"/>
4255 <param name="no_cleanup" value="false"/>
4256 <param name="all_PSMs" value="true"/>
4257 <param name="group_level" value="true"/>
4258 <param name="log2_states" value="0"/>
4259 <section name="prob">
4260 <param name="protein" value="0.0"/>
4261 <param name="peptide" value="0.0"/>
4262 <param name="spurious" value="0.0"/>
4263 </section>
4264 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4265 <output name="ctd_out" ftype="xml">
4266 <assert_contents>
4267 <is_valid_xml/>
4268 </assert_contents>
4269 </output>
4270 </test>
4271 <test expect_num_outputs="2">
4272 <conditional name="adv_opts_cond">
4273 <param name="adv_opts_selector" value="advanced"/>
4274 <param name="keep_zero_group" value="false"/>
4275 <param name="accuracy" value=""/>
4276 <param name="log2_states_precalc" value="0"/>
4277 <param name="force" value="false"/>
4278 <param name="test" value="true"/>
4279 </conditional>
4280 <param name="in" value="FidoAdapter_4_input.idXML"/>
4281 <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4282 <param name="separate_runs" value="false"/>
4283 <param name="greedy_group_resolution" value="false"/>
4284 <param name="no_cleanup" value="false"/>
4285 <param name="all_PSMs" value="false"/>
4286 <param name="group_level" value="false"/>
4287 <param name="log2_states" value="0"/>
4288 <section name="prob">
4289 <param name="protein" value="0.0"/>
4290 <param name="peptide" value="0.0"/>
4291 <param name="spurious" value="0.0"/>
4292 </section>
4293 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4294 <output name="ctd_out" ftype="xml">
4295 <assert_contents>
4296 <is_valid_xml/>
4297 </assert_contents>
4298 </output>
4299 </test>
4300 <test expect_num_outputs="2">
4301 <conditional name="adv_opts_cond">
4302 <param name="adv_opts_selector" value="advanced"/>
4303 <param name="keep_zero_group" value="false"/>
4304 <param name="accuracy" value=""/>
4305 <param name="log2_states_precalc" value="0"/>
4306 <param name="force" value="false"/>
4307 <param name="test" value="true"/>
4308 </conditional>
4309 <param name="in" value="FidoAdapter_5_input.idXML"/>
4310 <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4311 <param name="separate_runs" value="false"/>
4312 <param name="greedy_group_resolution" value="true"/>
4313 <param name="no_cleanup" value="false"/>
4314 <param name="all_PSMs" value="false"/>
4315 <param name="group_level" value="false"/>
4316 <param name="log2_states" value="0"/>
4317 <section name="prob">
4318 <param name="protein" value="0.0"/>
4319 <param name="peptide" value="0.0"/>
4320 <param name="spurious" value="0.0"/>
4321 </section>
4322 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4323 <output name="ctd_out" ftype="xml">
4324 <assert_contents>
4325 <is_valid_xml/>
4326 </assert_contents>
4327 </output>
4328 </test>
4329 <test expect_num_outputs="2">
4330 <conditional name="adv_opts_cond">
4331 <param name="adv_opts_selector" value="advanced"/>
4332 <param name="keep_zero_group" value="false"/>
4333 <param name="accuracy" value=""/>
4334 <param name="log2_states_precalc" value="0"/>
4335 <param name="force" value="false"/>
4336 <param name="test" value="true"/>
4337 </conditional>
4338 <param name="in" value="FidoAdapter_1_input.idXML"/>
4339 <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4340 <param name="separate_runs" value="false"/>
4341 <param name="greedy_group_resolution" value="false"/>
4342 <param name="no_cleanup" value="false"/>
4343 <param name="all_PSMs" value="false"/>
4344 <param name="group_level" value="false"/>
4345 <param name="log2_states" value="0"/>
4346 <section name="prob">
4347 <param name="protein" value="0.9"/>
4348 <param name="peptide" value="0.01"/>
4349 <param name="spurious" value="0.0"/>
4350 </section>
4351 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4352 <output name="ctd_out" ftype="xml">
4353 <assert_contents>
4354 <is_valid_xml/>
4355 </assert_contents>
4356 </output>
4357 </test>
4358 </xml>
4359 <xml name="autotest_FileConverter">
4360 <test expect_num_outputs="2">
4361 <conditional name="adv_opts_cond">
4362 <param name="adv_opts_selector" value="advanced"/>
4363 <param name="UID_postprocessing" value="ensure"/>
4364 <param name="TIC_DTA2D" value="false"/>
4365 <param name="MGF_compact" value="false"/>
4366 <param name="force_MaxQuant_compatibility" value="false"/>
4367 <param name="convert_to_chromatograms" value="false"/>
4368 <param name="force_TPP_compatibility" value="false"/>
4369 <param name="change_im_format" value="none"/>
4370 <param name="write_scan_index" value="true"/>
4371 <param name="lossy_compression" value="false"/>
4372 <param name="lossy_mass_accuracy" value="-1.0"/>
4373 <param name="process_lowmemory" value="false"/>
4374 <param name="no_peak_picking" value="false"/>
4375 <param name="force" value="false"/>
4376 <param name="test" value="true"/>
4377 </conditional>
4378 <param name="in" value="FileConverter_1_input.mzData"/>
4379 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4380 <param name="out_type" value="mzML"/>
4381 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4382 <output name="ctd_out" ftype="xml">
4383 <assert_contents>
4384 <is_valid_xml/>
4385 </assert_contents>
4386 </output>
4387 </test>
4388 <test expect_num_outputs="2">
4389 <conditional name="adv_opts_cond">
4390 <param name="adv_opts_selector" value="advanced"/>
4391 <param name="UID_postprocessing" value="ensure"/>
4392 <param name="TIC_DTA2D" value="false"/>
4393 <param name="MGF_compact" value="false"/>
4394 <param name="force_MaxQuant_compatibility" value="false"/>
4395 <param name="convert_to_chromatograms" value="false"/>
4396 <param name="force_TPP_compatibility" value="false"/>
4397 <param name="change_im_format" value="none"/>
4398 <param name="write_scan_index" value="true"/>
4399 <param name="lossy_compression" value="false"/>
4400 <param name="lossy_mass_accuracy" value="-1.0"/>
4401 <param name="process_lowmemory" value="false"/>
4402 <param name="no_peak_picking" value="false"/>
4403 <param name="force" value="false"/>
4404 <param name="test" value="true"/>
4405 </conditional>
4406 <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
4407 <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4408 <param name="out_type" value="mzML"/>
4409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4410 <output name="ctd_out" ftype="xml">
4411 <assert_contents>
4412 <is_valid_xml/>
4413 </assert_contents>
4414 </output>
4415 </test>
4416 <test expect_num_outputs="2">
4417 <conditional name="adv_opts_cond">
4418 <param name="adv_opts_selector" value="advanced"/>
4419 <param name="UID_postprocessing" value="ensure"/>
4420 <param name="TIC_DTA2D" value="false"/>
4421 <param name="MGF_compact" value="false"/>
4422 <param name="force_MaxQuant_compatibility" value="false"/>
4423 <param name="convert_to_chromatograms" value="false"/>
4424 <param name="force_TPP_compatibility" value="false"/>
4425 <param name="change_im_format" value="none"/>
4426 <param name="write_scan_index" value="true"/>
4427 <param name="lossy_compression" value="false"/>
4428 <param name="lossy_mass_accuracy" value="-1.0"/>
4429 <param name="process_lowmemory" value="false"/>
4430 <param name="no_peak_picking" value="false"/>
4431 <param name="force" value="false"/>
4432 <param name="test" value="true"/>
4433 </conditional>
4434 <param name="in" value="FileConverter_3_input.featureXML"/>
4435 <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4436 <param name="out_type" value="mzML"/>
4437 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4438 <output name="ctd_out" ftype="xml">
4439 <assert_contents>
4440 <is_valid_xml/>
4441 </assert_contents>
4442 </output>
4443 </test>
4444 <test expect_num_outputs="2">
4445 <conditional name="adv_opts_cond">
4446 <param name="adv_opts_selector" value="advanced"/>
4447 <param name="UID_postprocessing" value="ensure"/>
4448 <param name="TIC_DTA2D" value="false"/>
4449 <param name="MGF_compact" value="false"/>
4450 <param name="force_MaxQuant_compatibility" value="false"/>
4451 <param name="convert_to_chromatograms" value="false"/>
4452 <param name="force_TPP_compatibility" value="false"/>
4453 <param name="change_im_format" value="none"/>
4454 <param name="write_scan_index" value="true"/>
4455 <param name="lossy_compression" value="false"/>
4456 <param name="lossy_mass_accuracy" value="-1.0"/>
4457 <param name="process_lowmemory" value="false"/>
4458 <param name="no_peak_picking" value="false"/>
4459 <param name="force" value="false"/>
4460 <param name="test" value="true"/>
4461 </conditional>
4462 <param name="in" value="FileConverter_4_input.mzXML"/>
4463 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4464 <param name="out_type" value="mzML"/>
4465 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4466 <output name="ctd_out" ftype="xml">
4467 <assert_contents>
4468 <is_valid_xml/>
4469 </assert_contents>
4470 </output>
4471 </test>
4472 <test expect_num_outputs="2">
4473 <conditional name="adv_opts_cond">
4474 <param name="adv_opts_selector" value="advanced"/>
4475 <param name="UID_postprocessing" value="ensure"/>
4476 <param name="TIC_DTA2D" value="false"/>
4477 <param name="MGF_compact" value="false"/>
4478 <param name="force_MaxQuant_compatibility" value="false"/>
4479 <param name="convert_to_chromatograms" value="false"/>
4480 <param name="force_TPP_compatibility" value="false"/>
4481 <param name="change_im_format" value="none"/>
4482 <param name="write_scan_index" value="true"/>
4483 <param name="lossy_compression" value="false"/>
4484 <param name="lossy_mass_accuracy" value="-1.0"/>
4485 <param name="process_lowmemory" value="false"/>
4486 <param name="no_peak_picking" value="false"/>
4487 <param name="force" value="false"/>
4488 <param name="test" value="true"/>
4489 </conditional>
4490 <param name="in" value="FileConverter_5_input.mzML"/>
4491 <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4492 <param name="out_type" value="mzXML"/>
4493 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4494 <output name="ctd_out" ftype="xml">
4495 <assert_contents>
4496 <is_valid_xml/>
4497 </assert_contents>
4498 </output>
4499 </test>
4500 <test expect_num_outputs="2">
4501 <conditional name="adv_opts_cond">
4502 <param name="adv_opts_selector" value="advanced"/>
4503 <param name="UID_postprocessing" value="ensure"/>
4504 <param name="TIC_DTA2D" value="false"/>
4505 <param name="MGF_compact" value="false"/>
4506 <param name="force_MaxQuant_compatibility" value="false"/>
4507 <param name="convert_to_chromatograms" value="false"/>
4508 <param name="force_TPP_compatibility" value="false"/>
4509 <param name="change_im_format" value="none"/>
4510 <param name="write_scan_index" value="true"/>
4511 <param name="lossy_compression" value="false"/>
4512 <param name="lossy_mass_accuracy" value="-1.0"/>
4513 <param name="process_lowmemory" value="false"/>
4514 <param name="no_peak_picking" value="false"/>
4515 <param name="force" value="false"/>
4516 <param name="test" value="true"/>
4517 </conditional>
4518 <param name="in" value="FileConverter_6_input.mzML"/>
4519 <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4520 <param name="out_type" value="mzXML"/>
4521 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4522 <output name="ctd_out" ftype="xml">
4523 <assert_contents>
4524 <is_valid_xml/>
4525 </assert_contents>
4526 </output>
4527 </test>
4528 <test expect_num_outputs="2">
4529 <conditional name="adv_opts_cond">
4530 <param name="adv_opts_selector" value="advanced"/>
4531 <param name="UID_postprocessing" value="ensure"/>
4532 <param name="TIC_DTA2D" value="false"/>
4533 <param name="MGF_compact" value="false"/>
4534 <param name="force_MaxQuant_compatibility" value="false"/>
4535 <param name="convert_to_chromatograms" value="false"/>
4536 <param name="force_TPP_compatibility" value="false"/>
4537 <param name="change_im_format" value="none"/>
4538 <param name="write_scan_index" value="true"/>
4539 <param name="lossy_compression" value="false"/>
4540 <param name="lossy_mass_accuracy" value="-1.0"/>
4541 <param name="process_lowmemory" value="false"/>
4542 <param name="no_peak_picking" value="false"/>
4543 <param name="force" value="false"/>
4544 <param name="test" value="true"/>
4545 </conditional>
4546 <param name="in" value="FileConverter_7_input.consensusXML"/>
4547 <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4548 <param name="out_type" value="featureXML"/>
4549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4550 <output name="ctd_out" ftype="xml">
4551 <assert_contents>
4552 <is_valid_xml/>
4553 </assert_contents>
4554 </output>
4555 </test>
4556 <test expect_num_outputs="2">
4557 <conditional name="adv_opts_cond">
4558 <param name="adv_opts_selector" value="advanced"/>
4559 <param name="UID_postprocessing" value="ensure"/>
4560 <param name="TIC_DTA2D" value="false"/>
4561 <param name="MGF_compact" value="false"/>
4562 <param name="force_MaxQuant_compatibility" value="false"/>
4563 <param name="convert_to_chromatograms" value="false"/>
4564 <param name="force_TPP_compatibility" value="false"/>
4565 <param name="change_im_format" value="none"/>
4566 <param name="write_scan_index" value="true"/>
4567 <param name="lossy_compression" value="false"/>
4568 <param name="lossy_mass_accuracy" value="-1.0"/>
4569 <param name="process_lowmemory" value="false"/>
4570 <param name="no_peak_picking" value="false"/>
4571 <param name="force" value="false"/>
4572 <param name="test" value="true"/>
4573 </conditional>
4574 <param name="in" value="FileConverter_8_input.mzML"/>
4575 <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/>
4576 <param name="out_type" value="mzData"/>
4577 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4578 <output name="ctd_out" ftype="xml">
4579 <assert_contents>
4580 <is_valid_xml/>
4581 </assert_contents>
4582 </output>
4583 </test>
4584 <test expect_num_outputs="2">
4585 <conditional name="adv_opts_cond">
4586 <param name="adv_opts_selector" value="advanced"/>
4587 <param name="UID_postprocessing" value="ensure"/>
4588 <param name="TIC_DTA2D" value="false"/>
4589 <param name="MGF_compact" value="false"/>
4590 <param name="force_MaxQuant_compatibility" value="false"/>
4591 <param name="convert_to_chromatograms" value="false"/>
4592 <param name="force_TPP_compatibility" value="false"/>
4593 <param name="change_im_format" value="none"/>
4594 <param name="write_scan_index" value="true"/>
4595 <param name="lossy_compression" value="false"/>
4596 <param name="lossy_mass_accuracy" value="-1.0"/>
4597 <param name="process_lowmemory" value="false"/>
4598 <param name="no_peak_picking" value="false"/>
4599 <param name="force" value="false"/>
4600 <param name="test" value="true"/>
4601 </conditional>
4602 <param name="in" value="FileConverter_9_input.consensusXML"/>
4603 <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4604 <param name="out_type" value="featureXML"/>
4605 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4606 <output name="ctd_out" ftype="xml">
4607 <assert_contents>
4608 <is_valid_xml/>
4609 </assert_contents>
4610 </output>
4611 </test>
4612 <test expect_num_outputs="2">
4613 <conditional name="adv_opts_cond">
4614 <param name="adv_opts_selector" value="advanced"/>
4615 <param name="UID_postprocessing" value="ensure"/>
4616 <param name="TIC_DTA2D" value="false"/>
4617 <param name="MGF_compact" value="false"/>
4618 <param name="force_MaxQuant_compatibility" value="false"/>
4619 <param name="convert_to_chromatograms" value="false"/>
4620 <param name="force_TPP_compatibility" value="false"/>
4621 <param name="change_im_format" value="none"/>
4622 <param name="write_scan_index" value="true"/>
4623 <param name="lossy_compression" value="false"/>
4624 <param name="lossy_mass_accuracy" value="-1.0"/>
4625 <param name="process_lowmemory" value="false"/>
4626 <param name="no_peak_picking" value="false"/>
4627 <param name="force" value="false"/>
4628 <param name="test" value="true"/>
4629 </conditional>
4630 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
4631 <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4632 <param name="out_type" value="featureXML"/>
4633 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4634 <output name="ctd_out" ftype="xml">
4635 <assert_contents>
4636 <is_valid_xml/>
4637 </assert_contents>
4638 </output>
4639 </test>
4640 <test expect_num_outputs="2">
4641 <conditional name="adv_opts_cond">
4642 <param name="adv_opts_selector" value="advanced"/>
4643 <param name="UID_postprocessing" value="ensure"/>
4644 <param name="TIC_DTA2D" value="false"/>
4645 <param name="MGF_compact" value="false"/>
4646 <param name="force_MaxQuant_compatibility" value="false"/>
4647 <param name="convert_to_chromatograms" value="false"/>
4648 <param name="force_TPP_compatibility" value="false"/>
4649 <param name="change_im_format" value="none"/>
4650 <param name="write_scan_index" value="true"/>
4651 <param name="lossy_compression" value="false"/>
4652 <param name="lossy_mass_accuracy" value="-1.0"/>
4653 <param name="process_lowmemory" value="false"/>
4654 <param name="no_peak_picking" value="false"/>
4655 <param name="force" value="false"/>
4656 <param name="test" value="true"/>
4657 </conditional>
4658 <param name="in" value="FileConverter_11_input.peplist"/>
4659 <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4660 <param name="out_type" value="featureXML"/>
4661 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4662 <output name="ctd_out" ftype="xml">
4663 <assert_contents>
4664 <is_valid_xml/>
4665 </assert_contents>
4666 </output>
4667 </test>
4668 <test expect_num_outputs="2">
4669 <conditional name="adv_opts_cond">
4670 <param name="adv_opts_selector" value="advanced"/>
4671 <param name="UID_postprocessing" value="ensure"/>
4672 <param name="TIC_DTA2D" value="false"/>
4673 <param name="MGF_compact" value="false"/>
4674 <param name="force_MaxQuant_compatibility" value="false"/>
4675 <param name="convert_to_chromatograms" value="false"/>
4676 <param name="force_TPP_compatibility" value="false"/>
4677 <param name="change_im_format" value="none"/>
4678 <param name="write_scan_index" value="true"/>
4679 <param name="lossy_compression" value="false"/>
4680 <param name="lossy_mass_accuracy" value="-1.0"/>
4681 <param name="process_lowmemory" value="false"/>
4682 <param name="no_peak_picking" value="false"/>
4683 <param name="force" value="false"/>
4684 <param name="test" value="true"/>
4685 </conditional>
4686 <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
4687 <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4688 <param name="out_type" value="featureXML"/>
4689 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4690 <output name="ctd_out" ftype="xml">
4691 <assert_contents>
4692 <is_valid_xml/>
4693 </assert_contents>
4694 </output>
4695 </test>
4696 <test expect_num_outputs="2">
4697 <conditional name="adv_opts_cond">
4698 <param name="adv_opts_selector" value="advanced"/>
4699 <param name="UID_postprocessing" value="ensure"/>
4700 <param name="TIC_DTA2D" value="false"/>
4701 <param name="MGF_compact" value="false"/>
4702 <param name="force_MaxQuant_compatibility" value="false"/>
4703 <param name="convert_to_chromatograms" value="false"/>
4704 <param name="force_TPP_compatibility" value="false"/>
4705 <param name="change_im_format" value="none"/>
4706 <param name="write_scan_index" value="true"/>
4707 <param name="lossy_compression" value="false"/>
4708 <param name="lossy_mass_accuracy" value="-1.0"/>
4709 <param name="process_lowmemory" value="false"/>
4710 <param name="no_peak_picking" value="false"/>
4711 <param name="force" value="false"/>
4712 <param name="test" value="true"/>
4713 </conditional>
4714 <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
4715 <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4716 <param name="out_type" value="featureXML"/>
4717 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4718 <output name="ctd_out" ftype="xml">
4719 <assert_contents>
4720 <is_valid_xml/>
4721 </assert_contents>
4722 </output>
4723 </test>
4724 <test expect_num_outputs="2">
4725 <conditional name="adv_opts_cond">
4726 <param name="adv_opts_selector" value="advanced"/>
4727 <param name="UID_postprocessing" value="ensure"/>
4728 <param name="TIC_DTA2D" value="false"/>
4729 <param name="MGF_compact" value="false"/>
4730 <param name="force_MaxQuant_compatibility" value="false"/>
4731 <param name="convert_to_chromatograms" value="false"/>
4732 <param name="force_TPP_compatibility" value="false"/>
4733 <param name="change_im_format" value="none"/>
4734 <param name="write_scan_index" value="true"/>
4735 <param name="lossy_compression" value="false"/>
4736 <param name="lossy_mass_accuracy" value="-1.0"/>
4737 <param name="process_lowmemory" value="false"/>
4738 <param name="no_peak_picking" value="false"/>
4739 <param name="force" value="false"/>
4740 <param name="test" value="true"/>
4741 </conditional>
4742 <param name="in" value="FileConverter_9_output.featureXML"/>
4743 <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4744 <param name="out_type" value="consensusXML"/>
4745 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4746 <output name="ctd_out" ftype="xml">
4747 <assert_contents>
4748 <is_valid_xml/>
4749 </assert_contents>
4750 </output>
4751 </test>
4752 <test expect_num_outputs="2">
4753 <conditional name="adv_opts_cond">
4754 <param name="adv_opts_selector" value="advanced"/>
4755 <param name="UID_postprocessing" value="ensure"/>
4756 <param name="TIC_DTA2D" value="false"/>
4757 <param name="MGF_compact" value="false"/>
4758 <param name="force_MaxQuant_compatibility" value="false"/>
4759 <param name="convert_to_chromatograms" value="false"/>
4760 <param name="force_TPP_compatibility" value="false"/>
4761 <param name="change_im_format" value="none"/>
4762 <param name="write_scan_index" value="true"/>
4763 <param name="lossy_compression" value="false"/>
4764 <param name="lossy_mass_accuracy" value="-1.0"/>
4765 <param name="process_lowmemory" value="false"/>
4766 <param name="no_peak_picking" value="false"/>
4767 <param name="force" value="false"/>
4768 <param name="test" value="true"/>
4769 </conditional>
4770 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
4771 <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4772 <param name="out_type" value="consensusXML"/>
4773 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4774 <output name="ctd_out" ftype="xml">
4775 <assert_contents>
4776 <is_valid_xml/>
4777 </assert_contents>
4778 </output>
4779 </test>
4780 <test expect_num_outputs="2">
4781 <conditional name="adv_opts_cond">
4782 <param name="adv_opts_selector" value="advanced"/>
4783 <param name="UID_postprocessing" value="ensure"/>
4784 <param name="TIC_DTA2D" value="false"/>
4785 <param name="MGF_compact" value="false"/>
4786 <param name="force_MaxQuant_compatibility" value="false"/>
4787 <param name="convert_to_chromatograms" value="false"/>
4788 <param name="force_TPP_compatibility" value="false"/>
4789 <param name="change_im_format" value="none"/>
4790 <param name="write_scan_index" value="true"/>
4791 <param name="lossy_compression" value="false"/>
4792 <param name="lossy_mass_accuracy" value="-1.0"/>
4793 <param name="process_lowmemory" value="false"/>
4794 <param name="no_peak_picking" value="false"/>
4795 <param name="force" value="false"/>
4796 <param name="test" value="true"/>
4797 </conditional>
4798 <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
4799 <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4800 <param name="out_type" value="consensusXML"/>
4801 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4802 <output name="ctd_out" ftype="xml">
4803 <assert_contents>
4804 <is_valid_xml/>
4805 </assert_contents>
4806 </output>
4807 </test>
4808 <test expect_num_outputs="2">
4809 <conditional name="adv_opts_cond">
4810 <param name="adv_opts_selector" value="advanced"/>
4811 <param name="UID_postprocessing" value="ensure"/>
4812 <param name="TIC_DTA2D" value="false"/>
4813 <param name="MGF_compact" value="false"/>
4814 <param name="force_MaxQuant_compatibility" value="false"/>
4815 <param name="convert_to_chromatograms" value="false"/>
4816 <param name="force_TPP_compatibility" value="false"/>
4817 <param name="change_im_format" value="none"/>
4818 <param name="write_scan_index" value="true"/>
4819 <param name="lossy_compression" value="false"/>
4820 <param name="lossy_mass_accuracy" value="-1.0"/>
4821 <param name="process_lowmemory" value="false"/>
4822 <param name="no_peak_picking" value="false"/>
4823 <param name="force" value="false"/>
4824 <param name="test" value="true"/>
4825 </conditional>
4826 <param name="in" value="FileConverter_17_input.consensusXML"/>
4827 <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/>
4828 <param name="out_type" value="csv"/>
4829 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4830 <output name="ctd_out" ftype="xml">
4831 <assert_contents>
4832 <is_valid_xml/>
4833 </assert_contents>
4834 </output>
4835 </test>
4836 <test expect_num_outputs="2">
4837 <conditional name="adv_opts_cond">
4838 <param name="adv_opts_selector" value="advanced"/>
4839 <param name="UID_postprocessing" value="ensure"/>
4840 <param name="TIC_DTA2D" value="false"/>
4841 <param name="MGF_compact" value="false"/>
4842 <param name="force_MaxQuant_compatibility" value="false"/>
4843 <param name="convert_to_chromatograms" value="false"/>
4844 <param name="force_TPP_compatibility" value="false"/>
4845 <param name="change_im_format" value="none"/>
4846 <param name="write_scan_index" value="true"/>
4847 <param name="lossy_compression" value="false"/>
4848 <param name="lossy_mass_accuracy" value="-1.0"/>
4849 <param name="process_lowmemory" value="false"/>
4850 <param name="no_peak_picking" value="false"/>
4851 <param name="force" value="false"/>
4852 <param name="test" value="true"/>
4853 </conditional>
4854 <param name="in" value="FileConverter_17_input.consensusXML"/>
4855 <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/>
4856 <param name="out_type" value="csv"/>
4857 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4858 <output name="ctd_out" ftype="xml">
4859 <assert_contents>
4860 <is_valid_xml/>
4861 </assert_contents>
4862 </output>
4863 </test>
4864 <test expect_num_outputs="2">
4865 <conditional name="adv_opts_cond">
4866 <param name="adv_opts_selector" value="advanced"/>
4867 <param name="UID_postprocessing" value="ensure"/>
4868 <param name="TIC_DTA2D" value="false"/>
4869 <param name="MGF_compact" value="false"/>
4870 <param name="force_MaxQuant_compatibility" value="false"/>
4871 <param name="convert_to_chromatograms" value="false"/>
4872 <param name="force_TPP_compatibility" value="false"/>
4873 <param name="change_im_format" value="none"/>
4874 <param name="write_scan_index" value="true"/>
4875 <param name="lossy_compression" value="false"/>
4876 <param name="lossy_mass_accuracy" value="-1.0"/>
4877 <param name="process_lowmemory" value="true"/>
4878 <param name="no_peak_picking" value="false"/>
4879 <param name="force" value="false"/>
4880 <param name="test" value="true"/>
4881 </conditional>
4882 <param name="in" value="FileFilter_1_input.mzML"/>
4883 <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4884 <param name="out_type" value="mzML"/>
4885 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4886 <output name="ctd_out" ftype="xml">
4887 <assert_contents>
4888 <is_valid_xml/>
4889 </assert_contents>
4890 </output>
4891 </test>
4892 <test expect_num_outputs="2">
4893 <conditional name="adv_opts_cond">
4894 <param name="adv_opts_selector" value="advanced"/>
4895 <param name="UID_postprocessing" value="ensure"/>
4896 <param name="TIC_DTA2D" value="false"/>
4897 <param name="MGF_compact" value="false"/>
4898 <param name="force_MaxQuant_compatibility" value="false"/>
4899 <param name="convert_to_chromatograms" value="false"/>
4900 <param name="force_TPP_compatibility" value="false"/>
4901 <param name="change_im_format" value="none"/>
4902 <param name="write_scan_index" value="true"/>
4903 <param name="lossy_compression" value="false"/>
4904 <param name="lossy_mass_accuracy" value="-1.0"/>
4905 <param name="process_lowmemory" value="false"/>
4906 <param name="no_peak_picking" value="false"/>
4907 <param name="force" value="false"/>
4908 <param name="test" value="true"/>
4909 </conditional>
4910 <param name="in" value="FileConverter_20_input.featureXML"/>
4911 <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4912 <param name="out_type" value="featureXML"/>
4913 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4914 <output name="ctd_out" ftype="xml">
4915 <assert_contents>
4916 <is_valid_xml/>
4917 </assert_contents>
4918 </output>
4919 </test>
4920 <test expect_num_outputs="2">
4921 <conditional name="adv_opts_cond">
4922 <param name="adv_opts_selector" value="advanced"/>
4923 <param name="UID_postprocessing" value="ensure"/>
4924 <param name="TIC_DTA2D" value="false"/>
4925 <param name="MGF_compact" value="false"/>
4926 <param name="force_MaxQuant_compatibility" value="false"/>
4927 <param name="convert_to_chromatograms" value="false"/>
4928 <param name="force_TPP_compatibility" value="false"/>
4929 <param name="change_im_format" value="none"/>
4930 <param name="write_scan_index" value="true"/>
4931 <param name="lossy_compression" value="false"/>
4932 <param name="lossy_mass_accuracy" value="-1.0"/>
4933 <param name="process_lowmemory" value="true"/>
4934 <param name="no_peak_picking" value="false"/>
4935 <param name="force" value="false"/>
4936 <param name="test" value="true"/>
4937 </conditional>
4938 <param name="in" value="FileConverter_4_input.mzXML"/>
4939 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4940 <param name="out_type" value="mzML"/>
4941 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4942 <output name="ctd_out" ftype="xml">
4943 <assert_contents>
4944 <is_valid_xml/>
4945 </assert_contents>
4946 </output>
4947 </test>
4948 <test expect_num_outputs="2">
4949 <conditional name="adv_opts_cond">
4950 <param name="adv_opts_selector" value="advanced"/>
4951 <param name="UID_postprocessing" value="ensure"/>
4952 <param name="TIC_DTA2D" value="false"/>
4953 <param name="MGF_compact" value="false"/>
4954 <param name="force_MaxQuant_compatibility" value="false"/>
4955 <param name="convert_to_chromatograms" value="false"/>
4956 <param name="force_TPP_compatibility" value="false"/>
4957 <param name="change_im_format" value="none"/>
4958 <param name="write_scan_index" value="true"/>
4959 <param name="lossy_compression" value="false"/>
4960 <param name="lossy_mass_accuracy" value="-1.0"/>
4961 <param name="process_lowmemory" value="false"/>
4962 <param name="no_peak_picking" value="false"/>
4963 <param name="force" value="false"/>
4964 <param name="test" value="true"/>
4965 </conditional>
4966 <param name="in" value="FileConverter_23_input.mzML"/>
4967 <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4968 <param name="out_type" value="mzML"/>
4969 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4970 <output name="ctd_out" ftype="xml">
4971 <assert_contents>
4972 <is_valid_xml/>
4973 </assert_contents>
4974 </output>
4975 </test>
4976 <test expect_num_outputs="2">
4977 <conditional name="adv_opts_cond">
4978 <param name="adv_opts_selector" value="advanced"/>
4979 <param name="UID_postprocessing" value="ensure"/>
4980 <param name="TIC_DTA2D" value="false"/>
4981 <param name="MGF_compact" value="false"/>
4982 <param name="force_MaxQuant_compatibility" value="false"/>
4983 <param name="convert_to_chromatograms" value="false"/>
4984 <param name="force_TPP_compatibility" value="false"/>
4985 <param name="change_im_format" value="none"/>
4986 <param name="write_scan_index" value="true"/>
4987 <param name="lossy_compression" value="true"/>
4988 <param name="lossy_mass_accuracy" value="0.0001"/>
4989 <param name="process_lowmemory" value="true"/>
4990 <param name="no_peak_picking" value="false"/>
4991 <param name="force" value="false"/>
4992 <param name="test" value="true"/>
4993 </conditional>
4994 <param name="in" value="FileFilter_1_input.mzML"/>
4995 <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4996 <param name="out_type" value="mzML"/>
4997 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4998 <output name="ctd_out" ftype="xml">
4999 <assert_contents>
5000 <is_valid_xml/>
5001 </assert_contents>
5002 </output>
5003 </test>
5004 <test expect_num_outputs="2">
5005 <conditional name="adv_opts_cond">
5006 <param name="adv_opts_selector" value="advanced"/>
5007 <param name="UID_postprocessing" value="ensure"/>
5008 <param name="TIC_DTA2D" value="false"/>
5009 <param name="MGF_compact" value="false"/>
5010 <param name="force_MaxQuant_compatibility" value="false"/>
5011 <param name="convert_to_chromatograms" value="false"/>
5012 <param name="force_TPP_compatibility" value="false"/>
5013 <param name="change_im_format" value="none"/>
5014 <param name="write_scan_index" value="true"/>
5015 <param name="lossy_compression" value="true"/>
5016 <param name="lossy_mass_accuracy" value="-1.0"/>
5017 <param name="process_lowmemory" value="true"/>
5018 <param name="no_peak_picking" value="false"/>
5019 <param name="force" value="false"/>
5020 <param name="test" value="true"/>
5021 </conditional>
5022 <param name="in" value="FileFilter_1_input.mzML"/>
5023 <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5024 <param name="out_type" value="mzML"/>
5025 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5026 <output name="ctd_out" ftype="xml">
5027 <assert_contents>
5028 <is_valid_xml/>
5029 </assert_contents>
5030 </output>
5031 </test>
5032 <test expect_num_outputs="2">
5033 <conditional name="adv_opts_cond">
5034 <param name="adv_opts_selector" value="advanced"/>
5035 <param name="UID_postprocessing" value="ensure"/>
5036 <param name="TIC_DTA2D" value="false"/>
5037 <param name="MGF_compact" value="false"/>
5038 <param name="force_MaxQuant_compatibility" value="true"/>
5039 <param name="convert_to_chromatograms" value="false"/>
5040 <param name="force_TPP_compatibility" value="false"/>
5041 <param name="change_im_format" value="none"/>
5042 <param name="write_scan_index" value="true"/>
5043 <param name="lossy_compression" value="false"/>
5044 <param name="lossy_mass_accuracy" value="-1.0"/>
5045 <param name="process_lowmemory" value="false"/>
5046 <param name="no_peak_picking" value="false"/>
5047 <param name="force" value="false"/>
5048 <param name="test" value="true"/>
5049 </conditional>
5050 <param name="in" value="FileFilter_1_input.mzML"/>
5051 <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
5052 <param name="out_type" value="mzXML"/>
5053 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5054 <output name="ctd_out" ftype="xml">
5055 <assert_contents>
5056 <is_valid_xml/>
5057 </assert_contents>
5058 </output>
5059 </test>
5060 <test expect_num_outputs="2">
5061 <conditional name="adv_opts_cond">
5062 <param name="adv_opts_selector" value="advanced"/>
5063 <param name="UID_postprocessing" value="ensure"/>
5064 <param name="TIC_DTA2D" value="false"/>
5065 <param name="MGF_compact" value="false"/>
5066 <param name="force_MaxQuant_compatibility" value="true"/>
5067 <param name="convert_to_chromatograms" value="false"/>
5068 <param name="force_TPP_compatibility" value="false"/>
5069 <param name="change_im_format" value="none"/>
5070 <param name="write_scan_index" value="true"/>
5071 <param name="lossy_compression" value="false"/>
5072 <param name="lossy_mass_accuracy" value="-1.0"/>
5073 <param name="process_lowmemory" value="false"/>
5074 <param name="no_peak_picking" value="false"/>
5075 <param name="force" value="false"/>
5076 <param name="test" value="true"/>
5077 </conditional>
5078 <param name="in" value="FileConverter_26_output.mzXML"/>
5079 <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
5080 <param name="out_type" value="mzXML"/>
5081 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5082 <output name="ctd_out" ftype="xml">
5083 <assert_contents>
5084 <is_valid_xml/>
5085 </assert_contents>
5086 </output>
5087 </test>
5088 <test expect_num_outputs="2">
5089 <conditional name="adv_opts_cond">
5090 <param name="adv_opts_selector" value="advanced"/>
5091 <param name="UID_postprocessing" value="ensure"/>
5092 <param name="TIC_DTA2D" value="false"/>
5093 <param name="MGF_compact" value="false"/>
5094 <param name="force_MaxQuant_compatibility" value="false"/>
5095 <param name="convert_to_chromatograms" value="true"/>
5096 <param name="force_TPP_compatibility" value="false"/>
5097 <param name="change_im_format" value="none"/>
5098 <param name="write_scan_index" value="true"/>
5099 <param name="lossy_compression" value="false"/>
5100 <param name="lossy_mass_accuracy" value="-1.0"/>
5101 <param name="process_lowmemory" value="false"/>
5102 <param name="no_peak_picking" value="false"/>
5103 <param name="force" value="false"/>
5104 <param name="test" value="true"/>
5105 </conditional>
5106 <param name="in" value="FileConverter_27_input.mzML"/>
5107 <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5108 <param name="out_type" value="mzML"/>
5109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5110 <output name="ctd_out" ftype="xml">
5111 <assert_contents>
5112 <is_valid_xml/>
5113 </assert_contents>
5114 </output>
5115 </test>
5116 <test expect_num_outputs="2">
5117 <conditional name="adv_opts_cond">
5118 <param name="adv_opts_selector" value="advanced"/>
5119 <param name="UID_postprocessing" value="ensure"/>
5120 <param name="TIC_DTA2D" value="false"/>
5121 <param name="MGF_compact" value="false"/>
5122 <param name="force_MaxQuant_compatibility" value="false"/>
5123 <param name="convert_to_chromatograms" value="true"/>
5124 <param name="force_TPP_compatibility" value="false"/>
5125 <param name="change_im_format" value="none"/>
5126 <param name="write_scan_index" value="true"/>
5127 <param name="lossy_compression" value="false"/>
5128 <param name="lossy_mass_accuracy" value="-1.0"/>
5129 <param name="process_lowmemory" value="false"/>
5130 <param name="no_peak_picking" value="false"/>
5131 <param name="force" value="false"/>
5132 <param name="test" value="true"/>
5133 </conditional>
5134 <param name="in" value="FileConverter_28_input.mzML"/>
5135 <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5136 <param name="out_type" value="mzML"/>
5137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5138 <output name="ctd_out" ftype="xml">
5139 <assert_contents>
5140 <is_valid_xml/>
5141 </assert_contents>
5142 </output>
5143 </test>
5144 <test expect_num_outputs="2">
5145 <conditional name="adv_opts_cond">
5146 <param name="adv_opts_selector" value="advanced"/>
5147 <param name="UID_postprocessing" value="ensure"/>
5148 <param name="TIC_DTA2D" value="false"/>
5149 <param name="MGF_compact" value="false"/>
5150 <param name="force_MaxQuant_compatibility" value="false"/>
5151 <param name="convert_to_chromatograms" value="false"/>
5152 <param name="force_TPP_compatibility" value="false"/>
5153 <param name="change_im_format" value="none"/>
5154 <param name="write_scan_index" value="true"/>
5155 <param name="lossy_compression" value="true"/>
5156 <param name="lossy_mass_accuracy" value="1e-05"/>
5157 <param name="process_lowmemory" value="true"/>
5158 <param name="no_peak_picking" value="false"/>
5159 <param name="force" value="false"/>
5160 <param name="test" value="true"/>
5161 </conditional>
5162 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
5163 <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5164 <param name="out_type" value="mzML"/>
5165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5166 <output name="ctd_out" ftype="xml">
5167 <assert_contents>
5168 <is_valid_xml/>
5169 </assert_contents>
5170 </output>
5171 </test>
5172 <test expect_num_outputs="2">
5173 <conditional name="adv_opts_cond">
5174 <param name="adv_opts_selector" value="advanced"/>
5175 <param name="UID_postprocessing" value="ensure"/>
5176 <param name="TIC_DTA2D" value="false"/>
5177 <param name="MGF_compact" value="false"/>
5178 <param name="force_MaxQuant_compatibility" value="false"/>
5179 <param name="convert_to_chromatograms" value="false"/>
5180 <param name="force_TPP_compatibility" value="false"/>
5181 <param name="change_im_format" value="none"/>
5182 <param name="write_scan_index" value="true"/>
5183 <param name="lossy_compression" value="false"/>
5184 <param name="lossy_mass_accuracy" value="-1.0"/>
5185 <param name="process_lowmemory" value="false"/>
5186 <param name="no_peak_picking" value="false"/>
5187 <param name="force" value="false"/>
5188 <param name="test" value="true"/>
5189 </conditional>
5190 <param name="in" value="FileConverter_29_output.mzML"/>
5191 <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/>
5192 <param name="out_type" value="mzML"/>
5193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5194 <output name="ctd_out" ftype="xml">
5195 <assert_contents>
5196 <is_valid_xml/>
5197 </assert_contents>
5198 </output>
5199 </test>
5200 <test expect_num_outputs="2">
5201 <conditional name="adv_opts_cond">
5202 <param name="adv_opts_selector" value="advanced"/>
5203 <param name="UID_postprocessing" value="ensure"/>
5204 <param name="TIC_DTA2D" value="false"/>
5205 <param name="MGF_compact" value="false"/>
5206 <param name="force_MaxQuant_compatibility" value="false"/>
5207 <param name="convert_to_chromatograms" value="false"/>
5208 <param name="force_TPP_compatibility" value="false"/>
5209 <param name="change_im_format" value="multiple"/>
5210 <param name="write_scan_index" value="true"/>
5211 <param name="lossy_compression" value="false"/>
5212 <param name="lossy_mass_accuracy" value="-1.0"/>
5213 <param name="process_lowmemory" value="false"/>
5214 <param name="no_peak_picking" value="false"/>
5215 <param name="force" value="false"/>
5216 <param name="test" value="true"/>
5217 </conditional>
5218 <param name="in" value="FileConverter_30_input.mzML"/>
5219 <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5220 <param name="out_type" value="mzML"/>
5221 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5222 <output name="ctd_out" ftype="xml">
5223 <assert_contents>
5224 <is_valid_xml/>
5225 </assert_contents>
5226 </output>
5227 </test>
5228 <test expect_num_outputs="2">
5229 <conditional name="adv_opts_cond">
5230 <param name="adv_opts_selector" value="advanced"/>
5231 <param name="UID_postprocessing" value="ensure"/>
5232 <param name="TIC_DTA2D" value="false"/>
5233 <param name="MGF_compact" value="false"/>
5234 <param name="force_MaxQuant_compatibility" value="false"/>
5235 <param name="convert_to_chromatograms" value="false"/>
5236 <param name="force_TPP_compatibility" value="false"/>
5237 <param name="change_im_format" value="single"/>
5238 <param name="write_scan_index" value="true"/>
5239 <param name="lossy_compression" value="false"/>
5240 <param name="lossy_mass_accuracy" value="-1.0"/>
5241 <param name="process_lowmemory" value="false"/>
5242 <param name="no_peak_picking" value="false"/>
5243 <param name="force" value="false"/>
5244 <param name="test" value="true"/>
5245 </conditional>
5246 <param name="in" value="FileConverter_30_output.mzML"/>
5247 <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5248 <param name="out_type" value="mzML"/>
5249 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5250 <output name="ctd_out" ftype="xml">
5251 <assert_contents>
5252 <is_valid_xml/>
5253 </assert_contents>
5254 </output>
5255 </test>
5256 <test expect_num_outputs="2">
5257 <conditional name="adv_opts_cond">
5258 <param name="adv_opts_selector" value="advanced"/>
5259 <param name="UID_postprocessing" value="ensure"/>
5260 <param name="TIC_DTA2D" value="false"/>
5261 <param name="MGF_compact" value="false"/>
5262 <param name="force_MaxQuant_compatibility" value="false"/>
5263 <param name="convert_to_chromatograms" value="false"/>
5264 <param name="force_TPP_compatibility" value="false"/>
5265 <param name="change_im_format" value="none"/>
5266 <param name="write_scan_index" value="true"/>
5267 <param name="lossy_compression" value="false"/>
5268 <param name="lossy_mass_accuracy" value="-1.0"/>
5269 <param name="process_lowmemory" value="false"/>
5270 <param name="no_peak_picking" value="false"/>
5271 <param name="force" value="false"/>
5272 <param name="test" value="true"/>
5273 </conditional>
5274 <param name="in" value="FileConverter_32_input.mzML"/>
5275 <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5276 <param name="out_type" value="mzML"/>
5277 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5278 <output name="ctd_out" ftype="xml">
5279 <assert_contents>
5280 <is_valid_xml/>
5281 </assert_contents>
5282 </output>
5283 </test>
5284 <test expect_num_outputs="2">
5285 <conditional name="adv_opts_cond">
5286 <param name="adv_opts_selector" value="advanced"/>
5287 <param name="UID_postprocessing" value="ensure"/>
5288 <param name="TIC_DTA2D" value="false"/>
5289 <param name="MGF_compact" value="false"/>
5290 <param name="force_MaxQuant_compatibility" value="false"/>
5291 <param name="convert_to_chromatograms" value="false"/>
5292 <param name="force_TPP_compatibility" value="false"/>
5293 <param name="change_im_format" value="none"/>
5294 <param name="write_scan_index" value="true"/>
5295 <param name="lossy_compression" value="false"/>
5296 <param name="lossy_mass_accuracy" value="-1.0"/>
5297 <param name="process_lowmemory" value="false"/>
5298 <param name="no_peak_picking" value="false"/>
5299 <param name="force" value="false"/>
5300 <param name="test" value="true"/>
5301 </conditional>
5302 <param name="in" value="ginkgotoxin-ms-switching.raw"/>
5303 <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5304 <param name="out_type" value="mzml"/>
5305 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5306 <output name="ctd_out" ftype="xml">
5307 <assert_contents>
5308 <is_valid_xml/>
5309 </assert_contents>
5310 </output>
5311 </test>
5312 </xml>
5313 <xml name="autotest_FileFilter">
5314 <test expect_num_outputs="2">
5315 <conditional name="adv_opts_cond">
5316 <param name="adv_opts_selector" value="advanced"/>
5317 <param name="force" value="false"/>
5318 <param name="test" value="true"/>
5319 </conditional>
5320 <param name="in" value="FileFilter_1_input.mzML"/>
5321 <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5322 <param name="out_type" value="mzML"/>
5323 <param name="rt" value=":30"/>
5324 <param name="mz" value=":1000"/>
5325 <param name="int" value=":20000"/>
5326 <param name="sort" value="false"/>
5327 <section name="peak_options">
5328 <param name="sn" value="0.0"/>
5329 <param name="rm_pc_charge" value=""/>
5330 <param name="pc_mz_range" value=":"/>
5331 <param name="pc_mz_list" value=""/>
5332 <param name="level" value="1 2 3"/>
5333 <param name="sort_peaks" value="false"/>
5334 <param name="no_chromatograms" value="false"/>
5335 <param name="remove_chromatograms" value="false"/>
5336 <param name="remove_empty" value="false"/>
5337 <param name="mz_precision" value="64"/>
5338 <param name="int_precision" value="32"/>
5339 <param name="indexed_file" value="true"/>
5340 <param name="zlib_compression" value="false"/>
5341 <section name="numpress">
5342 <param name="masstime" value="none"/>
5343 <param name="lossy_mass_accuracy" value="-1.0"/>
5344 <param name="intensity" value="none"/>
5345 <param name="float_da" value="none"/>
5346 </section>
5347 </section>
5348 <section name="spectra">
5349 <param name="remove_zoom" value="false"/>
5350 <param name="remove_mode" value=""/>
5351 <param name="remove_activation" value=""/>
5352 <param name="remove_collision_energy" value=":"/>
5353 <param name="remove_isolation_window_width" value=":"/>
5354 <param name="select_zoom" value="false"/>
5355 <param name="select_mode" value=""/>
5356 <param name="select_activation" value=""/>
5357 <param name="select_collision_energy" value=":"/>
5358 <param name="select_isolation_window_width" value=":"/>
5359 <param name="select_polarity" value=""/>
5360 <section name="blackorwhitelist">
5361 <param name="similarity_threshold" value="-1.0"/>
5362 <param name="rt" value="0.01"/>
5363 <param name="mz" value="0.01"/>
5364 <param name="use_ppm_tolerance" value="false"/>
5365 <param name="blacklist" value="true"/>
5366 </section>
5367 </section>
5368 <section name="feature">
5369 <param name="q" value=":"/>
5370 </section>
5371 <section name="consensus">
5372 <param name="map" value=""/>
5373 <param name="map_and" value="false"/>
5374 <section name="blackorwhitelist">
5375 <param name="blacklist" value="true"/>
5376 <param name="maps" value=""/>
5377 <param name="rt" value="60.0"/>
5378 <param name="mz" value="0.01"/>
5379 <param name="use_ppm_tolerance" value="false"/>
5380 </section>
5381 </section>
5382 <section name="f_and_c">
5383 <param name="charge" value=":"/>
5384 <param name="size" value=":"/>
5385 <param name="remove_meta" value=""/>
5386 </section>
5387 <section name="id">
5388 <param name="remove_clashes" value="false"/>
5389 <param name="keep_best_score_id" value="false"/>
5390 <param name="sequences_whitelist" value=""/>
5391 <param name="sequence_comparison_method" value="substring"/>
5392 <param name="accessions_whitelist" value=""/>
5393 <param name="remove_annotated_features" value="false"/>
5394 <param name="remove_unannotated_features" value="false"/>
5395 <param name="remove_unassigned_ids" value="false"/>
5396 <param name="rt" value="0.1"/>
5397 <param name="mz" value="0.001"/>
5398 <param name="blacklist_imperfect" value="false"/>
5399 </section>
5400 <section name="algorithm">
5401 <section name="SignalToNoise">
5402 <param name="max_intensity" value="-1"/>
5403 <param name="auto_max_stdev_factor" value="3.0"/>
5404 <param name="auto_max_percentile" value="95"/>
5405 <param name="auto_mode" value="0"/>
5406 <param name="win_len" value="200.0"/>
5407 <param name="bin_count" value="30"/>
5408 <param name="min_required_elements" value="10"/>
5409 <param name="noise_for_empty_window" value="1e+20"/>
5410 <param name="write_log_messages" value="true"/>
5411 </section>
5412 </section>
5413 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5414 <output name="ctd_out" ftype="xml">
5415 <assert_contents>
5416 <is_valid_xml/>
5417 </assert_contents>
5418 </output>
5419 </test>
5420 <test expect_num_outputs="2">
5421 <conditional name="adv_opts_cond">
5422 <param name="adv_opts_selector" value="advanced"/>
5423 <param name="force" value="false"/>
5424 <param name="test" value="true"/>
5425 </conditional>
5426 <param name="in" value="FileFilter_1_input.mzML"/>
5427 <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5428 <param name="out_type" value="mzML"/>
5429 <param name="rt" value="30:"/>
5430 <param name="mz" value="1000:"/>
5431 <param name="int" value="100:"/>
5432 <param name="sort" value="false"/>
5433 <section name="peak_options">
5434 <param name="sn" value="0.0"/>
5435 <param name="rm_pc_charge" value=""/>
5436 <param name="pc_mz_range" value=":"/>
5437 <param name="pc_mz_list" value=""/>
5438 <param name="level" value="1 2 3"/>
5439 <param name="sort_peaks" value="false"/>
5440 <param name="no_chromatograms" value="false"/>
5441 <param name="remove_chromatograms" value="false"/>
5442 <param name="remove_empty" value="false"/>
5443 <param name="mz_precision" value="64"/>
5444 <param name="int_precision" value="32"/>
5445 <param name="indexed_file" value="true"/>
5446 <param name="zlib_compression" value="false"/>
5447 <section name="numpress">
5448 <param name="masstime" value="none"/>
5449 <param name="lossy_mass_accuracy" value="-1.0"/>
5450 <param name="intensity" value="none"/>
5451 <param name="float_da" value="none"/>
5452 </section>
5453 </section>
5454 <section name="spectra">
5455 <param name="remove_zoom" value="false"/>
5456 <param name="remove_mode" value=""/>
5457 <param name="remove_activation" value=""/>
5458 <param name="remove_collision_energy" value=":"/>
5459 <param name="remove_isolation_window_width" value=":"/>
5460 <param name="select_zoom" value="false"/>
5461 <param name="select_mode" value=""/>
5462 <param name="select_activation" value=""/>
5463 <param name="select_collision_energy" value=":"/>
5464 <param name="select_isolation_window_width" value=":"/>
5465 <param name="select_polarity" value=""/>
5466 <section name="blackorwhitelist">
5467 <param name="similarity_threshold" value="-1.0"/>
5468 <param name="rt" value="0.01"/>
5469 <param name="mz" value="0.01"/>
5470 <param name="use_ppm_tolerance" value="false"/>
5471 <param name="blacklist" value="true"/>
5472 </section>
5473 </section>
5474 <section name="feature">
5475 <param name="q" value=":"/>
5476 </section>
5477 <section name="consensus">
5478 <param name="map" value=""/>
5479 <param name="map_and" value="false"/>
5480 <section name="blackorwhitelist">
5481 <param name="blacklist" value="true"/>
5482 <param name="maps" value=""/>
5483 <param name="rt" value="60.0"/>
5484 <param name="mz" value="0.01"/>
5485 <param name="use_ppm_tolerance" value="false"/>
5486 </section>
5487 </section>
5488 <section name="f_and_c">
5489 <param name="charge" value=":"/>
5490 <param name="size" value=":"/>
5491 <param name="remove_meta" value=""/>
5492 </section>
5493 <section name="id">
5494 <param name="remove_clashes" value="false"/>
5495 <param name="keep_best_score_id" value="false"/>
5496 <param name="sequences_whitelist" value=""/>
5497 <param name="sequence_comparison_method" value="substring"/>
5498 <param name="accessions_whitelist" value=""/>
5499 <param name="remove_annotated_features" value="false"/>
5500 <param name="remove_unannotated_features" value="false"/>
5501 <param name="remove_unassigned_ids" value="false"/>
5502 <param name="rt" value="0.1"/>
5503 <param name="mz" value="0.001"/>
5504 <param name="blacklist_imperfect" value="false"/>
5505 </section>
5506 <section name="algorithm">
5507 <section name="SignalToNoise">
5508 <param name="max_intensity" value="-1"/>
5509 <param name="auto_max_stdev_factor" value="3.0"/>
5510 <param name="auto_max_percentile" value="95"/>
5511 <param name="auto_mode" value="0"/>
5512 <param name="win_len" value="200.0"/>
5513 <param name="bin_count" value="30"/>
5514 <param name="min_required_elements" value="10"/>
5515 <param name="noise_for_empty_window" value="1e+20"/>
5516 <param name="write_log_messages" value="true"/>
5517 </section>
5518 </section>
5519 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5520 <output name="ctd_out" ftype="xml">
5521 <assert_contents>
5522 <is_valid_xml/>
5523 </assert_contents>
5524 </output>
5525 </test>
5526 <test expect_num_outputs="2">
5527 <conditional name="adv_opts_cond">
5528 <param name="adv_opts_selector" value="advanced"/>
5529 <param name="force" value="false"/>
5530 <param name="test" value="true"/>
5531 </conditional>
5532 <param name="in" value="FileFilter_1_input.mzML"/>
5533 <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5534 <param name="out_type" value="mzML"/>
5535 <param name="rt" value=":"/>
5536 <param name="mz" value=":"/>
5537 <param name="int" value=":"/>
5538 <param name="sort" value="false"/>
5539 <section name="peak_options">
5540 <param name="sn" value="0.0"/>
5541 <param name="rm_pc_charge" value=""/>
5542 <param name="pc_mz_range" value=":"/>
5543 <param name="pc_mz_list" value=""/>
5544 <param name="level" value="2"/>
5545 <param name="sort_peaks" value="false"/>
5546 <param name="no_chromatograms" value="false"/>
5547 <param name="remove_chromatograms" value="false"/>
5548 <param name="remove_empty" value="false"/>
5549 <param name="mz_precision" value="64"/>
5550 <param name="int_precision" value="32"/>
5551 <param name="indexed_file" value="true"/>
5552 <param name="zlib_compression" value="false"/>
5553 <section name="numpress">
5554 <param name="masstime" value="none"/>
5555 <param name="lossy_mass_accuracy" value="-1.0"/>
5556 <param name="intensity" value="none"/>
5557 <param name="float_da" value="none"/>
5558 </section>
5559 </section>
5560 <section name="spectra">
5561 <param name="remove_zoom" value="false"/>
5562 <param name="remove_mode" value=""/>
5563 <param name="remove_activation" value=""/>
5564 <param name="remove_collision_energy" value=":"/>
5565 <param name="remove_isolation_window_width" value=":"/>
5566 <param name="select_zoom" value="false"/>
5567 <param name="select_mode" value=""/>
5568 <param name="select_activation" value=""/>
5569 <param name="select_collision_energy" value=":"/>
5570 <param name="select_isolation_window_width" value=":"/>
5571 <param name="select_polarity" value=""/>
5572 <section name="blackorwhitelist">
5573 <param name="similarity_threshold" value="-1.0"/>
5574 <param name="rt" value="0.01"/>
5575 <param name="mz" value="0.01"/>
5576 <param name="use_ppm_tolerance" value="false"/>
5577 <param name="blacklist" value="true"/>
5578 </section>
5579 </section>
5580 <section name="feature">
5581 <param name="q" value=":"/>
5582 </section>
5583 <section name="consensus">
5584 <param name="map" value=""/>
5585 <param name="map_and" value="false"/>
5586 <section name="blackorwhitelist">
5587 <param name="blacklist" value="true"/>
5588 <param name="maps" value=""/>
5589 <param name="rt" value="60.0"/>
5590 <param name="mz" value="0.01"/>
5591 <param name="use_ppm_tolerance" value="false"/>
5592 </section>
5593 </section>
5594 <section name="f_and_c">
5595 <param name="charge" value=":"/>
5596 <param name="size" value=":"/>
5597 <param name="remove_meta" value=""/>
5598 </section>
5599 <section name="id">
5600 <param name="remove_clashes" value="false"/>
5601 <param name="keep_best_score_id" value="false"/>
5602 <param name="sequences_whitelist" value=""/>
5603 <param name="sequence_comparison_method" value="substring"/>
5604 <param name="accessions_whitelist" value=""/>
5605 <param name="remove_annotated_features" value="false"/>
5606 <param name="remove_unannotated_features" value="false"/>
5607 <param name="remove_unassigned_ids" value="false"/>
5608 <param name="rt" value="0.1"/>
5609 <param name="mz" value="0.001"/>
5610 <param name="blacklist_imperfect" value="false"/>
5611 </section>
5612 <section name="algorithm">
5613 <section name="SignalToNoise">
5614 <param name="max_intensity" value="-1"/>
5615 <param name="auto_max_stdev_factor" value="3.0"/>
5616 <param name="auto_max_percentile" value="95"/>
5617 <param name="auto_mode" value="0"/>
5618 <param name="win_len" value="200.0"/>
5619 <param name="bin_count" value="30"/>
5620 <param name="min_required_elements" value="10"/>
5621 <param name="noise_for_empty_window" value="1e+20"/>
5622 <param name="write_log_messages" value="true"/>
5623 </section>
5624 </section>
5625 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5626 <output name="ctd_out" ftype="xml">
5627 <assert_contents>
5628 <is_valid_xml/>
5629 </assert_contents>
5630 </output>
5631 </test>
5632 <test expect_num_outputs="2">
5633 <conditional name="adv_opts_cond">
5634 <param name="adv_opts_selector" value="advanced"/>
5635 <param name="force" value="false"/>
5636 <param name="test" value="true"/>
5637 </conditional>
5638 <param name="in" value="FileFilter_4_input.mzML"/>
5639 <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5640 <param name="out_type" value="mzML"/>
5641 <param name="rt" value=":"/>
5642 <param name="mz" value=":"/>
5643 <param name="int" value=":"/>
5644 <param name="sort" value="false"/>
5645 <section name="peak_options">
5646 <param name="sn" value="0.0"/>
5647 <param name="rm_pc_charge" value=""/>
5648 <param name="pc_mz_range" value=":"/>
5649 <param name="pc_mz_list" value=""/>
5650 <param name="level" value="1 2 3"/>
5651 <param name="sort_peaks" value="false"/>
5652 <param name="no_chromatograms" value="false"/>
5653 <param name="remove_chromatograms" value="false"/>
5654 <param name="remove_empty" value="false"/>
5655 <param name="mz_precision" value="64"/>
5656 <param name="int_precision" value="32"/>
5657 <param name="indexed_file" value="true"/>
5658 <param name="zlib_compression" value="false"/>
5659 <section name="numpress">
5660 <param name="masstime" value="none"/>
5661 <param name="lossy_mass_accuracy" value="-1.0"/>
5662 <param name="intensity" value="none"/>
5663 <param name="float_da" value="none"/>
5664 </section>
5665 </section>
5666 <section name="spectra">
5667 <param name="remove_zoom" value="true"/>
5668 <param name="remove_mode" value=""/>
5669 <param name="remove_activation" value=""/>
5670 <param name="remove_collision_energy" value=":"/>
5671 <param name="remove_isolation_window_width" value=":"/>
5672 <param name="select_zoom" value="false"/>
5673 <param name="select_mode" value=""/>
5674 <param name="select_activation" value=""/>
5675 <param name="select_collision_energy" value=":"/>
5676 <param name="select_isolation_window_width" value=":"/>
5677 <param name="select_polarity" value=""/>
5678 <section name="blackorwhitelist">
5679 <param name="similarity_threshold" value="-1.0"/>
5680 <param name="rt" value="0.01"/>
5681 <param name="mz" value="0.01"/>
5682 <param name="use_ppm_tolerance" value="false"/>
5683 <param name="blacklist" value="true"/>
5684 </section>
5685 </section>
5686 <section name="feature">
5687 <param name="q" value=":"/>
5688 </section>
5689 <section name="consensus">
5690 <param name="map" value=""/>
5691 <param name="map_and" value="false"/>
5692 <section name="blackorwhitelist">
5693 <param name="blacklist" value="true"/>
5694 <param name="maps" value=""/>
5695 <param name="rt" value="60.0"/>
5696 <param name="mz" value="0.01"/>
5697 <param name="use_ppm_tolerance" value="false"/>
5698 </section>
5699 </section>
5700 <section name="f_and_c">
5701 <param name="charge" value=":"/>
5702 <param name="size" value=":"/>
5703 <param name="remove_meta" value=""/>
5704 </section>
5705 <section name="id">
5706 <param name="remove_clashes" value="false"/>
5707 <param name="keep_best_score_id" value="false"/>
5708 <param name="sequences_whitelist" value=""/>
5709 <param name="sequence_comparison_method" value="substring"/>
5710 <param name="accessions_whitelist" value=""/>
5711 <param name="remove_annotated_features" value="false"/>
5712 <param name="remove_unannotated_features" value="false"/>
5713 <param name="remove_unassigned_ids" value="false"/>
5714 <param name="rt" value="0.1"/>
5715 <param name="mz" value="0.001"/>
5716 <param name="blacklist_imperfect" value="false"/>
5717 </section>
5718 <section name="algorithm">
5719 <section name="SignalToNoise">
5720 <param name="max_intensity" value="-1"/>
5721 <param name="auto_max_stdev_factor" value="3.0"/>
5722 <param name="auto_max_percentile" value="95"/>
5723 <param name="auto_mode" value="0"/>
5724 <param name="win_len" value="200.0"/>
5725 <param name="bin_count" value="30"/>
5726 <param name="min_required_elements" value="10"/>
5727 <param name="noise_for_empty_window" value="1e+20"/>
5728 <param name="write_log_messages" value="true"/>
5729 </section>
5730 </section>
5731 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5732 <output name="ctd_out" ftype="xml">
5733 <assert_contents>
5734 <is_valid_xml/>
5735 </assert_contents>
5736 </output>
5737 </test>
5738 <test expect_num_outputs="2">
5739 <conditional name="adv_opts_cond">
5740 <param name="adv_opts_selector" value="advanced"/>
5741 <param name="force" value="false"/>
5742 <param name="test" value="true"/>
5743 </conditional>
5744 <param name="in" value="FileFilter_5_input.featureXML"/>
5745 <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
5746 <param name="out_type" value="featureXML"/>
5747 <param name="rt" value=":1000"/>
5748 <param name="mz" value=":480"/>
5749 <param name="int" value=":79000"/>
5750 <param name="sort" value="false"/>
5751 <section name="peak_options">
5752 <param name="sn" value="0.0"/>
5753 <param name="rm_pc_charge" value=""/>
5754 <param name="pc_mz_range" value=":"/>
5755 <param name="pc_mz_list" value=""/>
5756 <param name="level" value="1 2 3"/>
5757 <param name="sort_peaks" value="false"/>
5758 <param name="no_chromatograms" value="false"/>
5759 <param name="remove_chromatograms" value="false"/>
5760 <param name="remove_empty" value="false"/>
5761 <param name="mz_precision" value="64"/>
5762 <param name="int_precision" value="32"/>
5763 <param name="indexed_file" value="true"/>
5764 <param name="zlib_compression" value="false"/>
5765 <section name="numpress">
5766 <param name="masstime" value="none"/>
5767 <param name="lossy_mass_accuracy" value="-1.0"/>
5768 <param name="intensity" value="none"/>
5769 <param name="float_da" value="none"/>
5770 </section>
5771 </section>
5772 <section name="spectra">
5773 <param name="remove_zoom" value="false"/>
5774 <param name="remove_mode" value=""/>
5775 <param name="remove_activation" value=""/>
5776 <param name="remove_collision_energy" value=":"/>
5777 <param name="remove_isolation_window_width" value=":"/>
5778 <param name="select_zoom" value="false"/>
5779 <param name="select_mode" value=""/>
5780 <param name="select_activation" value=""/>
5781 <param name="select_collision_energy" value=":"/>
5782 <param name="select_isolation_window_width" value=":"/>
5783 <param name="select_polarity" value=""/>
5784 <section name="blackorwhitelist">
5785 <param name="similarity_threshold" value="-1.0"/>
5786 <param name="rt" value="0.01"/>
5787 <param name="mz" value="0.01"/>
5788 <param name="use_ppm_tolerance" value="false"/>
5789 <param name="blacklist" value="true"/>
5790 </section>
5791 </section>
5792 <section name="feature">
5793 <param name="q" value=":0.6"/>
5794 </section>
5795 <section name="consensus">
5796 <param name="map" value=""/>
5797 <param name="map_and" value="false"/>
5798 <section name="blackorwhitelist">
5799 <param name="blacklist" value="true"/>
5800 <param name="maps" value=""/>
5801 <param name="rt" value="60.0"/>
5802 <param name="mz" value="0.01"/>
5803 <param name="use_ppm_tolerance" value="false"/>
5804 </section>
5805 </section>
5806 <section name="f_and_c">
5807 <param name="charge" value=":3"/>
5808 <param name="size" value=":"/>
5809 <param name="remove_meta" value=""/>
5810 </section>
5811 <section name="id">
5812 <param name="remove_clashes" value="false"/>
5813 <param name="keep_best_score_id" value="false"/>
5814 <param name="sequences_whitelist" value=""/>
5815 <param name="sequence_comparison_method" value="substring"/>
5816 <param name="accessions_whitelist" value=""/>
5817 <param name="remove_annotated_features" value="false"/>
5818 <param name="remove_unannotated_features" value="false"/>
5819 <param name="remove_unassigned_ids" value="false"/>
5820 <param name="rt" value="0.1"/>
5821 <param name="mz" value="0.001"/>
5822 <param name="blacklist_imperfect" value="false"/>
5823 </section>
5824 <section name="algorithm">
5825 <section name="SignalToNoise">
5826 <param name="max_intensity" value="-1"/>
5827 <param name="auto_max_stdev_factor" value="3.0"/>
5828 <param name="auto_max_percentile" value="95"/>
5829 <param name="auto_mode" value="0"/>
5830 <param name="win_len" value="200.0"/>
5831 <param name="bin_count" value="30"/>
5832 <param name="min_required_elements" value="10"/>
5833 <param name="noise_for_empty_window" value="1e+20"/>
5834 <param name="write_log_messages" value="true"/>
5835 </section>
5836 </section>
5837 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5838 <output name="ctd_out" ftype="xml">
5839 <assert_contents>
5840 <is_valid_xml/>
5841 </assert_contents>
5842 </output>
5843 </test>
5844 <test expect_num_outputs="2">
5845 <conditional name="adv_opts_cond">
5846 <param name="adv_opts_selector" value="advanced"/>
5847 <param name="force" value="false"/>
5848 <param name="test" value="true"/>
5849 </conditional>
5850 <param name="in" value="FileFilter_5_input.featureXML"/>
5851 <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
5852 <param name="out_type" value="featureXML"/>
5853 <param name="rt" value="1000:"/>
5854 <param name="mz" value="440:"/>
5855 <param name="int" value="70000:"/>
5856 <param name="sort" value="false"/>
5857 <section name="peak_options">
5858 <param name="sn" value="0.0"/>
5859 <param name="rm_pc_charge" value=""/>
5860 <param name="pc_mz_range" value=":"/>
5861 <param name="pc_mz_list" value=""/>
5862 <param name="level" value="1 2 3"/>
5863 <param name="sort_peaks" value="false"/>
5864 <param name="no_chromatograms" value="false"/>
5865 <param name="remove_chromatograms" value="false"/>
5866 <param name="remove_empty" value="false"/>
5867 <param name="mz_precision" value="64"/>
5868 <param name="int_precision" value="32"/>
5869 <param name="indexed_file" value="true"/>
5870 <param name="zlib_compression" value="false"/>
5871 <section name="numpress">
5872 <param name="masstime" value="none"/>
5873 <param name="lossy_mass_accuracy" value="-1.0"/>
5874 <param name="intensity" value="none"/>
5875 <param name="float_da" value="none"/>
5876 </section>
5877 </section>
5878 <section name="spectra">
5879 <param name="remove_zoom" value="false"/>
5880 <param name="remove_mode" value=""/>
5881 <param name="remove_activation" value=""/>
5882 <param name="remove_collision_energy" value=":"/>
5883 <param name="remove_isolation_window_width" value=":"/>
5884 <param name="select_zoom" value="false"/>
5885 <param name="select_mode" value=""/>
5886 <param name="select_activation" value=""/>
5887 <param name="select_collision_energy" value=":"/>
5888 <param name="select_isolation_window_width" value=":"/>
5889 <param name="select_polarity" value=""/>
5890 <section name="blackorwhitelist">
5891 <param name="similarity_threshold" value="-1.0"/>
5892 <param name="rt" value="0.01"/>
5893 <param name="mz" value="0.01"/>
5894 <param name="use_ppm_tolerance" value="false"/>
5895 <param name="blacklist" value="true"/>
5896 </section>
5897 </section>
5898 <section name="feature">
5899 <param name="q" value="0.51:"/>
5900 </section>
5901 <section name="consensus">
5902 <param name="map" value=""/>
5903 <param name="map_and" value="false"/>
5904 <section name="blackorwhitelist">
5905 <param name="blacklist" value="true"/>
5906 <param name="maps" value=""/>
5907 <param name="rt" value="60.0"/>
5908 <param name="mz" value="0.01"/>
5909 <param name="use_ppm_tolerance" value="false"/>
5910 </section>
5911 </section>
5912 <section name="f_and_c">
5913 <param name="charge" value="3:"/>
5914 <param name="size" value=":"/>
5915 <param name="remove_meta" value=""/>
5916 </section>
5917 <section name="id">
5918 <param name="remove_clashes" value="false"/>
5919 <param name="keep_best_score_id" value="false"/>
5920 <param name="sequences_whitelist" value=""/>
5921 <param name="sequence_comparison_method" value="substring"/>
5922 <param name="accessions_whitelist" value=""/>
5923 <param name="remove_annotated_features" value="false"/>
5924 <param name="remove_unannotated_features" value="false"/>
5925 <param name="remove_unassigned_ids" value="false"/>
5926 <param name="rt" value="0.1"/>
5927 <param name="mz" value="0.001"/>
5928 <param name="blacklist_imperfect" value="false"/>
5929 </section>
5930 <section name="algorithm">
5931 <section name="SignalToNoise">
5932 <param name="max_intensity" value="-1"/>
5933 <param name="auto_max_stdev_factor" value="3.0"/>
5934 <param name="auto_max_percentile" value="95"/>
5935 <param name="auto_mode" value="0"/>
5936 <param name="win_len" value="200.0"/>
5937 <param name="bin_count" value="30"/>
5938 <param name="min_required_elements" value="10"/>
5939 <param name="noise_for_empty_window" value="1e+20"/>
5940 <param name="write_log_messages" value="true"/>
5941 </section>
5942 </section>
5943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5944 <output name="ctd_out" ftype="xml">
5945 <assert_contents>
5946 <is_valid_xml/>
5947 </assert_contents>
5948 </output>
5949 </test>
5950 <test expect_num_outputs="2">
5951 <conditional name="adv_opts_cond">
5952 <param name="adv_opts_selector" value="advanced"/>
5953 <param name="force" value="false"/>
5954 <param name="test" value="true"/>
5955 </conditional>
5956 <param name="in" value="FileFilter_7_input.mzML"/>
5957 <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5958 <param name="out_type" value="mzML"/>
5959 <param name="rt" value=":"/>
5960 <param name="mz" value=":"/>
5961 <param name="int" value="7000:"/>
5962 <param name="sort" value="false"/>
5963 <section name="peak_options">
5964 <param name="sn" value="0.0"/>
5965 <param name="rm_pc_charge" value=""/>
5966 <param name="pc_mz_range" value=":"/>
5967 <param name="pc_mz_list" value=""/>
5968 <param name="level" value="1 2 3"/>
5969 <param name="sort_peaks" value="false"/>
5970 <param name="no_chromatograms" value="false"/>
5971 <param name="remove_chromatograms" value="false"/>
5972 <param name="remove_empty" value="false"/>
5973 <param name="mz_precision" value="64"/>
5974 <param name="int_precision" value="32"/>
5975 <param name="indexed_file" value="true"/>
5976 <param name="zlib_compression" value="false"/>
5977 <section name="numpress">
5978 <param name="masstime" value="none"/>
5979 <param name="lossy_mass_accuracy" value="-1.0"/>
5980 <param name="intensity" value="none"/>
5981 <param name="float_da" value="none"/>
5982 </section>
5983 </section>
5984 <section name="spectra">
5985 <param name="remove_zoom" value="false"/>
5986 <param name="remove_mode" value=""/>
5987 <param name="remove_activation" value=""/>
5988 <param name="remove_collision_energy" value=":"/>
5989 <param name="remove_isolation_window_width" value=":"/>
5990 <param name="select_zoom" value="false"/>
5991 <param name="select_mode" value=""/>
5992 <param name="select_activation" value=""/>
5993 <param name="select_collision_energy" value=":"/>
5994 <param name="select_isolation_window_width" value=":"/>
5995 <param name="select_polarity" value=""/>
5996 <section name="blackorwhitelist">
5997 <param name="similarity_threshold" value="-1.0"/>
5998 <param name="rt" value="0.01"/>
5999 <param name="mz" value="0.01"/>
6000 <param name="use_ppm_tolerance" value="false"/>
6001 <param name="blacklist" value="true"/>
6002 </section>
6003 </section>
6004 <section name="feature">
6005 <param name="q" value=":"/>
6006 </section>
6007 <section name="consensus">
6008 <param name="map" value=""/>
6009 <param name="map_and" value="false"/>
6010 <section name="blackorwhitelist">
6011 <param name="blacklist" value="true"/>
6012 <param name="maps" value=""/>
6013 <param name="rt" value="60.0"/>
6014 <param name="mz" value="0.01"/>
6015 <param name="use_ppm_tolerance" value="false"/>
6016 </section>
6017 </section>
6018 <section name="f_and_c">
6019 <param name="charge" value=":"/>
6020 <param name="size" value=":"/>
6021 <param name="remove_meta" value=""/>
6022 </section>
6023 <section name="id">
6024 <param name="remove_clashes" value="false"/>
6025 <param name="keep_best_score_id" value="false"/>
6026 <param name="sequences_whitelist" value=""/>
6027 <param name="sequence_comparison_method" value="substring"/>
6028 <param name="accessions_whitelist" value=""/>
6029 <param name="remove_annotated_features" value="false"/>
6030 <param name="remove_unannotated_features" value="false"/>
6031 <param name="remove_unassigned_ids" value="false"/>
6032 <param name="rt" value="0.1"/>
6033 <param name="mz" value="0.001"/>
6034 <param name="blacklist_imperfect" value="false"/>
6035 </section>
6036 <section name="algorithm">
6037 <section name="SignalToNoise">
6038 <param name="max_intensity" value="-1"/>
6039 <param name="auto_max_stdev_factor" value="3.0"/>
6040 <param name="auto_max_percentile" value="95"/>
6041 <param name="auto_mode" value="0"/>
6042 <param name="win_len" value="200.0"/>
6043 <param name="bin_count" value="30"/>
6044 <param name="min_required_elements" value="10"/>
6045 <param name="noise_for_empty_window" value="1e+20"/>
6046 <param name="write_log_messages" value="true"/>
6047 </section>
6048 </section>
6049 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6050 <output name="ctd_out" ftype="xml">
6051 <assert_contents>
6052 <is_valid_xml/>
6053 </assert_contents>
6054 </output>
6055 </test>
6056 <test expect_num_outputs="2">
6057 <conditional name="adv_opts_cond">
6058 <param name="adv_opts_selector" value="advanced"/>
6059 <param name="force" value="false"/>
6060 <param name="test" value="true"/>
6061 </conditional>
6062 <param name="in" value="FileFilter_8_input.consensusXML"/>
6063 <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
6064 <param name="out_type" value="consensusXML"/>
6065 <param name="rt" value="600:1400"/>
6066 <param name="mz" value="700:2300"/>
6067 <param name="int" value="1100:6000"/>
6068 <param name="sort" value="false"/>
6069 <section name="peak_options">
6070 <param name="sn" value="0.0"/>
6071 <param name="rm_pc_charge" value=""/>
6072 <param name="pc_mz_range" value=":"/>
6073 <param name="pc_mz_list" value=""/>
6074 <param name="level" value="1 2 3"/>
6075 <param name="sort_peaks" value="false"/>
6076 <param name="no_chromatograms" value="false"/>
6077 <param name="remove_chromatograms" value="false"/>
6078 <param name="remove_empty" value="false"/>
6079 <param name="mz_precision" value="64"/>
6080 <param name="int_precision" value="32"/>
6081 <param name="indexed_file" value="true"/>
6082 <param name="zlib_compression" value="false"/>
6083 <section name="numpress">
6084 <param name="masstime" value="none"/>
6085 <param name="lossy_mass_accuracy" value="-1.0"/>
6086 <param name="intensity" value="none"/>
6087 <param name="float_da" value="none"/>
6088 </section>
6089 </section>
6090 <section name="spectra">
6091 <param name="remove_zoom" value="false"/>
6092 <param name="remove_mode" value=""/>
6093 <param name="remove_activation" value=""/>
6094 <param name="remove_collision_energy" value=":"/>
6095 <param name="remove_isolation_window_width" value=":"/>
6096 <param name="select_zoom" value="false"/>
6097 <param name="select_mode" value=""/>
6098 <param name="select_activation" value=""/>
6099 <param name="select_collision_energy" value=":"/>
6100 <param name="select_isolation_window_width" value=":"/>
6101 <param name="select_polarity" value=""/>
6102 <section name="blackorwhitelist">
6103 <param name="similarity_threshold" value="-1.0"/>
6104 <param name="rt" value="0.01"/>
6105 <param name="mz" value="0.01"/>
6106 <param name="use_ppm_tolerance" value="false"/>
6107 <param name="blacklist" value="true"/>
6108 </section>
6109 </section>
6110 <section name="feature">
6111 <param name="q" value=":"/>
6112 </section>
6113 <section name="consensus">
6114 <param name="map" value=""/>
6115 <param name="map_and" value="false"/>
6116 <section name="blackorwhitelist">
6117 <param name="blacklist" value="true"/>
6118 <param name="maps" value=""/>
6119 <param name="rt" value="60.0"/>
6120 <param name="mz" value="0.01"/>
6121 <param name="use_ppm_tolerance" value="false"/>
6122 </section>
6123 </section>
6124 <section name="f_and_c">
6125 <param name="charge" value=":"/>
6126 <param name="size" value=":"/>
6127 <param name="remove_meta" value=""/>
6128 </section>
6129 <section name="id">
6130 <param name="remove_clashes" value="false"/>
6131 <param name="keep_best_score_id" value="false"/>
6132 <param name="sequences_whitelist" value=""/>
6133 <param name="sequence_comparison_method" value="substring"/>
6134 <param name="accessions_whitelist" value=""/>
6135 <param name="remove_annotated_features" value="false"/>
6136 <param name="remove_unannotated_features" value="false"/>
6137 <param name="remove_unassigned_ids" value="false"/>
6138 <param name="rt" value="0.1"/>
6139 <param name="mz" value="0.001"/>
6140 <param name="blacklist_imperfect" value="false"/>
6141 </section>
6142 <section name="algorithm">
6143 <section name="SignalToNoise">
6144 <param name="max_intensity" value="-1"/>
6145 <param name="auto_max_stdev_factor" value="3.0"/>
6146 <param name="auto_max_percentile" value="95"/>
6147 <param name="auto_mode" value="0"/>
6148 <param name="win_len" value="200.0"/>
6149 <param name="bin_count" value="30"/>
6150 <param name="min_required_elements" value="10"/>
6151 <param name="noise_for_empty_window" value="1e+20"/>
6152 <param name="write_log_messages" value="true"/>
6153 </section>
6154 </section>
6155 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6156 <output name="ctd_out" ftype="xml">
6157 <assert_contents>
6158 <is_valid_xml/>
6159 </assert_contents>
6160 </output>
6161 </test>
6162 <test expect_num_outputs="2">
6163 <conditional name="adv_opts_cond">
6164 <param name="adv_opts_selector" value="advanced"/>
6165 <param name="force" value="false"/>
6166 <param name="test" value="true"/>
6167 </conditional>
6168 <param name="in" value="FileFilter_9_input.mzML"/>
6169 <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
6170 <param name="out_type" value="mzML"/>
6171 <param name="rt" value=":"/>
6172 <param name="mz" value=":"/>
6173 <param name="int" value=":"/>
6174 <param name="sort" value="false"/>
6175 <section name="peak_options">
6176 <param name="sn" value="0.0"/>
6177 <param name="rm_pc_charge" value=""/>
6178 <param name="pc_mz_range" value=":"/>
6179 <param name="pc_mz_list" value=""/>
6180 <param name="level" value="1 2 3"/>
6181 <param name="sort_peaks" value="false"/>
6182 <param name="no_chromatograms" value="false"/>
6183 <param name="remove_chromatograms" value="false"/>
6184 <param name="remove_empty" value="false"/>
6185 <param name="mz_precision" value="64"/>
6186 <param name="int_precision" value="32"/>
6187 <param name="indexed_file" value="true"/>
6188 <param name="zlib_compression" value="false"/>
6189 <section name="numpress">
6190 <param name="masstime" value="none"/>
6191 <param name="lossy_mass_accuracy" value="-1.0"/>
6192 <param name="intensity" value="none"/>
6193 <param name="float_da" value="none"/>
6194 </section>
6195 </section>
6196 <section name="spectra">
6197 <param name="remove_zoom" value="false"/>
6198 <param name="remove_mode" value="SelectedIonMonitoring"/>
6199 <param name="remove_activation" value=""/>
6200 <param name="remove_collision_energy" value=":"/>
6201 <param name="remove_isolation_window_width" value=":"/>
6202 <param name="select_zoom" value="false"/>
6203 <param name="select_mode" value=""/>
6204 <param name="select_activation" value=""/>
6205 <param name="select_collision_energy" value=":"/>
6206 <param name="select_isolation_window_width" value=":"/>
6207 <param name="select_polarity" value=""/>
6208 <section name="blackorwhitelist">
6209 <param name="similarity_threshold" value="-1.0"/>
6210 <param name="rt" value="0.01"/>
6211 <param name="mz" value="0.01"/>
6212 <param name="use_ppm_tolerance" value="false"/>
6213 <param name="blacklist" value="true"/>
6214 </section>
6215 </section>
6216 <section name="feature">
6217 <param name="q" value=":"/>
6218 </section>
6219 <section name="consensus">
6220 <param name="map" value=""/>
6221 <param name="map_and" value="false"/>
6222 <section name="blackorwhitelist">
6223 <param name="blacklist" value="true"/>
6224 <param name="maps" value=""/>
6225 <param name="rt" value="60.0"/>
6226 <param name="mz" value="0.01"/>
6227 <param name="use_ppm_tolerance" value="false"/>
6228 </section>
6229 </section>
6230 <section name="f_and_c">
6231 <param name="charge" value=":"/>
6232 <param name="size" value=":"/>
6233 <param name="remove_meta" value=""/>
6234 </section>
6235 <section name="id">
6236 <param name="remove_clashes" value="false"/>
6237 <param name="keep_best_score_id" value="false"/>
6238 <param name="sequences_whitelist" value=""/>
6239 <param name="sequence_comparison_method" value="substring"/>
6240 <param name="accessions_whitelist" value=""/>
6241 <param name="remove_annotated_features" value="false"/>
6242 <param name="remove_unannotated_features" value="false"/>
6243 <param name="remove_unassigned_ids" value="false"/>
6244 <param name="rt" value="0.1"/>
6245 <param name="mz" value="0.001"/>
6246 <param name="blacklist_imperfect" value="false"/>
6247 </section>
6248 <section name="algorithm">
6249 <section name="SignalToNoise">
6250 <param name="max_intensity" value="-1"/>
6251 <param name="auto_max_stdev_factor" value="3.0"/>
6252 <param name="auto_max_percentile" value="95"/>
6253 <param name="auto_mode" value="0"/>
6254 <param name="win_len" value="200.0"/>
6255 <param name="bin_count" value="30"/>
6256 <param name="min_required_elements" value="10"/>
6257 <param name="noise_for_empty_window" value="1e+20"/>
6258 <param name="write_log_messages" value="true"/>
6259 </section>
6260 </section>
6261 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6262 <output name="ctd_out" ftype="xml">
6263 <assert_contents>
6264 <is_valid_xml/>
6265 </assert_contents>
6266 </output>
6267 </test>
6268 <test expect_num_outputs="2">
6269 <conditional name="adv_opts_cond">
6270 <param name="adv_opts_selector" value="advanced"/>
6271 <param name="force" value="false"/>
6272 <param name="test" value="true"/>
6273 </conditional>
6274 <param name="in" value="FileFilter_10_input.mzML"/>
6275 <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
6276 <param name="out_type" value="mzML"/>
6277 <param name="rt" value=":"/>
6278 <param name="mz" value=":"/>
6279 <param name="int" value=":"/>
6280 <param name="sort" value="false"/>
6281 <section name="peak_options">
6282 <param name="sn" value="0.0"/>
6283 <param name="rm_pc_charge" value=""/>
6284 <param name="pc_mz_range" value=":"/>
6285 <param name="pc_mz_list" value=""/>
6286 <param name="level" value="1 2 3"/>
6287 <param name="sort_peaks" value="false"/>
6288 <param name="no_chromatograms" value="false"/>
6289 <param name="remove_chromatograms" value="false"/>
6290 <param name="remove_empty" value="false"/>
6291 <param name="mz_precision" value="64"/>
6292 <param name="int_precision" value="32"/>
6293 <param name="indexed_file" value="true"/>
6294 <param name="zlib_compression" value="false"/>
6295 <section name="numpress">
6296 <param name="masstime" value="none"/>
6297 <param name="lossy_mass_accuracy" value="-1.0"/>
6298 <param name="intensity" value="none"/>
6299 <param name="float_da" value="none"/>
6300 </section>
6301 </section>
6302 <section name="spectra">
6303 <param name="remove_zoom" value="false"/>
6304 <param name="remove_mode" value=""/>
6305 <param name="remove_activation" value="Collision-induced dissociation"/>
6306 <param name="remove_collision_energy" value=":"/>
6307 <param name="remove_isolation_window_width" value=":"/>
6308 <param name="select_zoom" value="false"/>
6309 <param name="select_mode" value=""/>
6310 <param name="select_activation" value=""/>
6311 <param name="select_collision_energy" value=":"/>
6312 <param name="select_isolation_window_width" value=":"/>
6313 <param name="select_polarity" value=""/>
6314 <section name="blackorwhitelist">
6315 <param name="similarity_threshold" value="-1.0"/>
6316 <param name="rt" value="0.01"/>
6317 <param name="mz" value="0.01"/>
6318 <param name="use_ppm_tolerance" value="false"/>
6319 <param name="blacklist" value="true"/>
6320 </section>
6321 </section>
6322 <section name="feature">
6323 <param name="q" value=":"/>
6324 </section>
6325 <section name="consensus">
6326 <param name="map" value=""/>
6327 <param name="map_and" value="false"/>
6328 <section name="blackorwhitelist">
6329 <param name="blacklist" value="true"/>
6330 <param name="maps" value=""/>
6331 <param name="rt" value="60.0"/>
6332 <param name="mz" value="0.01"/>
6333 <param name="use_ppm_tolerance" value="false"/>
6334 </section>
6335 </section>
6336 <section name="f_and_c">
6337 <param name="charge" value=":"/>
6338 <param name="size" value=":"/>
6339 <param name="remove_meta" value=""/>
6340 </section>
6341 <section name="id">
6342 <param name="remove_clashes" value="false"/>
6343 <param name="keep_best_score_id" value="false"/>
6344 <param name="sequences_whitelist" value=""/>
6345 <param name="sequence_comparison_method" value="substring"/>
6346 <param name="accessions_whitelist" value=""/>
6347 <param name="remove_annotated_features" value="false"/>
6348 <param name="remove_unannotated_features" value="false"/>
6349 <param name="remove_unassigned_ids" value="false"/>
6350 <param name="rt" value="0.1"/>
6351 <param name="mz" value="0.001"/>
6352 <param name="blacklist_imperfect" value="false"/>
6353 </section>
6354 <section name="algorithm">
6355 <section name="SignalToNoise">
6356 <param name="max_intensity" value="-1"/>
6357 <param name="auto_max_stdev_factor" value="3.0"/>
6358 <param name="auto_max_percentile" value="95"/>
6359 <param name="auto_mode" value="0"/>
6360 <param name="win_len" value="200.0"/>
6361 <param name="bin_count" value="30"/>
6362 <param name="min_required_elements" value="10"/>
6363 <param name="noise_for_empty_window" value="1e+20"/>
6364 <param name="write_log_messages" value="true"/>
6365 </section>
6366 </section>
6367 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6368 <output name="ctd_out" ftype="xml">
6369 <assert_contents>
6370 <is_valid_xml/>
6371 </assert_contents>
6372 </output>
6373 </test>
6374 <test expect_num_outputs="2">
6375 <conditional name="adv_opts_cond">
6376 <param name="adv_opts_selector" value="advanced"/>
6377 <param name="force" value="false"/>
6378 <param name="test" value="true"/>
6379 </conditional>
6380 <param name="in" value="FileFilter_11_input.mzML"/>
6381 <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
6382 <param name="out_type" value="mzML"/>
6383 <param name="rt" value=":"/>
6384 <param name="mz" value=":"/>
6385 <param name="int" value=":"/>
6386 <param name="sort" value="false"/>
6387 <section name="peak_options">
6388 <param name="sn" value="0.0"/>
6389 <param name="rm_pc_charge" value=""/>
6390 <param name="pc_mz_range" value=":"/>
6391 <param name="pc_mz_list" value=""/>
6392 <param name="level" value="1 2 3"/>
6393 <param name="sort_peaks" value="false"/>
6394 <param name="no_chromatograms" value="false"/>
6395 <param name="remove_chromatograms" value="false"/>
6396 <param name="remove_empty" value="false"/>
6397 <param name="mz_precision" value="64"/>
6398 <param name="int_precision" value="32"/>
6399 <param name="indexed_file" value="true"/>
6400 <param name="zlib_compression" value="false"/>
6401 <section name="numpress">
6402 <param name="masstime" value="none"/>
6403 <param name="lossy_mass_accuracy" value="-1.0"/>
6404 <param name="intensity" value="none"/>
6405 <param name="float_da" value="none"/>
6406 </section>
6407 </section>
6408 <section name="spectra">
6409 <param name="remove_zoom" value="false"/>
6410 <param name="remove_mode" value=""/>
6411 <param name="remove_activation" value="Plasma desorption"/>
6412 <param name="remove_collision_energy" value=":"/>
6413 <param name="remove_isolation_window_width" value=":"/>
6414 <param name="select_zoom" value="false"/>
6415 <param name="select_mode" value=""/>
6416 <param name="select_activation" value=""/>
6417 <param name="select_collision_energy" value=":"/>
6418 <param name="select_isolation_window_width" value=":"/>
6419 <param name="select_polarity" value=""/>
6420 <section name="blackorwhitelist">
6421 <param name="similarity_threshold" value="-1.0"/>
6422 <param name="rt" value="0.01"/>
6423 <param name="mz" value="0.01"/>
6424 <param name="use_ppm_tolerance" value="false"/>
6425 <param name="blacklist" value="true"/>
6426 </section>
6427 </section>
6428 <section name="feature">
6429 <param name="q" value=":"/>
6430 </section>
6431 <section name="consensus">
6432 <param name="map" value=""/>
6433 <param name="map_and" value="false"/>
6434 <section name="blackorwhitelist">
6435 <param name="blacklist" value="true"/>
6436 <param name="maps" value=""/>
6437 <param name="rt" value="60.0"/>
6438 <param name="mz" value="0.01"/>
6439 <param name="use_ppm_tolerance" value="false"/>
6440 </section>
6441 </section>
6442 <section name="f_and_c">
6443 <param name="charge" value=":"/>
6444 <param name="size" value=":"/>
6445 <param name="remove_meta" value=""/>
6446 </section>
6447 <section name="id">
6448 <param name="remove_clashes" value="false"/>
6449 <param name="keep_best_score_id" value="false"/>
6450 <param name="sequences_whitelist" value=""/>
6451 <param name="sequence_comparison_method" value="substring"/>
6452 <param name="accessions_whitelist" value=""/>
6453 <param name="remove_annotated_features" value="false"/>
6454 <param name="remove_unannotated_features" value="false"/>
6455 <param name="remove_unassigned_ids" value="false"/>
6456 <param name="rt" value="0.1"/>
6457 <param name="mz" value="0.001"/>
6458 <param name="blacklist_imperfect" value="false"/>
6459 </section>
6460 <section name="algorithm">
6461 <section name="SignalToNoise">
6462 <param name="max_intensity" value="-1"/>
6463 <param name="auto_max_stdev_factor" value="3.0"/>
6464 <param name="auto_max_percentile" value="95"/>
6465 <param name="auto_mode" value="0"/>
6466 <param name="win_len" value="200.0"/>
6467 <param name="bin_count" value="30"/>
6468 <param name="min_required_elements" value="10"/>
6469 <param name="noise_for_empty_window" value="1e+20"/>
6470 <param name="write_log_messages" value="true"/>
6471 </section>
6472 </section>
6473 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6474 <output name="ctd_out" ftype="xml">
6475 <assert_contents>
6476 <is_valid_xml/>
6477 </assert_contents>
6478 </output>
6479 </test>
6480 <test expect_num_outputs="2">
6481 <conditional name="adv_opts_cond">
6482 <param name="adv_opts_selector" value="advanced"/>
6483 <param name="force" value="false"/>
6484 <param name="test" value="true"/>
6485 </conditional>
6486 <param name="in" value="FileFilter_12_input.mzML"/>
6487 <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
6488 <param name="out_type" value="mzML"/>
6489 <param name="rt" value=":"/>
6490 <param name="mz" value=":"/>
6491 <param name="int" value=":"/>
6492 <param name="sort" value="false"/>
6493 <section name="peak_options">
6494 <param name="sn" value="0.0"/>
6495 <param name="rm_pc_charge" value=""/>
6496 <param name="pc_mz_range" value=":"/>
6497 <param name="pc_mz_list" value=""/>
6498 <param name="level" value="1 2 3"/>
6499 <param name="sort_peaks" value="false"/>
6500 <param name="no_chromatograms" value="false"/>
6501 <param name="remove_chromatograms" value="true"/>
6502 <param name="remove_empty" value="false"/>
6503 <param name="mz_precision" value="64"/>
6504 <param name="int_precision" value="32"/>
6505 <param name="indexed_file" value="true"/>
6506 <param name="zlib_compression" value="false"/>
6507 <section name="numpress">
6508 <param name="masstime" value="none"/>
6509 <param name="lossy_mass_accuracy" value="-1.0"/>
6510 <param name="intensity" value="none"/>
6511 <param name="float_da" value="none"/>
6512 </section>
6513 </section>
6514 <section name="spectra">
6515 <param name="remove_zoom" value="false"/>
6516 <param name="remove_mode" value=""/>
6517 <param name="remove_activation" value=""/>
6518 <param name="remove_collision_energy" value=":"/>
6519 <param name="remove_isolation_window_width" value=":"/>
6520 <param name="select_zoom" value="false"/>
6521 <param name="select_mode" value=""/>
6522 <param name="select_activation" value=""/>
6523 <param name="select_collision_energy" value=":"/>
6524 <param name="select_isolation_window_width" value=":"/>
6525 <param name="select_polarity" value=""/>
6526 <section name="blackorwhitelist">
6527 <param name="similarity_threshold" value="-1.0"/>
6528 <param name="rt" value="0.01"/>
6529 <param name="mz" value="0.01"/>
6530 <param name="use_ppm_tolerance" value="false"/>
6531 <param name="blacklist" value="true"/>
6532 </section>
6533 </section>
6534 <section name="feature">
6535 <param name="q" value=":"/>
6536 </section>
6537 <section name="consensus">
6538 <param name="map" value=""/>
6539 <param name="map_and" value="false"/>
6540 <section name="blackorwhitelist">
6541 <param name="blacklist" value="true"/>
6542 <param name="maps" value=""/>
6543 <param name="rt" value="60.0"/>
6544 <param name="mz" value="0.01"/>
6545 <param name="use_ppm_tolerance" value="false"/>
6546 </section>
6547 </section>
6548 <section name="f_and_c">
6549 <param name="charge" value=":"/>
6550 <param name="size" value=":"/>
6551 <param name="remove_meta" value=""/>
6552 </section>
6553 <section name="id">
6554 <param name="remove_clashes" value="false"/>
6555 <param name="keep_best_score_id" value="false"/>
6556 <param name="sequences_whitelist" value=""/>
6557 <param name="sequence_comparison_method" value="substring"/>
6558 <param name="accessions_whitelist" value=""/>
6559 <param name="remove_annotated_features" value="false"/>
6560 <param name="remove_unannotated_features" value="false"/>
6561 <param name="remove_unassigned_ids" value="false"/>
6562 <param name="rt" value="0.1"/>
6563 <param name="mz" value="0.001"/>
6564 <param name="blacklist_imperfect" value="false"/>
6565 </section>
6566 <section name="algorithm">
6567 <section name="SignalToNoise">
6568 <param name="max_intensity" value="-1"/>
6569 <param name="auto_max_stdev_factor" value="3.0"/>
6570 <param name="auto_max_percentile" value="95"/>
6571 <param name="auto_mode" value="0"/>
6572 <param name="win_len" value="200.0"/>
6573 <param name="bin_count" value="30"/>
6574 <param name="min_required_elements" value="10"/>
6575 <param name="noise_for_empty_window" value="1e+20"/>
6576 <param name="write_log_messages" value="true"/>
6577 </section>
6578 </section>
6579 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6580 <output name="ctd_out" ftype="xml">
6581 <assert_contents>
6582 <is_valid_xml/>
6583 </assert_contents>
6584 </output>
6585 </test>
6586 <test expect_num_outputs="2">
6587 <conditional name="adv_opts_cond">
6588 <param name="adv_opts_selector" value="advanced"/>
6589 <param name="force" value="false"/>
6590 <param name="test" value="true"/>
6591 </conditional>
6592 <param name="in" value="FileFilter_13_input.consensusXML"/>
6593 <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
6594 <param name="out_type" value="featureXML"/>
6595 <param name="rt" value=":"/>
6596 <param name="mz" value=":"/>
6597 <param name="int" value=":"/>
6598 <param name="sort" value="false"/>
6599 <section name="peak_options">
6600 <param name="sn" value="0.0"/>
6601 <param name="rm_pc_charge" value=""/>
6602 <param name="pc_mz_range" value=":"/>
6603 <param name="pc_mz_list" value=""/>
6604 <param name="level" value="1 2 3"/>
6605 <param name="sort_peaks" value="false"/>
6606 <param name="no_chromatograms" value="false"/>
6607 <param name="remove_chromatograms" value="false"/>
6608 <param name="remove_empty" value="false"/>
6609 <param name="mz_precision" value="64"/>
6610 <param name="int_precision" value="32"/>
6611 <param name="indexed_file" value="true"/>
6612 <param name="zlib_compression" value="false"/>
6613 <section name="numpress">
6614 <param name="masstime" value="none"/>
6615 <param name="lossy_mass_accuracy" value="-1.0"/>
6616 <param name="intensity" value="none"/>
6617 <param name="float_da" value="none"/>
6618 </section>
6619 </section>
6620 <section name="spectra">
6621 <param name="remove_zoom" value="false"/>
6622 <param name="remove_mode" value=""/>
6623 <param name="remove_activation" value=""/>
6624 <param name="remove_collision_energy" value=":"/>
6625 <param name="remove_isolation_window_width" value=":"/>
6626 <param name="select_zoom" value="false"/>
6627 <param name="select_mode" value=""/>
6628 <param name="select_activation" value=""/>
6629 <param name="select_collision_energy" value=":"/>
6630 <param name="select_isolation_window_width" value=":"/>
6631 <param name="select_polarity" value=""/>
6632 <section name="blackorwhitelist">
6633 <param name="similarity_threshold" value="-1.0"/>
6634 <param name="rt" value="0.01"/>
6635 <param name="mz" value="0.01"/>
6636 <param name="use_ppm_tolerance" value="false"/>
6637 <param name="blacklist" value="true"/>
6638 </section>
6639 </section>
6640 <section name="feature">
6641 <param name="q" value=":"/>
6642 </section>
6643 <section name="consensus">
6644 <param name="map" value="2"/>
6645 <param name="map_and" value="false"/>
6646 <section name="blackorwhitelist">
6647 <param name="blacklist" value="true"/>
6648 <param name="maps" value=""/>
6649 <param name="rt" value="60.0"/>
6650 <param name="mz" value="0.01"/>
6651 <param name="use_ppm_tolerance" value="false"/>
6652 </section>
6653 </section>
6654 <section name="f_and_c">
6655 <param name="charge" value=":"/>
6656 <param name="size" value=":"/>
6657 <param name="remove_meta" value=""/>
6658 </section>
6659 <section name="id">
6660 <param name="remove_clashes" value="false"/>
6661 <param name="keep_best_score_id" value="false"/>
6662 <param name="sequences_whitelist" value=""/>
6663 <param name="sequence_comparison_method" value="substring"/>
6664 <param name="accessions_whitelist" value=""/>
6665 <param name="remove_annotated_features" value="false"/>
6666 <param name="remove_unannotated_features" value="false"/>
6667 <param name="remove_unassigned_ids" value="false"/>
6668 <param name="rt" value="0.1"/>
6669 <param name="mz" value="0.001"/>
6670 <param name="blacklist_imperfect" value="false"/>
6671 </section>
6672 <section name="algorithm">
6673 <section name="SignalToNoise">
6674 <param name="max_intensity" value="-1"/>
6675 <param name="auto_max_stdev_factor" value="3.0"/>
6676 <param name="auto_max_percentile" value="95"/>
6677 <param name="auto_mode" value="0"/>
6678 <param name="win_len" value="200.0"/>
6679 <param name="bin_count" value="30"/>
6680 <param name="min_required_elements" value="10"/>
6681 <param name="noise_for_empty_window" value="1e+20"/>
6682 <param name="write_log_messages" value="true"/>
6683 </section>
6684 </section>
6685 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6686 <output name="ctd_out" ftype="xml">
6687 <assert_contents>
6688 <is_valid_xml/>
6689 </assert_contents>
6690 </output>
6691 </test>
6692 <test expect_num_outputs="2">
6693 <conditional name="adv_opts_cond">
6694 <param name="adv_opts_selector" value="advanced"/>
6695 <param name="force" value="false"/>
6696 <param name="test" value="true"/>
6697 </conditional>
6698 <param name="in" value="FileFilter_14_input.consensusXML"/>
6699 <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
6700 <param name="out_type" value="consensusXML"/>
6701 <param name="rt" value=":"/>
6702 <param name="mz" value=":"/>
6703 <param name="int" value=":"/>
6704 <param name="sort" value="false"/>
6705 <section name="peak_options">
6706 <param name="sn" value="0.0"/>
6707 <param name="rm_pc_charge" value=""/>
6708 <param name="pc_mz_range" value=":"/>
6709 <param name="pc_mz_list" value=""/>
6710 <param name="level" value="1 2 3"/>
6711 <param name="sort_peaks" value="false"/>
6712 <param name="no_chromatograms" value="false"/>
6713 <param name="remove_chromatograms" value="false"/>
6714 <param name="remove_empty" value="false"/>
6715 <param name="mz_precision" value="64"/>
6716 <param name="int_precision" value="32"/>
6717 <param name="indexed_file" value="true"/>
6718 <param name="zlib_compression" value="false"/>
6719 <section name="numpress">
6720 <param name="masstime" value="none"/>
6721 <param name="lossy_mass_accuracy" value="-1.0"/>
6722 <param name="intensity" value="none"/>
6723 <param name="float_da" value="none"/>
6724 </section>
6725 </section>
6726 <section name="spectra">
6727 <param name="remove_zoom" value="false"/>
6728 <param name="remove_mode" value=""/>
6729 <param name="remove_activation" value=""/>
6730 <param name="remove_collision_energy" value=":"/>
6731 <param name="remove_isolation_window_width" value=":"/>
6732 <param name="select_zoom" value="false"/>
6733 <param name="select_mode" value=""/>
6734 <param name="select_activation" value=""/>
6735 <param name="select_collision_energy" value=":"/>
6736 <param name="select_isolation_window_width" value=":"/>
6737 <param name="select_polarity" value=""/>
6738 <section name="blackorwhitelist">
6739 <param name="similarity_threshold" value="-1.0"/>
6740 <param name="rt" value="0.01"/>
6741 <param name="mz" value="0.01"/>
6742 <param name="use_ppm_tolerance" value="false"/>
6743 <param name="blacklist" value="true"/>
6744 </section>
6745 </section>
6746 <section name="feature">
6747 <param name="q" value=":"/>
6748 </section>
6749 <section name="consensus">
6750 <param name="map" value="0 2"/>
6751 <param name="map_and" value="false"/>
6752 <section name="blackorwhitelist">
6753 <param name="blacklist" value="true"/>
6754 <param name="maps" value=""/>
6755 <param name="rt" value="60.0"/>
6756 <param name="mz" value="0.01"/>
6757 <param name="use_ppm_tolerance" value="false"/>
6758 </section>
6759 </section>
6760 <section name="f_and_c">
6761 <param name="charge" value=":"/>
6762 <param name="size" value=":"/>
6763 <param name="remove_meta" value=""/>
6764 </section>
6765 <section name="id">
6766 <param name="remove_clashes" value="false"/>
6767 <param name="keep_best_score_id" value="false"/>
6768 <param name="sequences_whitelist" value=""/>
6769 <param name="sequence_comparison_method" value="substring"/>
6770 <param name="accessions_whitelist" value=""/>
6771 <param name="remove_annotated_features" value="false"/>
6772 <param name="remove_unannotated_features" value="false"/>
6773 <param name="remove_unassigned_ids" value="false"/>
6774 <param name="rt" value="0.1"/>
6775 <param name="mz" value="0.001"/>
6776 <param name="blacklist_imperfect" value="false"/>
6777 </section>
6778 <section name="algorithm">
6779 <section name="SignalToNoise">
6780 <param name="max_intensity" value="-1"/>
6781 <param name="auto_max_stdev_factor" value="3.0"/>
6782 <param name="auto_max_percentile" value="95"/>
6783 <param name="auto_mode" value="0"/>
6784 <param name="win_len" value="200.0"/>
6785 <param name="bin_count" value="30"/>
6786 <param name="min_required_elements" value="10"/>
6787 <param name="noise_for_empty_window" value="1e+20"/>
6788 <param name="write_log_messages" value="true"/>
6789 </section>
6790 </section>
6791 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6792 <output name="ctd_out" ftype="xml">
6793 <assert_contents>
6794 <is_valid_xml/>
6795 </assert_contents>
6796 </output>
6797 </test>
6798 <test expect_num_outputs="2">
6799 <conditional name="adv_opts_cond">
6800 <param name="adv_opts_selector" value="advanced"/>
6801 <param name="force" value="false"/>
6802 <param name="test" value="true"/>
6803 </conditional>
6804 <param name="in" value="FileFilter_15_input.featureXML"/>
6805 <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
6806 <param name="out_type" value="featurexml"/>
6807 <param name="rt" value=":"/>
6808 <param name="mz" value=":"/>
6809 <param name="int" value=":"/>
6810 <param name="sort" value="false"/>
6811 <section name="peak_options">
6812 <param name="sn" value="0.0"/>
6813 <param name="rm_pc_charge" value=""/>
6814 <param name="pc_mz_range" value=":"/>
6815 <param name="pc_mz_list" value=""/>
6816 <param name="level" value="1 2 3"/>
6817 <param name="sort_peaks" value="false"/>
6818 <param name="no_chromatograms" value="false"/>
6819 <param name="remove_chromatograms" value="false"/>
6820 <param name="remove_empty" value="false"/>
6821 <param name="mz_precision" value="64"/>
6822 <param name="int_precision" value="32"/>
6823 <param name="indexed_file" value="true"/>
6824 <param name="zlib_compression" value="false"/>
6825 <section name="numpress">
6826 <param name="masstime" value="none"/>
6827 <param name="lossy_mass_accuracy" value="-1.0"/>
6828 <param name="intensity" value="none"/>
6829 <param name="float_da" value="none"/>
6830 </section>
6831 </section>
6832 <section name="spectra">
6833 <param name="remove_zoom" value="false"/>
6834 <param name="remove_mode" value=""/>
6835 <param name="remove_activation" value=""/>
6836 <param name="remove_collision_energy" value=":"/>
6837 <param name="remove_isolation_window_width" value=":"/>
6838 <param name="select_zoom" value="false"/>
6839 <param name="select_mode" value=""/>
6840 <param name="select_activation" value=""/>
6841 <param name="select_collision_energy" value=":"/>
6842 <param name="select_isolation_window_width" value=":"/>
6843 <param name="select_polarity" value=""/>
6844 <section name="blackorwhitelist">
6845 <param name="similarity_threshold" value="-1.0"/>
6846 <param name="rt" value="0.01"/>
6847 <param name="mz" value="0.01"/>
6848 <param name="use_ppm_tolerance" value="false"/>
6849 <param name="blacklist" value="true"/>
6850 </section>
6851 </section>
6852 <section name="feature">
6853 <param name="q" value=":"/>
6854 </section>
6855 <section name="consensus">
6856 <param name="map" value=""/>
6857 <param name="map_and" value="false"/>
6858 <section name="blackorwhitelist">
6859 <param name="blacklist" value="true"/>
6860 <param name="maps" value=""/>
6861 <param name="rt" value="60.0"/>
6862 <param name="mz" value="0.01"/>
6863 <param name="use_ppm_tolerance" value="false"/>
6864 </section>
6865 </section>
6866 <section name="f_and_c">
6867 <param name="charge" value=":"/>
6868 <param name="size" value=":"/>
6869 <param name="remove_meta" value=""/>
6870 </section>
6871 <section name="id">
6872 <param name="remove_clashes" value="false"/>
6873 <param name="keep_best_score_id" value="false"/>
6874 <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
6875 <param name="sequence_comparison_method" value="substring"/>
6876 <param name="accessions_whitelist" value=""/>
6877 <param name="remove_annotated_features" value="false"/>
6878 <param name="remove_unannotated_features" value="false"/>
6879 <param name="remove_unassigned_ids" value="true"/>
6880 <param name="rt" value="0.1"/>
6881 <param name="mz" value="0.001"/>
6882 <param name="blacklist_imperfect" value="false"/>
6883 </section>
6884 <section name="algorithm">
6885 <section name="SignalToNoise">
6886 <param name="max_intensity" value="-1"/>
6887 <param name="auto_max_stdev_factor" value="3.0"/>
6888 <param name="auto_max_percentile" value="95"/>
6889 <param name="auto_mode" value="0"/>
6890 <param name="win_len" value="200.0"/>
6891 <param name="bin_count" value="30"/>
6892 <param name="min_required_elements" value="10"/>
6893 <param name="noise_for_empty_window" value="1e+20"/>
6894 <param name="write_log_messages" value="true"/>
6895 </section>
6896 </section>
6897 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6898 <output name="ctd_out" ftype="xml">
6899 <assert_contents>
6900 <is_valid_xml/>
6901 </assert_contents>
6902 </output>
6903 </test>
6904 <test expect_num_outputs="2">
6905 <conditional name="adv_opts_cond">
6906 <param name="adv_opts_selector" value="advanced"/>
6907 <param name="force" value="false"/>
6908 <param name="test" value="true"/>
6909 </conditional>
6910 <param name="in" value="FileFilter_15_input.featureXML"/>
6911 <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
6912 <param name="out_type" value="featurexml"/>
6913 <param name="rt" value="3000:4000"/>
6914 <param name="mz" value="400:600"/>
6915 <param name="int" value=":"/>
6916 <param name="sort" value="false"/>
6917 <section name="peak_options">
6918 <param name="sn" value="0.0"/>
6919 <param name="rm_pc_charge" value=""/>
6920 <param name="pc_mz_range" value=":"/>
6921 <param name="pc_mz_list" value=""/>
6922 <param name="level" value="1 2 3"/>
6923 <param name="sort_peaks" value="false"/>
6924 <param name="no_chromatograms" value="false"/>
6925 <param name="remove_chromatograms" value="false"/>
6926 <param name="remove_empty" value="false"/>
6927 <param name="mz_precision" value="64"/>
6928 <param name="int_precision" value="32"/>
6929 <param name="indexed_file" value="true"/>
6930 <param name="zlib_compression" value="false"/>
6931 <section name="numpress">
6932 <param name="masstime" value="none"/>
6933 <param name="lossy_mass_accuracy" value="-1.0"/>
6934 <param name="intensity" value="none"/>
6935 <param name="float_da" value="none"/>
6936 </section>
6937 </section>
6938 <section name="spectra">
6939 <param name="remove_zoom" value="false"/>
6940 <param name="remove_mode" value=""/>
6941 <param name="remove_activation" value=""/>
6942 <param name="remove_collision_energy" value=":"/>
6943 <param name="remove_isolation_window_width" value=":"/>
6944 <param name="select_zoom" value="false"/>
6945 <param name="select_mode" value=""/>
6946 <param name="select_activation" value=""/>
6947 <param name="select_collision_energy" value=":"/>
6948 <param name="select_isolation_window_width" value=":"/>
6949 <param name="select_polarity" value=""/>
6950 <section name="blackorwhitelist">
6951 <param name="similarity_threshold" value="-1.0"/>
6952 <param name="rt" value="0.01"/>
6953 <param name="mz" value="0.01"/>
6954 <param name="use_ppm_tolerance" value="false"/>
6955 <param name="blacklist" value="true"/>
6956 </section>
6957 </section>
6958 <section name="feature">
6959 <param name="q" value=":"/>
6960 </section>
6961 <section name="consensus">
6962 <param name="map" value=""/>
6963 <param name="map_and" value="false"/>
6964 <section name="blackorwhitelist">
6965 <param name="blacklist" value="true"/>
6966 <param name="maps" value=""/>
6967 <param name="rt" value="60.0"/>
6968 <param name="mz" value="0.01"/>
6969 <param name="use_ppm_tolerance" value="false"/>
6970 </section>
6971 </section>
6972 <section name="f_and_c">
6973 <param name="charge" value=":"/>
6974 <param name="size" value=":"/>
6975 <param name="remove_meta" value=""/>
6976 </section>
6977 <section name="id">
6978 <param name="remove_clashes" value="false"/>
6979 <param name="keep_best_score_id" value="false"/>
6980 <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
6981 <param name="sequence_comparison_method" value="substring"/>
6982 <param name="accessions_whitelist" value=""/>
6983 <param name="remove_annotated_features" value="false"/>
6984 <param name="remove_unannotated_features" value="false"/>
6985 <param name="remove_unassigned_ids" value="true"/>
6986 <param name="rt" value="0.1"/>
6987 <param name="mz" value="0.001"/>
6988 <param name="blacklist_imperfect" value="false"/>
6989 </section>
6990 <section name="algorithm">
6991 <section name="SignalToNoise">
6992 <param name="max_intensity" value="-1"/>
6993 <param name="auto_max_stdev_factor" value="3.0"/>
6994 <param name="auto_max_percentile" value="95"/>
6995 <param name="auto_mode" value="0"/>
6996 <param name="win_len" value="200.0"/>
6997 <param name="bin_count" value="30"/>
6998 <param name="min_required_elements" value="10"/>
6999 <param name="noise_for_empty_window" value="1e+20"/>
7000 <param name="write_log_messages" value="true"/>
7001 </section>
7002 </section>
7003 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7004 <output name="ctd_out" ftype="xml">
7005 <assert_contents>
7006 <is_valid_xml/>
7007 </assert_contents>
7008 </output>
7009 </test>
7010 <test expect_num_outputs="2">
7011 <conditional name="adv_opts_cond">
7012 <param name="adv_opts_selector" value="advanced"/>
7013 <param name="force" value="false"/>
7014 <param name="test" value="true"/>
7015 </conditional>
7016 <param name="in" value="FileFilter_15_input.featureXML"/>
7017 <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
7018 <param name="out_type" value="featurexml"/>
7019 <param name="rt" value="3000:4000"/>
7020 <param name="mz" value="400:600"/>
7021 <param name="int" value=":"/>
7022 <param name="sort" value="false"/>
7023 <section name="peak_options">
7024 <param name="sn" value="0.0"/>
7025 <param name="rm_pc_charge" value=""/>
7026 <param name="pc_mz_range" value=":"/>
7027 <param name="pc_mz_list" value=""/>
7028 <param name="level" value="1 2 3"/>
7029 <param name="sort_peaks" value="false"/>
7030 <param name="no_chromatograms" value="false"/>
7031 <param name="remove_chromatograms" value="false"/>
7032 <param name="remove_empty" value="false"/>
7033 <param name="mz_precision" value="64"/>
7034 <param name="int_precision" value="32"/>
7035 <param name="indexed_file" value="true"/>
7036 <param name="zlib_compression" value="false"/>
7037 <section name="numpress">
7038 <param name="masstime" value="none"/>
7039 <param name="lossy_mass_accuracy" value="-1.0"/>
7040 <param name="intensity" value="none"/>
7041 <param name="float_da" value="none"/>
7042 </section>
7043 </section>
7044 <section name="spectra">
7045 <param name="remove_zoom" value="false"/>
7046 <param name="remove_mode" value=""/>
7047 <param name="remove_activation" value=""/>
7048 <param name="remove_collision_energy" value=":"/>
7049 <param name="remove_isolation_window_width" value=":"/>
7050 <param name="select_zoom" value="false"/>
7051 <param name="select_mode" value=""/>
7052 <param name="select_activation" value=""/>
7053 <param name="select_collision_energy" value=":"/>
7054 <param name="select_isolation_window_width" value=":"/>
7055 <param name="select_polarity" value=""/>
7056 <section name="blackorwhitelist">
7057 <param name="similarity_threshold" value="-1.0"/>
7058 <param name="rt" value="0.01"/>
7059 <param name="mz" value="0.01"/>
7060 <param name="use_ppm_tolerance" value="false"/>
7061 <param name="blacklist" value="true"/>
7062 </section>
7063 </section>
7064 <section name="feature">
7065 <param name="q" value=":"/>
7066 </section>
7067 <section name="consensus">
7068 <param name="map" value=""/>
7069 <param name="map_and" value="false"/>
7070 <section name="blackorwhitelist">
7071 <param name="blacklist" value="true"/>
7072 <param name="maps" value=""/>
7073 <param name="rt" value="60.0"/>
7074 <param name="mz" value="0.01"/>
7075 <param name="use_ppm_tolerance" value="false"/>
7076 </section>
7077 </section>
7078 <section name="f_and_c">
7079 <param name="charge" value=":"/>
7080 <param name="size" value=":"/>
7081 <param name="remove_meta" value=""/>
7082 </section>
7083 <section name="id">
7084 <param name="remove_clashes" value="false"/>
7085 <param name="keep_best_score_id" value="false"/>
7086 <param name="sequences_whitelist" value=""/>
7087 <param name="sequence_comparison_method" value="substring"/>
7088 <param name="accessions_whitelist" value=""/>
7089 <param name="remove_annotated_features" value="true"/>
7090 <param name="remove_unannotated_features" value="false"/>
7091 <param name="remove_unassigned_ids" value="false"/>
7092 <param name="rt" value="0.1"/>
7093 <param name="mz" value="0.001"/>
7094 <param name="blacklist_imperfect" value="false"/>
7095 </section>
7096 <section name="algorithm">
7097 <section name="SignalToNoise">
7098 <param name="max_intensity" value="-1"/>
7099 <param name="auto_max_stdev_factor" value="3.0"/>
7100 <param name="auto_max_percentile" value="95"/>
7101 <param name="auto_mode" value="0"/>
7102 <param name="win_len" value="200.0"/>
7103 <param name="bin_count" value="30"/>
7104 <param name="min_required_elements" value="10"/>
7105 <param name="noise_for_empty_window" value="1e+20"/>
7106 <param name="write_log_messages" value="true"/>
7107 </section>
7108 </section>
7109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7110 <output name="ctd_out" ftype="xml">
7111 <assert_contents>
7112 <is_valid_xml/>
7113 </assert_contents>
7114 </output>
7115 </test>
7116 <test expect_num_outputs="2">
7117 <conditional name="adv_opts_cond">
7118 <param name="adv_opts_selector" value="advanced"/>
7119 <param name="force" value="false"/>
7120 <param name="test" value="true"/>
7121 </conditional>
7122 <param name="in" value="FileFilter_18_input.consensusXML"/>
7123 <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7124 <param name="out_type" value="consensusxml"/>
7125 <param name="rt" value=":"/>
7126 <param name="mz" value=":"/>
7127 <param name="int" value=":"/>
7128 <param name="sort" value="false"/>
7129 <section name="peak_options">
7130 <param name="sn" value="0.0"/>
7131 <param name="rm_pc_charge" value=""/>
7132 <param name="pc_mz_range" value=":"/>
7133 <param name="pc_mz_list" value=""/>
7134 <param name="level" value="1 2 3"/>
7135 <param name="sort_peaks" value="false"/>
7136 <param name="no_chromatograms" value="false"/>
7137 <param name="remove_chromatograms" value="false"/>
7138 <param name="remove_empty" value="false"/>
7139 <param name="mz_precision" value="64"/>
7140 <param name="int_precision" value="32"/>
7141 <param name="indexed_file" value="true"/>
7142 <param name="zlib_compression" value="false"/>
7143 <section name="numpress">
7144 <param name="masstime" value="none"/>
7145 <param name="lossy_mass_accuracy" value="-1.0"/>
7146 <param name="intensity" value="none"/>
7147 <param name="float_da" value="none"/>
7148 </section>
7149 </section>
7150 <section name="spectra">
7151 <param name="remove_zoom" value="false"/>
7152 <param name="remove_mode" value=""/>
7153 <param name="remove_activation" value=""/>
7154 <param name="remove_collision_energy" value=":"/>
7155 <param name="remove_isolation_window_width" value=":"/>
7156 <param name="select_zoom" value="false"/>
7157 <param name="select_mode" value=""/>
7158 <param name="select_activation" value=""/>
7159 <param name="select_collision_energy" value=":"/>
7160 <param name="select_isolation_window_width" value=":"/>
7161 <param name="select_polarity" value=""/>
7162 <section name="blackorwhitelist">
7163 <param name="similarity_threshold" value="-1.0"/>
7164 <param name="rt" value="0.01"/>
7165 <param name="mz" value="0.01"/>
7166 <param name="use_ppm_tolerance" value="false"/>
7167 <param name="blacklist" value="true"/>
7168 </section>
7169 </section>
7170 <section name="feature">
7171 <param name="q" value=":"/>
7172 </section>
7173 <section name="consensus">
7174 <param name="map" value=""/>
7175 <param name="map_and" value="false"/>
7176 <section name="blackorwhitelist">
7177 <param name="blacklist" value="true"/>
7178 <param name="maps" value=""/>
7179 <param name="rt" value="60.0"/>
7180 <param name="mz" value="0.01"/>
7181 <param name="use_ppm_tolerance" value="false"/>
7182 </section>
7183 </section>
7184 <section name="f_and_c">
7185 <param name="charge" value=":"/>
7186 <param name="size" value=":"/>
7187 <param name="remove_meta" value=""/>
7188 </section>
7189 <section name="id">
7190 <param name="remove_clashes" value="false"/>
7191 <param name="keep_best_score_id" value="false"/>
7192 <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
7193 <param name="sequence_comparison_method" value="substring"/>
7194 <param name="accessions_whitelist" value=""/>
7195 <param name="remove_annotated_features" value="false"/>
7196 <param name="remove_unannotated_features" value="false"/>
7197 <param name="remove_unassigned_ids" value="true"/>
7198 <param name="rt" value="0.1"/>
7199 <param name="mz" value="0.001"/>
7200 <param name="blacklist_imperfect" value="false"/>
7201 </section>
7202 <section name="algorithm">
7203 <section name="SignalToNoise">
7204 <param name="max_intensity" value="-1"/>
7205 <param name="auto_max_stdev_factor" value="3.0"/>
7206 <param name="auto_max_percentile" value="95"/>
7207 <param name="auto_mode" value="0"/>
7208 <param name="win_len" value="200.0"/>
7209 <param name="bin_count" value="30"/>
7210 <param name="min_required_elements" value="10"/>
7211 <param name="noise_for_empty_window" value="1e+20"/>
7212 <param name="write_log_messages" value="true"/>
7213 </section>
7214 </section>
7215 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7216 <output name="ctd_out" ftype="xml">
7217 <assert_contents>
7218 <is_valid_xml/>
7219 </assert_contents>
7220 </output>
7221 </test>
7222 <test expect_num_outputs="2">
7223 <conditional name="adv_opts_cond">
7224 <param name="adv_opts_selector" value="advanced"/>
7225 <param name="force" value="false"/>
7226 <param name="test" value="true"/>
7227 </conditional>
7228 <param name="in" value="FileFilter_18_input.consensusXML"/>
7229 <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7230 <param name="out_type" value="consensusxml"/>
7231 <param name="rt" value="3000:4000"/>
7232 <param name="mz" value="400:600"/>
7233 <param name="int" value=":"/>
7234 <param name="sort" value="false"/>
7235 <section name="peak_options">
7236 <param name="sn" value="0.0"/>
7237 <param name="rm_pc_charge" value=""/>
7238 <param name="pc_mz_range" value=":"/>
7239 <param name="pc_mz_list" value=""/>
7240 <param name="level" value="1 2 3"/>
7241 <param name="sort_peaks" value="false"/>
7242 <param name="no_chromatograms" value="false"/>
7243 <param name="remove_chromatograms" value="false"/>
7244 <param name="remove_empty" value="false"/>
7245 <param name="mz_precision" value="64"/>
7246 <param name="int_precision" value="32"/>
7247 <param name="indexed_file" value="true"/>
7248 <param name="zlib_compression" value="false"/>
7249 <section name="numpress">
7250 <param name="masstime" value="none"/>
7251 <param name="lossy_mass_accuracy" value="-1.0"/>
7252 <param name="intensity" value="none"/>
7253 <param name="float_da" value="none"/>
7254 </section>
7255 </section>
7256 <section name="spectra">
7257 <param name="remove_zoom" value="false"/>
7258 <param name="remove_mode" value=""/>
7259 <param name="remove_activation" value=""/>
7260 <param name="remove_collision_energy" value=":"/>
7261 <param name="remove_isolation_window_width" value=":"/>
7262 <param name="select_zoom" value="false"/>
7263 <param name="select_mode" value=""/>
7264 <param name="select_activation" value=""/>
7265 <param name="select_collision_energy" value=":"/>
7266 <param name="select_isolation_window_width" value=":"/>
7267 <param name="select_polarity" value=""/>
7268 <section name="blackorwhitelist">
7269 <param name="similarity_threshold" value="-1.0"/>
7270 <param name="rt" value="0.01"/>
7271 <param name="mz" value="0.01"/>
7272 <param name="use_ppm_tolerance" value="false"/>
7273 <param name="blacklist" value="true"/>
7274 </section>
7275 </section>
7276 <section name="feature">
7277 <param name="q" value=":"/>
7278 </section>
7279 <section name="consensus">
7280 <param name="map" value=""/>
7281 <param name="map_and" value="false"/>
7282 <section name="blackorwhitelist">
7283 <param name="blacklist" value="true"/>
7284 <param name="maps" value=""/>
7285 <param name="rt" value="60.0"/>
7286 <param name="mz" value="0.01"/>
7287 <param name="use_ppm_tolerance" value="false"/>
7288 </section>
7289 </section>
7290 <section name="f_and_c">
7291 <param name="charge" value=":"/>
7292 <param name="size" value=":"/>
7293 <param name="remove_meta" value=""/>
7294 </section>
7295 <section name="id">
7296 <param name="remove_clashes" value="false"/>
7297 <param name="keep_best_score_id" value="false"/>
7298 <param name="sequences_whitelist" value=""/>
7299 <param name="sequence_comparison_method" value="substring"/>
7300 <param name="accessions_whitelist" value=""/>
7301 <param name="remove_annotated_features" value="false"/>
7302 <param name="remove_unannotated_features" value="true"/>
7303 <param name="remove_unassigned_ids" value="false"/>
7304 <param name="rt" value="0.1"/>
7305 <param name="mz" value="0.001"/>
7306 <param name="blacklist_imperfect" value="false"/>
7307 </section>
7308 <section name="algorithm">
7309 <section name="SignalToNoise">
7310 <param name="max_intensity" value="-1"/>
7311 <param name="auto_max_stdev_factor" value="3.0"/>
7312 <param name="auto_max_percentile" value="95"/>
7313 <param name="auto_mode" value="0"/>
7314 <param name="win_len" value="200.0"/>
7315 <param name="bin_count" value="30"/>
7316 <param name="min_required_elements" value="10"/>
7317 <param name="noise_for_empty_window" value="1e+20"/>
7318 <param name="write_log_messages" value="true"/>
7319 </section>
7320 </section>
7321 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7322 <output name="ctd_out" ftype="xml">
7323 <assert_contents>
7324 <is_valid_xml/>
7325 </assert_contents>
7326 </output>
7327 </test>
7328 <test expect_num_outputs="2">
7329 <conditional name="adv_opts_cond">
7330 <param name="adv_opts_selector" value="advanced"/>
7331 <param name="force" value="false"/>
7332 <param name="test" value="true"/>
7333 </conditional>
7334 <param name="in" value="FileFilter_15_input.featureXML"/>
7335 <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
7336 <param name="out_type" value="featurexml"/>
7337 <param name="rt" value=":"/>
7338 <param name="mz" value=":"/>
7339 <param name="int" value=":"/>
7340 <param name="sort" value="false"/>
7341 <section name="peak_options">
7342 <param name="sn" value="0.0"/>
7343 <param name="rm_pc_charge" value=""/>
7344 <param name="pc_mz_range" value=":"/>
7345 <param name="pc_mz_list" value=""/>
7346 <param name="level" value="1 2 3"/>
7347 <param name="sort_peaks" value="false"/>
7348 <param name="no_chromatograms" value="false"/>
7349 <param name="remove_chromatograms" value="false"/>
7350 <param name="remove_empty" value="false"/>
7351 <param name="mz_precision" value="64"/>
7352 <param name="int_precision" value="32"/>
7353 <param name="indexed_file" value="true"/>
7354 <param name="zlib_compression" value="false"/>
7355 <section name="numpress">
7356 <param name="masstime" value="none"/>
7357 <param name="lossy_mass_accuracy" value="-1.0"/>
7358 <param name="intensity" value="none"/>
7359 <param name="float_da" value="none"/>
7360 </section>
7361 </section>
7362 <section name="spectra">
7363 <param name="remove_zoom" value="false"/>
7364 <param name="remove_mode" value=""/>
7365 <param name="remove_activation" value=""/>
7366 <param name="remove_collision_energy" value=":"/>
7367 <param name="remove_isolation_window_width" value=":"/>
7368 <param name="select_zoom" value="false"/>
7369 <param name="select_mode" value=""/>
7370 <param name="select_activation" value=""/>
7371 <param name="select_collision_energy" value=":"/>
7372 <param name="select_isolation_window_width" value=":"/>
7373 <param name="select_polarity" value=""/>
7374 <section name="blackorwhitelist">
7375 <param name="similarity_threshold" value="-1.0"/>
7376 <param name="rt" value="0.01"/>
7377 <param name="mz" value="0.01"/>
7378 <param name="use_ppm_tolerance" value="false"/>
7379 <param name="blacklist" value="true"/>
7380 </section>
7381 </section>
7382 <section name="feature">
7383 <param name="q" value=":"/>
7384 </section>
7385 <section name="consensus">
7386 <param name="map" value=""/>
7387 <param name="map_and" value="false"/>
7388 <section name="blackorwhitelist">
7389 <param name="blacklist" value="true"/>
7390 <param name="maps" value=""/>
7391 <param name="rt" value="60.0"/>
7392 <param name="mz" value="0.01"/>
7393 <param name="use_ppm_tolerance" value="false"/>
7394 </section>
7395 </section>
7396 <section name="f_and_c">
7397 <param name="charge" value=":"/>
7398 <param name="size" value=":"/>
7399 <param name="remove_meta" value=""/>
7400 </section>
7401 <section name="id">
7402 <param name="remove_clashes" value="false"/>
7403 <param name="keep_best_score_id" value="false"/>
7404 <param name="sequences_whitelist" value=""/>
7405 <param name="sequence_comparison_method" value="substring"/>
7406 <param name="accessions_whitelist" value="&quot;YDL217C&quot;"/>
7407 <param name="remove_annotated_features" value="false"/>
7408 <param name="remove_unannotated_features" value="false"/>
7409 <param name="remove_unassigned_ids" value="true"/>
7410 <param name="rt" value="0.1"/>
7411 <param name="mz" value="0.001"/>
7412 <param name="blacklist_imperfect" value="false"/>
7413 </section>
7414 <section name="algorithm">
7415 <section name="SignalToNoise">
7416 <param name="max_intensity" value="-1"/>
7417 <param name="auto_max_stdev_factor" value="3.0"/>
7418 <param name="auto_max_percentile" value="95"/>
7419 <param name="auto_mode" value="0"/>
7420 <param name="win_len" value="200.0"/>
7421 <param name="bin_count" value="30"/>
7422 <param name="min_required_elements" value="10"/>
7423 <param name="noise_for_empty_window" value="1e+20"/>
7424 <param name="write_log_messages" value="true"/>
7425 </section>
7426 </section>
7427 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7428 <output name="ctd_out" ftype="xml">
7429 <assert_contents>
7430 <is_valid_xml/>
7431 </assert_contents>
7432 </output>
7433 </test>
7434 <test expect_num_outputs="2">
7435 <conditional name="adv_opts_cond">
7436 <param name="adv_opts_selector" value="advanced"/>
7437 <param name="force" value="false"/>
7438 <param name="test" value="true"/>
7439 </conditional>
7440 <param name="in" value="FileFilter_15_input.featureXML"/>
7441 <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
7442 <param name="out_type" value="featurexml"/>
7443 <param name="rt" value=":"/>
7444 <param name="mz" value=":"/>
7445 <param name="int" value=":"/>
7446 <param name="sort" value="false"/>
7447 <section name="peak_options">
7448 <param name="sn" value="0.0"/>
7449 <param name="rm_pc_charge" value=""/>
7450 <param name="pc_mz_range" value=":"/>
7451 <param name="pc_mz_list" value=""/>
7452 <param name="level" value="1 2 3"/>
7453 <param name="sort_peaks" value="false"/>
7454 <param name="no_chromatograms" value="false"/>
7455 <param name="remove_chromatograms" value="false"/>
7456 <param name="remove_empty" value="false"/>
7457 <param name="mz_precision" value="64"/>
7458 <param name="int_precision" value="32"/>
7459 <param name="indexed_file" value="true"/>
7460 <param name="zlib_compression" value="false"/>
7461 <section name="numpress">
7462 <param name="masstime" value="none"/>
7463 <param name="lossy_mass_accuracy" value="-1.0"/>
7464 <param name="intensity" value="none"/>
7465 <param name="float_da" value="none"/>
7466 </section>
7467 </section>
7468 <section name="spectra">
7469 <param name="remove_zoom" value="false"/>
7470 <param name="remove_mode" value=""/>
7471 <param name="remove_activation" value=""/>
7472 <param name="remove_collision_energy" value=":"/>
7473 <param name="remove_isolation_window_width" value=":"/>
7474 <param name="select_zoom" value="false"/>
7475 <param name="select_mode" value=""/>
7476 <param name="select_activation" value=""/>
7477 <param name="select_collision_energy" value=":"/>
7478 <param name="select_isolation_window_width" value=":"/>
7479 <param name="select_polarity" value=""/>
7480 <section name="blackorwhitelist">
7481 <param name="similarity_threshold" value="-1.0"/>
7482 <param name="rt" value="0.01"/>
7483 <param name="mz" value="0.01"/>
7484 <param name="use_ppm_tolerance" value="false"/>
7485 <param name="blacklist" value="true"/>
7486 </section>
7487 </section>
7488 <section name="feature">
7489 <param name="q" value=":"/>
7490 </section>
7491 <section name="consensus">
7492 <param name="map" value=""/>
7493 <param name="map_and" value="false"/>
7494 <section name="blackorwhitelist">
7495 <param name="blacklist" value="true"/>
7496 <param name="maps" value=""/>
7497 <param name="rt" value="60.0"/>
7498 <param name="mz" value="0.01"/>
7499 <param name="use_ppm_tolerance" value="false"/>
7500 </section>
7501 </section>
7502 <section name="f_and_c">
7503 <param name="charge" value=":"/>
7504 <param name="size" value=":"/>
7505 <param name="remove_meta" value=""/>
7506 </section>
7507 <section name="id">
7508 <param name="remove_clashes" value="false"/>
7509 <param name="keep_best_score_id" value="true"/>
7510 <param name="sequences_whitelist" value=""/>
7511 <param name="sequence_comparison_method" value="substring"/>
7512 <param name="accessions_whitelist" value=""/>
7513 <param name="remove_annotated_features" value="false"/>
7514 <param name="remove_unannotated_features" value="true"/>
7515 <param name="remove_unassigned_ids" value="true"/>
7516 <param name="rt" value="0.1"/>
7517 <param name="mz" value="0.001"/>
7518 <param name="blacklist_imperfect" value="false"/>
7519 </section>
7520 <section name="algorithm">
7521 <section name="SignalToNoise">
7522 <param name="max_intensity" value="-1"/>
7523 <param name="auto_max_stdev_factor" value="3.0"/>
7524 <param name="auto_max_percentile" value="95"/>
7525 <param name="auto_mode" value="0"/>
7526 <param name="win_len" value="200.0"/>
7527 <param name="bin_count" value="30"/>
7528 <param name="min_required_elements" value="10"/>
7529 <param name="noise_for_empty_window" value="1e+20"/>
7530 <param name="write_log_messages" value="true"/>
7531 </section>
7532 </section>
7533 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7534 <output name="ctd_out" ftype="xml">
7535 <assert_contents>
7536 <is_valid_xml/>
7537 </assert_contents>
7538 </output>
7539 </test>
7540 <test expect_num_outputs="2">
7541 <conditional name="adv_opts_cond">
7542 <param name="adv_opts_selector" value="advanced"/>
7543 <param name="force" value="false"/>
7544 <param name="test" value="true"/>
7545 </conditional>
7546 <param name="in" value="FileFilter_22_input.consensusXML"/>
7547 <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7548 <param name="out_type" value="consensusxml"/>
7549 <param name="rt" value=":"/>
7550 <param name="mz" value=":"/>
7551 <param name="int" value=":"/>
7552 <param name="sort" value="false"/>
7553 <section name="peak_options">
7554 <param name="sn" value="0.0"/>
7555 <param name="rm_pc_charge" value=""/>
7556 <param name="pc_mz_range" value=":"/>
7557 <param name="pc_mz_list" value=""/>
7558 <param name="level" value="1 2 3"/>
7559 <param name="sort_peaks" value="false"/>
7560 <param name="no_chromatograms" value="false"/>
7561 <param name="remove_chromatograms" value="false"/>
7562 <param name="remove_empty" value="false"/>
7563 <param name="mz_precision" value="64"/>
7564 <param name="int_precision" value="32"/>
7565 <param name="indexed_file" value="true"/>
7566 <param name="zlib_compression" value="false"/>
7567 <section name="numpress">
7568 <param name="masstime" value="none"/>
7569 <param name="lossy_mass_accuracy" value="-1.0"/>
7570 <param name="intensity" value="none"/>
7571 <param name="float_da" value="none"/>
7572 </section>
7573 </section>
7574 <section name="spectra">
7575 <param name="remove_zoom" value="false"/>
7576 <param name="remove_mode" value=""/>
7577 <param name="remove_activation" value=""/>
7578 <param name="remove_collision_energy" value=":"/>
7579 <param name="remove_isolation_window_width" value=":"/>
7580 <param name="select_zoom" value="false"/>
7581 <param name="select_mode" value=""/>
7582 <param name="select_activation" value=""/>
7583 <param name="select_collision_energy" value=":"/>
7584 <param name="select_isolation_window_width" value=":"/>
7585 <param name="select_polarity" value=""/>
7586 <section name="blackorwhitelist">
7587 <param name="similarity_threshold" value="-1.0"/>
7588 <param name="rt" value="0.01"/>
7589 <param name="mz" value="0.01"/>
7590 <param name="use_ppm_tolerance" value="false"/>
7591 <param name="blacklist" value="true"/>
7592 </section>
7593 </section>
7594 <section name="feature">
7595 <param name="q" value=":"/>
7596 </section>
7597 <section name="consensus">
7598 <param name="map" value=""/>
7599 <param name="map_and" value="false"/>
7600 <section name="blackorwhitelist">
7601 <param name="blacklist" value="true"/>
7602 <param name="maps" value=""/>
7603 <param name="rt" value="60.0"/>
7604 <param name="mz" value="0.01"/>
7605 <param name="use_ppm_tolerance" value="false"/>
7606 </section>
7607 </section>
7608 <section name="f_and_c">
7609 <param name="charge" value=":"/>
7610 <param name="size" value=":"/>
7611 <param name="remove_meta" value="&quot;distinct_charges&quot; &quot;gt&quot; &quot;1,2&quot;"/>
7612 </section>
7613 <section name="id">
7614 <param name="remove_clashes" value="false"/>
7615 <param name="keep_best_score_id" value="false"/>
7616 <param name="sequences_whitelist" value=""/>
7617 <param name="sequence_comparison_method" value="substring"/>
7618 <param name="accessions_whitelist" value=""/>
7619 <param name="remove_annotated_features" value="false"/>
7620 <param name="remove_unannotated_features" value="false"/>
7621 <param name="remove_unassigned_ids" value="false"/>
7622 <param name="rt" value="0.1"/>
7623 <param name="mz" value="0.001"/>
7624 <param name="blacklist_imperfect" value="false"/>
7625 </section>
7626 <section name="algorithm">
7627 <section name="SignalToNoise">
7628 <param name="max_intensity" value="-1"/>
7629 <param name="auto_max_stdev_factor" value="3.0"/>
7630 <param name="auto_max_percentile" value="95"/>
7631 <param name="auto_mode" value="0"/>
7632 <param name="win_len" value="200.0"/>
7633 <param name="bin_count" value="30"/>
7634 <param name="min_required_elements" value="10"/>
7635 <param name="noise_for_empty_window" value="1e+20"/>
7636 <param name="write_log_messages" value="true"/>
7637 </section>
7638 </section>
7639 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7640 <output name="ctd_out" ftype="xml">
7641 <assert_contents>
7642 <is_valid_xml/>
7643 </assert_contents>
7644 </output>
7645 </test>
7646 <test expect_num_outputs="2">
7647 <conditional name="adv_opts_cond">
7648 <param name="adv_opts_selector" value="advanced"/>
7649 <param name="force" value="false"/>
7650 <param name="test" value="true"/>
7651 </conditional>
7652 <param name="in" value="FileFilter_22_input.consensusXML"/>
7653 <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7654 <param name="out_type" value="consensusxml"/>
7655 <param name="rt" value=":"/>
7656 <param name="mz" value=":"/>
7657 <param name="int" value=":"/>
7658 <param name="sort" value="false"/>
7659 <section name="peak_options">
7660 <param name="sn" value="0.0"/>
7661 <param name="rm_pc_charge" value=""/>
7662 <param name="pc_mz_range" value=":"/>
7663 <param name="pc_mz_list" value=""/>
7664 <param name="level" value="1 2 3"/>
7665 <param name="sort_peaks" value="false"/>
7666 <param name="no_chromatograms" value="false"/>
7667 <param name="remove_chromatograms" value="false"/>
7668 <param name="remove_empty" value="false"/>
7669 <param name="mz_precision" value="64"/>
7670 <param name="int_precision" value="32"/>
7671 <param name="indexed_file" value="true"/>
7672 <param name="zlib_compression" value="false"/>
7673 <section name="numpress">
7674 <param name="masstime" value="none"/>
7675 <param name="lossy_mass_accuracy" value="-1.0"/>
7676 <param name="intensity" value="none"/>
7677 <param name="float_da" value="none"/>
7678 </section>
7679 </section>
7680 <section name="spectra">
7681 <param name="remove_zoom" value="false"/>
7682 <param name="remove_mode" value=""/>
7683 <param name="remove_activation" value=""/>
7684 <param name="remove_collision_energy" value=":"/>
7685 <param name="remove_isolation_window_width" value=":"/>
7686 <param name="select_zoom" value="false"/>
7687 <param name="select_mode" value=""/>
7688 <param name="select_activation" value=""/>
7689 <param name="select_collision_energy" value=":"/>
7690 <param name="select_isolation_window_width" value=":"/>
7691 <param name="select_polarity" value=""/>
7692 <section name="blackorwhitelist">
7693 <param name="similarity_threshold" value="-1.0"/>
7694 <param name="rt" value="0.01"/>
7695 <param name="mz" value="0.01"/>
7696 <param name="use_ppm_tolerance" value="false"/>
7697 <param name="blacklist" value="true"/>
7698 </section>
7699 </section>
7700 <section name="feature">
7701 <param name="q" value=":"/>
7702 </section>
7703 <section name="consensus">
7704 <param name="map" value=""/>
7705 <param name="map_and" value="false"/>
7706 <section name="blackorwhitelist">
7707 <param name="blacklist" value="true"/>
7708 <param name="maps" value=""/>
7709 <param name="rt" value="60.0"/>
7710 <param name="mz" value="0.01"/>
7711 <param name="use_ppm_tolerance" value="false"/>
7712 </section>
7713 </section>
7714 <section name="f_and_c">
7715 <param name="charge" value=":"/>
7716 <param name="size" value=":"/>
7717 <param name="remove_meta" value="&quot;distinct_charges_size&quot; &quot;gt&quot; &quot;2&quot;"/>
7718 </section>
7719 <section name="id">
7720 <param name="remove_clashes" value="false"/>
7721 <param name="keep_best_score_id" value="false"/>
7722 <param name="sequences_whitelist" value=""/>
7723 <param name="sequence_comparison_method" value="substring"/>
7724 <param name="accessions_whitelist" value=""/>
7725 <param name="remove_annotated_features" value="false"/>
7726 <param name="remove_unannotated_features" value="false"/>
7727 <param name="remove_unassigned_ids" value="false"/>
7728 <param name="rt" value="0.1"/>
7729 <param name="mz" value="0.001"/>
7730 <param name="blacklist_imperfect" value="false"/>
7731 </section>
7732 <section name="algorithm">
7733 <section name="SignalToNoise">
7734 <param name="max_intensity" value="-1"/>
7735 <param name="auto_max_stdev_factor" value="3.0"/>
7736 <param name="auto_max_percentile" value="95"/>
7737 <param name="auto_mode" value="0"/>
7738 <param name="win_len" value="200.0"/>
7739 <param name="bin_count" value="30"/>
7740 <param name="min_required_elements" value="10"/>
7741 <param name="noise_for_empty_window" value="1e+20"/>
7742 <param name="write_log_messages" value="true"/>
7743 </section>
7744 </section>
7745 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7746 <output name="ctd_out" ftype="xml">
7747 <assert_contents>
7748 <is_valid_xml/>
7749 </assert_contents>
7750 </output>
7751 </test>
7752 <test expect_num_outputs="2">
7753 <conditional name="adv_opts_cond">
7754 <param name="adv_opts_selector" value="advanced"/>
7755 <param name="force" value="false"/>
7756 <param name="test" value="true"/>
7757 </conditional>
7758 <param name="in" value="FileFilter_22_input.consensusXML"/>
7759 <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7760 <param name="out_type" value="consensusxml"/>
7761 <param name="rt" value=":"/>
7762 <param name="mz" value=":"/>
7763 <param name="int" value=":"/>
7764 <param name="sort" value="false"/>
7765 <section name="peak_options">
7766 <param name="sn" value="0.0"/>
7767 <param name="rm_pc_charge" value=""/>
7768 <param name="pc_mz_range" value=":"/>
7769 <param name="pc_mz_list" value=""/>
7770 <param name="level" value="1 2 3"/>
7771 <param name="sort_peaks" value="false"/>
7772 <param name="no_chromatograms" value="false"/>
7773 <param name="remove_chromatograms" value="false"/>
7774 <param name="remove_empty" value="false"/>
7775 <param name="mz_precision" value="64"/>
7776 <param name="int_precision" value="32"/>
7777 <param name="indexed_file" value="true"/>
7778 <param name="zlib_compression" value="false"/>
7779 <section name="numpress">
7780 <param name="masstime" value="none"/>
7781 <param name="lossy_mass_accuracy" value="-1.0"/>
7782 <param name="intensity" value="none"/>
7783 <param name="float_da" value="none"/>
7784 </section>
7785 </section>
7786 <section name="spectra">
7787 <param name="remove_zoom" value="false"/>
7788 <param name="remove_mode" value=""/>
7789 <param name="remove_activation" value=""/>
7790 <param name="remove_collision_energy" value=":"/>
7791 <param name="remove_isolation_window_width" value=":"/>
7792 <param name="select_zoom" value="false"/>
7793 <param name="select_mode" value=""/>
7794 <param name="select_activation" value=""/>
7795 <param name="select_collision_energy" value=":"/>
7796 <param name="select_isolation_window_width" value=":"/>
7797 <param name="select_polarity" value=""/>
7798 <section name="blackorwhitelist">
7799 <param name="similarity_threshold" value="-1.0"/>
7800 <param name="rt" value="0.01"/>
7801 <param name="mz" value="0.01"/>
7802 <param name="use_ppm_tolerance" value="false"/>
7803 <param name="blacklist" value="true"/>
7804 </section>
7805 </section>
7806 <section name="feature">
7807 <param name="q" value=":"/>
7808 </section>
7809 <section name="consensus">
7810 <param name="map" value=""/>
7811 <param name="map_and" value="false"/>
7812 <section name="blackorwhitelist">
7813 <param name="blacklist" value="true"/>
7814 <param name="maps" value=""/>
7815 <param name="rt" value="60.0"/>
7816 <param name="mz" value="0.01"/>
7817 <param name="use_ppm_tolerance" value="false"/>
7818 </section>
7819 </section>
7820 <section name="f_and_c">
7821 <param name="charge" value=":"/>
7822 <param name="size" value=":"/>
7823 <param name="remove_meta" value="&quot;DOESNOTEXIST&quot; &quot;lt&quot; &quot;whatever&quot;"/>
7824 </section>
7825 <section name="id">
7826 <param name="remove_clashes" value="false"/>
7827 <param name="keep_best_score_id" value="false"/>
7828 <param name="sequences_whitelist" value=""/>
7829 <param name="sequence_comparison_method" value="substring"/>
7830 <param name="accessions_whitelist" value=""/>
7831 <param name="remove_annotated_features" value="false"/>
7832 <param name="remove_unannotated_features" value="false"/>
7833 <param name="remove_unassigned_ids" value="false"/>
7834 <param name="rt" value="0.1"/>
7835 <param name="mz" value="0.001"/>
7836 <param name="blacklist_imperfect" value="false"/>
7837 </section>
7838 <section name="algorithm">
7839 <section name="SignalToNoise">
7840 <param name="max_intensity" value="-1"/>
7841 <param name="auto_max_stdev_factor" value="3.0"/>
7842 <param name="auto_max_percentile" value="95"/>
7843 <param name="auto_mode" value="0"/>
7844 <param name="win_len" value="200.0"/>
7845 <param name="bin_count" value="30"/>
7846 <param name="min_required_elements" value="10"/>
7847 <param name="noise_for_empty_window" value="1e+20"/>
7848 <param name="write_log_messages" value="true"/>
7849 </section>
7850 </section>
7851 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7852 <output name="ctd_out" ftype="xml">
7853 <assert_contents>
7854 <is_valid_xml/>
7855 </assert_contents>
7856 </output>
7857 </test>
7858 <test expect_num_outputs="2">
7859 <conditional name="adv_opts_cond">
7860 <param name="adv_opts_selector" value="advanced"/>
7861 <param name="force" value="false"/>
7862 <param name="test" value="true"/>
7863 </conditional>
7864 <param name="in" value="FileFilter_25_input.mzML.gz"/>
7865 <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
7866 <param name="out_type" value="mzml"/>
7867 <param name="rt" value=":"/>
7868 <param name="mz" value=":"/>
7869 <param name="int" value=":"/>
7870 <param name="sort" value="false"/>
7871 <section name="peak_options">
7872 <param name="sn" value="0.0"/>
7873 <param name="rm_pc_charge" value=""/>
7874 <param name="pc_mz_range" value=":"/>
7875 <param name="pc_mz_list" value=""/>
7876 <param name="level" value="1 2 3"/>
7877 <param name="sort_peaks" value="false"/>
7878 <param name="no_chromatograms" value="false"/>
7879 <param name="remove_chromatograms" value="false"/>
7880 <param name="remove_empty" value="false"/>
7881 <param name="mz_precision" value="64"/>
7882 <param name="int_precision" value="32"/>
7883 <param name="indexed_file" value="true"/>
7884 <param name="zlib_compression" value="false"/>
7885 <section name="numpress">
7886 <param name="masstime" value="none"/>
7887 <param name="lossy_mass_accuracy" value="-1.0"/>
7888 <param name="intensity" value="none"/>
7889 <param name="float_da" value="none"/>
7890 </section>
7891 </section>
7892 <section name="spectra">
7893 <param name="remove_zoom" value="false"/>
7894 <param name="remove_mode" value=""/>
7895 <param name="remove_activation" value=""/>
7896 <param name="remove_collision_energy" value=":"/>
7897 <param name="remove_isolation_window_width" value=":"/>
7898 <param name="select_zoom" value="false"/>
7899 <param name="select_mode" value=""/>
7900 <param name="select_activation" value=""/>
7901 <param name="select_collision_energy" value=":"/>
7902 <param name="select_isolation_window_width" value=":"/>
7903 <param name="select_polarity" value=""/>
7904 <section name="blackorwhitelist">
7905 <param name="similarity_threshold" value="-1.0"/>
7906 <param name="rt" value="0.01"/>
7907 <param name="mz" value="0.01"/>
7908 <param name="use_ppm_tolerance" value="false"/>
7909 <param name="blacklist" value="true"/>
7910 </section>
7911 </section>
7912 <section name="feature">
7913 <param name="q" value=":"/>
7914 </section>
7915 <section name="consensus">
7916 <param name="map" value=""/>
7917 <param name="map_and" value="false"/>
7918 <section name="blackorwhitelist">
7919 <param name="blacklist" value="true"/>
7920 <param name="maps" value=""/>
7921 <param name="rt" value="60.0"/>
7922 <param name="mz" value="0.01"/>
7923 <param name="use_ppm_tolerance" value="false"/>
7924 </section>
7925 </section>
7926 <section name="f_and_c">
7927 <param name="charge" value=":"/>
7928 <param name="size" value=":"/>
7929 <param name="remove_meta" value=""/>
7930 </section>
7931 <section name="id">
7932 <param name="remove_clashes" value="false"/>
7933 <param name="keep_best_score_id" value="false"/>
7934 <param name="sequences_whitelist" value=""/>
7935 <param name="sequence_comparison_method" value="substring"/>
7936 <param name="accessions_whitelist" value=""/>
7937 <param name="remove_annotated_features" value="false"/>
7938 <param name="remove_unannotated_features" value="false"/>
7939 <param name="remove_unassigned_ids" value="false"/>
7940 <param name="blacklist" value="FileFilter_25_input.idXML"/>
7941 <param name="rt" value="1.0"/>
7942 <param name="mz" value="0.05"/>
7943 <param name="blacklist_imperfect" value="true"/>
7944 </section>
7945 <section name="algorithm">
7946 <section name="SignalToNoise">
7947 <param name="max_intensity" value="-1"/>
7948 <param name="auto_max_stdev_factor" value="3.0"/>
7949 <param name="auto_max_percentile" value="95"/>
7950 <param name="auto_mode" value="0"/>
7951 <param name="win_len" value="200.0"/>
7952 <param name="bin_count" value="30"/>
7953 <param name="min_required_elements" value="10"/>
7954 <param name="noise_for_empty_window" value="1e+20"/>
7955 <param name="write_log_messages" value="true"/>
7956 </section>
7957 </section>
7958 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7959 <output name="ctd_out" ftype="xml">
7960 <assert_contents>
7961 <is_valid_xml/>
7962 </assert_contents>
7963 </output>
7964 </test>
7965 <test expect_num_outputs="2">
7966 <conditional name="adv_opts_cond">
7967 <param name="adv_opts_selector" value="advanced"/>
7968 <param name="force" value="false"/>
7969 <param name="test" value="true"/>
7970 </conditional>
7971 <param name="in" value="FileFilter_25_input.mzML.gz"/>
7972 <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
7973 <param name="out_type" value="mzml"/>
7974 <param name="rt" value=":"/>
7975 <param name="mz" value=":"/>
7976 <param name="int" value=":"/>
7977 <param name="sort" value="false"/>
7978 <section name="peak_options">
7979 <param name="sn" value="0.0"/>
7980 <param name="rm_pc_charge" value=""/>
7981 <param name="pc_mz_range" value=":"/>
7982 <param name="pc_mz_list" value=""/>
7983 <param name="level" value="1 2 3"/>
7984 <param name="sort_peaks" value="false"/>
7985 <param name="no_chromatograms" value="false"/>
7986 <param name="remove_chromatograms" value="false"/>
7987 <param name="remove_empty" value="false"/>
7988 <param name="mz_precision" value="64"/>
7989 <param name="int_precision" value="32"/>
7990 <param name="indexed_file" value="true"/>
7991 <param name="zlib_compression" value="false"/>
7992 <section name="numpress">
7993 <param name="masstime" value="none"/>
7994 <param name="lossy_mass_accuracy" value="-1.0"/>
7995 <param name="intensity" value="none"/>
7996 <param name="float_da" value="none"/>
7997 </section>
7998 </section>
7999 <section name="spectra">
8000 <param name="remove_zoom" value="false"/>
8001 <param name="remove_mode" value=""/>
8002 <param name="remove_activation" value=""/>
8003 <param name="remove_collision_energy" value=":"/>
8004 <param name="remove_isolation_window_width" value=":"/>
8005 <param name="select_zoom" value="false"/>
8006 <param name="select_mode" value=""/>
8007 <param name="select_activation" value=""/>
8008 <param name="select_collision_energy" value=":"/>
8009 <param name="select_isolation_window_width" value=":"/>
8010 <param name="select_polarity" value=""/>
8011 <section name="blackorwhitelist">
8012 <param name="similarity_threshold" value="-1.0"/>
8013 <param name="rt" value="0.01"/>
8014 <param name="mz" value="0.01"/>
8015 <param name="use_ppm_tolerance" value="false"/>
8016 <param name="blacklist" value="true"/>
8017 </section>
8018 </section>
8019 <section name="feature">
8020 <param name="q" value=":"/>
8021 </section>
8022 <section name="consensus">
8023 <param name="map" value=""/>
8024 <param name="map_and" value="false"/>
8025 <section name="blackorwhitelist">
8026 <param name="blacklist" value="true"/>
8027 <param name="maps" value=""/>
8028 <param name="rt" value="60.0"/>
8029 <param name="mz" value="0.01"/>
8030 <param name="use_ppm_tolerance" value="false"/>
8031 </section>
8032 </section>
8033 <section name="f_and_c">
8034 <param name="charge" value=":"/>
8035 <param name="size" value=":"/>
8036 <param name="remove_meta" value=""/>
8037 </section>
8038 <section name="id">
8039 <param name="remove_clashes" value="false"/>
8040 <param name="keep_best_score_id" value="false"/>
8041 <param name="sequences_whitelist" value=""/>
8042 <param name="sequence_comparison_method" value="substring"/>
8043 <param name="accessions_whitelist" value=""/>
8044 <param name="remove_annotated_features" value="false"/>
8045 <param name="remove_unannotated_features" value="false"/>
8046 <param name="remove_unassigned_ids" value="false"/>
8047 <param name="blacklist" value="FileFilter_25_input.idXML"/>
8048 <param name="rt" value="0.1"/>
8049 <param name="mz" value="0.001"/>
8050 <param name="blacklist_imperfect" value="true"/>
8051 </section>
8052 <section name="algorithm">
8053 <section name="SignalToNoise">
8054 <param name="max_intensity" value="-1"/>
8055 <param name="auto_max_stdev_factor" value="3.0"/>
8056 <param name="auto_max_percentile" value="95"/>
8057 <param name="auto_mode" value="0"/>
8058 <param name="win_len" value="200.0"/>
8059 <param name="bin_count" value="30"/>
8060 <param name="min_required_elements" value="10"/>
8061 <param name="noise_for_empty_window" value="1e+20"/>
8062 <param name="write_log_messages" value="true"/>
8063 </section>
8064 </section>
8065 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8066 <output name="ctd_out" ftype="xml">
8067 <assert_contents>
8068 <is_valid_xml/>
8069 </assert_contents>
8070 </output>
8071 </test>
8072 <test expect_num_outputs="2">
8073 <conditional name="adv_opts_cond">
8074 <param name="adv_opts_selector" value="advanced"/>
8075 <param name="force" value="false"/>
8076 <param name="test" value="true"/>
8077 </conditional>
8078 <param name="in" value="FileFilter_28_input.mzML.gz"/>
8079 <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8080 <param name="out_type" value="mzml"/>
8081 <param name="rt" value=":"/>
8082 <param name="mz" value=":"/>
8083 <param name="int" value=":"/>
8084 <param name="sort" value="false"/>
8085 <section name="peak_options">
8086 <param name="sn" value="0.0"/>
8087 <param name="rm_pc_charge" value=""/>
8088 <param name="pc_mz_range" value="832:836"/>
8089 <param name="pc_mz_list" value=""/>
8090 <param name="level" value="2"/>
8091 <param name="sort_peaks" value="false"/>
8092 <param name="no_chromatograms" value="false"/>
8093 <param name="remove_chromatograms" value="false"/>
8094 <param name="remove_empty" value="false"/>
8095 <param name="mz_precision" value="64"/>
8096 <param name="int_precision" value="32"/>
8097 <param name="indexed_file" value="true"/>
8098 <param name="zlib_compression" value="false"/>
8099 <section name="numpress">
8100 <param name="masstime" value="none"/>
8101 <param name="lossy_mass_accuracy" value="-1.0"/>
8102 <param name="intensity" value="none"/>
8103 <param name="float_da" value="none"/>
8104 </section>
8105 </section>
8106 <section name="spectra">
8107 <param name="remove_zoom" value="false"/>
8108 <param name="remove_mode" value=""/>
8109 <param name="remove_activation" value=""/>
8110 <param name="remove_collision_energy" value=":"/>
8111 <param name="remove_isolation_window_width" value=":"/>
8112 <param name="select_zoom" value="false"/>
8113 <param name="select_mode" value=""/>
8114 <param name="select_activation" value=""/>
8115 <param name="select_collision_energy" value=":"/>
8116 <param name="select_isolation_window_width" value=":"/>
8117 <param name="select_polarity" value=""/>
8118 <section name="blackorwhitelist">
8119 <param name="similarity_threshold" value="-1.0"/>
8120 <param name="rt" value="0.01"/>
8121 <param name="mz" value="0.01"/>
8122 <param name="use_ppm_tolerance" value="false"/>
8123 <param name="blacklist" value="true"/>
8124 </section>
8125 </section>
8126 <section name="feature">
8127 <param name="q" value=":"/>
8128 </section>
8129 <section name="consensus">
8130 <param name="map" value=""/>
8131 <param name="map_and" value="false"/>
8132 <section name="blackorwhitelist">
8133 <param name="blacklist" value="true"/>
8134 <param name="maps" value=""/>
8135 <param name="rt" value="60.0"/>
8136 <param name="mz" value="0.01"/>
8137 <param name="use_ppm_tolerance" value="false"/>
8138 </section>
8139 </section>
8140 <section name="f_and_c">
8141 <param name="charge" value=":"/>
8142 <param name="size" value=":"/>
8143 <param name="remove_meta" value=""/>
8144 </section>
8145 <section name="id">
8146 <param name="remove_clashes" value="false"/>
8147 <param name="keep_best_score_id" value="false"/>
8148 <param name="sequences_whitelist" value=""/>
8149 <param name="sequence_comparison_method" value="substring"/>
8150 <param name="accessions_whitelist" value=""/>
8151 <param name="remove_annotated_features" value="false"/>
8152 <param name="remove_unannotated_features" value="false"/>
8153 <param name="remove_unassigned_ids" value="false"/>
8154 <param name="rt" value="0.1"/>
8155 <param name="mz" value="0.001"/>
8156 <param name="blacklist_imperfect" value="false"/>
8157 </section>
8158 <section name="algorithm">
8159 <section name="SignalToNoise">
8160 <param name="max_intensity" value="-1"/>
8161 <param name="auto_max_stdev_factor" value="3.0"/>
8162 <param name="auto_max_percentile" value="95"/>
8163 <param name="auto_mode" value="0"/>
8164 <param name="win_len" value="200.0"/>
8165 <param name="bin_count" value="30"/>
8166 <param name="min_required_elements" value="10"/>
8167 <param name="noise_for_empty_window" value="1e+20"/>
8168 <param name="write_log_messages" value="true"/>
8169 </section>
8170 </section>
8171 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8172 <output name="ctd_out" ftype="xml">
8173 <assert_contents>
8174 <is_valid_xml/>
8175 </assert_contents>
8176 </output>
8177 </test>
8178 <test expect_num_outputs="2">
8179 <conditional name="adv_opts_cond">
8180 <param name="adv_opts_selector" value="advanced"/>
8181 <param name="force" value="false"/>
8182 <param name="test" value="true"/>
8183 </conditional>
8184 <param name="in" value="FileFilter_28_input.mzML.gz"/>
8185 <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8186 <param name="out_type" value="mzml"/>
8187 <param name="rt" value=":"/>
8188 <param name="mz" value=":"/>
8189 <param name="int" value=":"/>
8190 <param name="sort" value="false"/>
8191 <section name="peak_options">
8192 <param name="sn" value="0.0"/>
8193 <param name="rm_pc_charge" value=""/>
8194 <param name="pc_mz_range" value="832:836"/>
8195 <param name="pc_mz_list" value=""/>
8196 <param name="level" value="1 2"/>
8197 <param name="sort_peaks" value="false"/>
8198 <param name="no_chromatograms" value="false"/>
8199 <param name="remove_chromatograms" value="false"/>
8200 <param name="remove_empty" value="false"/>
8201 <param name="mz_precision" value="64"/>
8202 <param name="int_precision" value="32"/>
8203 <param name="indexed_file" value="true"/>
8204 <param name="zlib_compression" value="false"/>
8205 <section name="numpress">
8206 <param name="masstime" value="none"/>
8207 <param name="lossy_mass_accuracy" value="-1.0"/>
8208 <param name="intensity" value="none"/>
8209 <param name="float_da" value="none"/>
8210 </section>
8211 </section>
8212 <section name="spectra">
8213 <param name="remove_zoom" value="false"/>
8214 <param name="remove_mode" value=""/>
8215 <param name="remove_activation" value=""/>
8216 <param name="remove_collision_energy" value=":"/>
8217 <param name="remove_isolation_window_width" value=":"/>
8218 <param name="select_zoom" value="false"/>
8219 <param name="select_mode" value=""/>
8220 <param name="select_activation" value=""/>
8221 <param name="select_collision_energy" value=":"/>
8222 <param name="select_isolation_window_width" value=":"/>
8223 <param name="select_polarity" value=""/>
8224 <section name="blackorwhitelist">
8225 <param name="similarity_threshold" value="-1.0"/>
8226 <param name="rt" value="0.01"/>
8227 <param name="mz" value="0.01"/>
8228 <param name="use_ppm_tolerance" value="false"/>
8229 <param name="blacklist" value="true"/>
8230 </section>
8231 </section>
8232 <section name="feature">
8233 <param name="q" value=":"/>
8234 </section>
8235 <section name="consensus">
8236 <param name="map" value=""/>
8237 <param name="map_and" value="false"/>
8238 <section name="blackorwhitelist">
8239 <param name="blacklist" value="true"/>
8240 <param name="maps" value=""/>
8241 <param name="rt" value="60.0"/>
8242 <param name="mz" value="0.01"/>
8243 <param name="use_ppm_tolerance" value="false"/>
8244 </section>
8245 </section>
8246 <section name="f_and_c">
8247 <param name="charge" value=":"/>
8248 <param name="size" value=":"/>
8249 <param name="remove_meta" value=""/>
8250 </section>
8251 <section name="id">
8252 <param name="remove_clashes" value="false"/>
8253 <param name="keep_best_score_id" value="false"/>
8254 <param name="sequences_whitelist" value=""/>
8255 <param name="sequence_comparison_method" value="substring"/>
8256 <param name="accessions_whitelist" value=""/>
8257 <param name="remove_annotated_features" value="false"/>
8258 <param name="remove_unannotated_features" value="false"/>
8259 <param name="remove_unassigned_ids" value="false"/>
8260 <param name="rt" value="0.1"/>
8261 <param name="mz" value="0.001"/>
8262 <param name="blacklist_imperfect" value="false"/>
8263 </section>
8264 <section name="algorithm">
8265 <section name="SignalToNoise">
8266 <param name="max_intensity" value="-1"/>
8267 <param name="auto_max_stdev_factor" value="3.0"/>
8268 <param name="auto_max_percentile" value="95"/>
8269 <param name="auto_mode" value="0"/>
8270 <param name="win_len" value="200.0"/>
8271 <param name="bin_count" value="30"/>
8272 <param name="min_required_elements" value="10"/>
8273 <param name="noise_for_empty_window" value="1e+20"/>
8274 <param name="write_log_messages" value="true"/>
8275 </section>
8276 </section>
8277 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8278 <output name="ctd_out" ftype="xml">
8279 <assert_contents>
8280 <is_valid_xml/>
8281 </assert_contents>
8282 </output>
8283 </test>
8284 <test expect_num_outputs="2">
8285 <conditional name="adv_opts_cond">
8286 <param name="adv_opts_selector" value="advanced"/>
8287 <param name="force" value="false"/>
8288 <param name="test" value="true"/>
8289 </conditional>
8290 <param name="in" value="FileFilter_28_input.mzML.gz"/>
8291 <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8292 <param name="out_type" value="mzml"/>
8293 <param name="rt" value=":"/>
8294 <param name="mz" value=":"/>
8295 <param name="int" value=":"/>
8296 <param name="sort" value="false"/>
8297 <section name="peak_options">
8298 <param name="sn" value="0.0"/>
8299 <param name="rm_pc_charge" value=""/>
8300 <param name="pc_mz_range" value="832:836"/>
8301 <param name="pc_mz_list" value=""/>
8302 <param name="level" value="1 2"/>
8303 <param name="sort_peaks" value="false"/>
8304 <param name="no_chromatograms" value="false"/>
8305 <param name="remove_chromatograms" value="false"/>
8306 <param name="remove_empty" value="false"/>
8307 <param name="mz_precision" value="64"/>
8308 <param name="int_precision" value="32"/>
8309 <param name="indexed_file" value="true"/>
8310 <param name="zlib_compression" value="false"/>
8311 <section name="numpress">
8312 <param name="masstime" value="none"/>
8313 <param name="lossy_mass_accuracy" value="-1.0"/>
8314 <param name="intensity" value="none"/>
8315 <param name="float_da" value="none"/>
8316 </section>
8317 </section>
8318 <section name="spectra">
8319 <param name="remove_zoom" value="false"/>
8320 <param name="remove_mode" value=""/>
8321 <param name="remove_activation" value=""/>
8322 <param name="remove_collision_energy" value=":"/>
8323 <param name="remove_isolation_window_width" value=":"/>
8324 <param name="select_zoom" value="false"/>
8325 <param name="select_mode" value=""/>
8326 <param name="select_activation" value=""/>
8327 <param name="select_collision_energy" value=":"/>
8328 <param name="select_isolation_window_width" value=":"/>
8329 <param name="select_polarity" value=""/>
8330 <section name="blackorwhitelist">
8331 <param name="similarity_threshold" value="-1.0"/>
8332 <param name="rt" value="0.01"/>
8333 <param name="mz" value="0.01"/>
8334 <param name="use_ppm_tolerance" value="false"/>
8335 <param name="blacklist" value="true"/>
8336 </section>
8337 </section>
8338 <section name="feature">
8339 <param name="q" value=":"/>
8340 </section>
8341 <section name="consensus">
8342 <param name="map" value=""/>
8343 <param name="map_and" value="false"/>
8344 <section name="blackorwhitelist">
8345 <param name="blacklist" value="true"/>
8346 <param name="maps" value=""/>
8347 <param name="rt" value="60.0"/>
8348 <param name="mz" value="0.01"/>
8349 <param name="use_ppm_tolerance" value="false"/>
8350 </section>
8351 </section>
8352 <section name="f_and_c">
8353 <param name="charge" value=":"/>
8354 <param name="size" value=":"/>
8355 <param name="remove_meta" value=""/>
8356 </section>
8357 <section name="id">
8358 <param name="remove_clashes" value="false"/>
8359 <param name="keep_best_score_id" value="false"/>
8360 <param name="sequences_whitelist" value=""/>
8361 <param name="sequence_comparison_method" value="substring"/>
8362 <param name="accessions_whitelist" value=""/>
8363 <param name="remove_annotated_features" value="false"/>
8364 <param name="remove_unannotated_features" value="false"/>
8365 <param name="remove_unassigned_ids" value="false"/>
8366 <param name="rt" value="0.1"/>
8367 <param name="mz" value="0.001"/>
8368 <param name="blacklist_imperfect" value="false"/>
8369 </section>
8370 <section name="algorithm">
8371 <section name="SignalToNoise">
8372 <param name="max_intensity" value="-1"/>
8373 <param name="auto_max_stdev_factor" value="3.0"/>
8374 <param name="auto_max_percentile" value="95"/>
8375 <param name="auto_mode" value="0"/>
8376 <param name="win_len" value="200.0"/>
8377 <param name="bin_count" value="30"/>
8378 <param name="min_required_elements" value="10"/>
8379 <param name="noise_for_empty_window" value="1e+20"/>
8380 <param name="write_log_messages" value="true"/>
8381 </section>
8382 </section>
8383 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8384 <output name="ctd_out" ftype="xml">
8385 <assert_contents>
8386 <is_valid_xml/>
8387 </assert_contents>
8388 </output>
8389 </test>
8390 <test expect_num_outputs="2">
8391 <conditional name="adv_opts_cond">
8392 <param name="adv_opts_selector" value="advanced"/>
8393 <param name="force" value="false"/>
8394 <param name="test" value="true"/>
8395 </conditional>
8396 <param name="in" value="FileFilter_31_34_input.mzML"/>
8397 <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8398 <param name="out_type" value="mzml"/>
8399 <param name="rt" value=":"/>
8400 <param name="mz" value=":"/>
8401 <param name="int" value=":"/>
8402 <param name="sort" value="false"/>
8403 <section name="peak_options">
8404 <param name="sn" value="0.0"/>
8405 <param name="rm_pc_charge" value=""/>
8406 <param name="pc_mz_range" value=":"/>
8407 <param name="pc_mz_list" value=""/>
8408 <param name="level" value="1 2 3"/>
8409 <param name="sort_peaks" value="false"/>
8410 <param name="no_chromatograms" value="false"/>
8411 <param name="remove_chromatograms" value="false"/>
8412 <param name="remove_empty" value="false"/>
8413 <param name="mz_precision" value="64"/>
8414 <param name="int_precision" value="32"/>
8415 <param name="indexed_file" value="true"/>
8416 <param name="zlib_compression" value="false"/>
8417 <section name="numpress">
8418 <param name="masstime" value="none"/>
8419 <param name="lossy_mass_accuracy" value="-1.0"/>
8420 <param name="intensity" value="none"/>
8421 <param name="float_da" value="none"/>
8422 </section>
8423 </section>
8424 <section name="spectra">
8425 <param name="remove_zoom" value="false"/>
8426 <param name="remove_mode" value=""/>
8427 <param name="remove_activation" value=""/>
8428 <param name="remove_collision_energy" value=":"/>
8429 <param name="remove_isolation_window_width" value=":2"/>
8430 <param name="select_zoom" value="false"/>
8431 <param name="select_mode" value=""/>
8432 <param name="select_activation" value=""/>
8433 <param name="select_collision_energy" value=":"/>
8434 <param name="select_isolation_window_width" value=":"/>
8435 <param name="select_polarity" value=""/>
8436 <section name="blackorwhitelist">
8437 <param name="similarity_threshold" value="-1.0"/>
8438 <param name="rt" value="0.01"/>
8439 <param name="mz" value="0.01"/>
8440 <param name="use_ppm_tolerance" value="false"/>
8441 <param name="blacklist" value="true"/>
8442 </section>
8443 </section>
8444 <section name="feature">
8445 <param name="q" value=":"/>
8446 </section>
8447 <section name="consensus">
8448 <param name="map" value=""/>
8449 <param name="map_and" value="false"/>
8450 <section name="blackorwhitelist">
8451 <param name="blacklist" value="true"/>
8452 <param name="maps" value=""/>
8453 <param name="rt" value="60.0"/>
8454 <param name="mz" value="0.01"/>
8455 <param name="use_ppm_tolerance" value="false"/>
8456 </section>
8457 </section>
8458 <section name="f_and_c">
8459 <param name="charge" value=":"/>
8460 <param name="size" value=":"/>
8461 <param name="remove_meta" value=""/>
8462 </section>
8463 <section name="id">
8464 <param name="remove_clashes" value="false"/>
8465 <param name="keep_best_score_id" value="false"/>
8466 <param name="sequences_whitelist" value=""/>
8467 <param name="sequence_comparison_method" value="substring"/>
8468 <param name="accessions_whitelist" value=""/>
8469 <param name="remove_annotated_features" value="false"/>
8470 <param name="remove_unannotated_features" value="false"/>
8471 <param name="remove_unassigned_ids" value="false"/>
8472 <param name="rt" value="0.1"/>
8473 <param name="mz" value="0.001"/>
8474 <param name="blacklist_imperfect" value="false"/>
8475 </section>
8476 <section name="algorithm">
8477 <section name="SignalToNoise">
8478 <param name="max_intensity" value="-1"/>
8479 <param name="auto_max_stdev_factor" value="3.0"/>
8480 <param name="auto_max_percentile" value="95"/>
8481 <param name="auto_mode" value="0"/>
8482 <param name="win_len" value="200.0"/>
8483 <param name="bin_count" value="30"/>
8484 <param name="min_required_elements" value="10"/>
8485 <param name="noise_for_empty_window" value="1e+20"/>
8486 <param name="write_log_messages" value="true"/>
8487 </section>
8488 </section>
8489 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8490 <output name="ctd_out" ftype="xml">
8491 <assert_contents>
8492 <is_valid_xml/>
8493 </assert_contents>
8494 </output>
8495 </test>
8496 <test expect_num_outputs="2">
8497 <conditional name="adv_opts_cond">
8498 <param name="adv_opts_selector" value="advanced"/>
8499 <param name="force" value="false"/>
8500 <param name="test" value="true"/>
8501 </conditional>
8502 <param name="in" value="FileFilter_31_34_input.mzML"/>
8503 <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8504 <param name="out_type" value="mzml"/>
8505 <param name="rt" value=":"/>
8506 <param name="mz" value=":"/>
8507 <param name="int" value=":"/>
8508 <param name="sort" value="false"/>
8509 <section name="peak_options">
8510 <param name="sn" value="0.0"/>
8511 <param name="rm_pc_charge" value=""/>
8512 <param name="pc_mz_range" value=":"/>
8513 <param name="pc_mz_list" value=""/>
8514 <param name="level" value="1 2 3"/>
8515 <param name="sort_peaks" value="false"/>
8516 <param name="no_chromatograms" value="false"/>
8517 <param name="remove_chromatograms" value="false"/>
8518 <param name="remove_empty" value="false"/>
8519 <param name="mz_precision" value="64"/>
8520 <param name="int_precision" value="32"/>
8521 <param name="indexed_file" value="true"/>
8522 <param name="zlib_compression" value="false"/>
8523 <section name="numpress">
8524 <param name="masstime" value="none"/>
8525 <param name="lossy_mass_accuracy" value="-1.0"/>
8526 <param name="intensity" value="none"/>
8527 <param name="float_da" value="none"/>
8528 </section>
8529 </section>
8530 <section name="spectra">
8531 <param name="remove_zoom" value="false"/>
8532 <param name="remove_mode" value=""/>
8533 <param name="remove_activation" value=""/>
8534 <param name="remove_collision_energy" value=":"/>
8535 <param name="remove_isolation_window_width" value=":"/>
8536 <param name="select_zoom" value="false"/>
8537 <param name="select_mode" value=""/>
8538 <param name="select_activation" value=""/>
8539 <param name="select_collision_energy" value=":"/>
8540 <param name="select_isolation_window_width" value=":2"/>
8541 <param name="select_polarity" value=""/>
8542 <section name="blackorwhitelist">
8543 <param name="similarity_threshold" value="-1.0"/>
8544 <param name="rt" value="0.01"/>
8545 <param name="mz" value="0.01"/>
8546 <param name="use_ppm_tolerance" value="false"/>
8547 <param name="blacklist" value="true"/>
8548 </section>
8549 </section>
8550 <section name="feature">
8551 <param name="q" value=":"/>
8552 </section>
8553 <section name="consensus">
8554 <param name="map" value=""/>
8555 <param name="map_and" value="false"/>
8556 <section name="blackorwhitelist">
8557 <param name="blacklist" value="true"/>
8558 <param name="maps" value=""/>
8559 <param name="rt" value="60.0"/>
8560 <param name="mz" value="0.01"/>
8561 <param name="use_ppm_tolerance" value="false"/>
8562 </section>
8563 </section>
8564 <section name="f_and_c">
8565 <param name="charge" value=":"/>
8566 <param name="size" value=":"/>
8567 <param name="remove_meta" value=""/>
8568 </section>
8569 <section name="id">
8570 <param name="remove_clashes" value="false"/>
8571 <param name="keep_best_score_id" value="false"/>
8572 <param name="sequences_whitelist" value=""/>
8573 <param name="sequence_comparison_method" value="substring"/>
8574 <param name="accessions_whitelist" value=""/>
8575 <param name="remove_annotated_features" value="false"/>
8576 <param name="remove_unannotated_features" value="false"/>
8577 <param name="remove_unassigned_ids" value="false"/>
8578 <param name="rt" value="0.1"/>
8579 <param name="mz" value="0.001"/>
8580 <param name="blacklist_imperfect" value="false"/>
8581 </section>
8582 <section name="algorithm">
8583 <section name="SignalToNoise">
8584 <param name="max_intensity" value="-1"/>
8585 <param name="auto_max_stdev_factor" value="3.0"/>
8586 <param name="auto_max_percentile" value="95"/>
8587 <param name="auto_mode" value="0"/>
8588 <param name="win_len" value="200.0"/>
8589 <param name="bin_count" value="30"/>
8590 <param name="min_required_elements" value="10"/>
8591 <param name="noise_for_empty_window" value="1e+20"/>
8592 <param name="write_log_messages" value="true"/>
8593 </section>
8594 </section>
8595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8596 <output name="ctd_out" ftype="xml">
8597 <assert_contents>
8598 <is_valid_xml/>
8599 </assert_contents>
8600 </output>
8601 </test>
8602 <test expect_num_outputs="2">
8603 <conditional name="adv_opts_cond">
8604 <param name="adv_opts_selector" value="advanced"/>
8605 <param name="force" value="false"/>
8606 <param name="test" value="true"/>
8607 </conditional>
8608 <param name="in" value="FileFilter_31_34_input.mzML"/>
8609 <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8610 <param name="out_type" value="mzml"/>
8611 <param name="rt" value=":"/>
8612 <param name="mz" value=":"/>
8613 <param name="int" value=":"/>
8614 <param name="sort" value="false"/>
8615 <section name="peak_options">
8616 <param name="sn" value="0.0"/>
8617 <param name="rm_pc_charge" value=""/>
8618 <param name="pc_mz_range" value=":"/>
8619 <param name="pc_mz_list" value=""/>
8620 <param name="level" value="1 2 3"/>
8621 <param name="sort_peaks" value="false"/>
8622 <param name="no_chromatograms" value="false"/>
8623 <param name="remove_chromatograms" value="false"/>
8624 <param name="remove_empty" value="false"/>
8625 <param name="mz_precision" value="64"/>
8626 <param name="int_precision" value="32"/>
8627 <param name="indexed_file" value="true"/>
8628 <param name="zlib_compression" value="false"/>
8629 <section name="numpress">
8630 <param name="masstime" value="none"/>
8631 <param name="lossy_mass_accuracy" value="-1.0"/>
8632 <param name="intensity" value="none"/>
8633 <param name="float_da" value="none"/>
8634 </section>
8635 </section>
8636 <section name="spectra">
8637 <param name="remove_zoom" value="false"/>
8638 <param name="remove_mode" value=""/>
8639 <param name="remove_activation" value=""/>
8640 <param name="remove_collision_energy" value=":35"/>
8641 <param name="remove_isolation_window_width" value=":"/>
8642 <param name="select_zoom" value="false"/>
8643 <param name="select_mode" value=""/>
8644 <param name="select_activation" value=""/>
8645 <param name="select_collision_energy" value=":"/>
8646 <param name="select_isolation_window_width" value=":"/>
8647 <param name="select_polarity" value=""/>
8648 <section name="blackorwhitelist">
8649 <param name="similarity_threshold" value="-1.0"/>
8650 <param name="rt" value="0.01"/>
8651 <param name="mz" value="0.01"/>
8652 <param name="use_ppm_tolerance" value="false"/>
8653 <param name="blacklist" value="true"/>
8654 </section>
8655 </section>
8656 <section name="feature">
8657 <param name="q" value=":"/>
8658 </section>
8659 <section name="consensus">
8660 <param name="map" value=""/>
8661 <param name="map_and" value="false"/>
8662 <section name="blackorwhitelist">
8663 <param name="blacklist" value="true"/>
8664 <param name="maps" value=""/>
8665 <param name="rt" value="60.0"/>
8666 <param name="mz" value="0.01"/>
8667 <param name="use_ppm_tolerance" value="false"/>
8668 </section>
8669 </section>
8670 <section name="f_and_c">
8671 <param name="charge" value=":"/>
8672 <param name="size" value=":"/>
8673 <param name="remove_meta" value=""/>
8674 </section>
8675 <section name="id">
8676 <param name="remove_clashes" value="false"/>
8677 <param name="keep_best_score_id" value="false"/>
8678 <param name="sequences_whitelist" value=""/>
8679 <param name="sequence_comparison_method" value="substring"/>
8680 <param name="accessions_whitelist" value=""/>
8681 <param name="remove_annotated_features" value="false"/>
8682 <param name="remove_unannotated_features" value="false"/>
8683 <param name="remove_unassigned_ids" value="false"/>
8684 <param name="rt" value="0.1"/>
8685 <param name="mz" value="0.001"/>
8686 <param name="blacklist_imperfect" value="false"/>
8687 </section>
8688 <section name="algorithm">
8689 <section name="SignalToNoise">
8690 <param name="max_intensity" value="-1"/>
8691 <param name="auto_max_stdev_factor" value="3.0"/>
8692 <param name="auto_max_percentile" value="95"/>
8693 <param name="auto_mode" value="0"/>
8694 <param name="win_len" value="200.0"/>
8695 <param name="bin_count" value="30"/>
8696 <param name="min_required_elements" value="10"/>
8697 <param name="noise_for_empty_window" value="1e+20"/>
8698 <param name="write_log_messages" value="true"/>
8699 </section>
8700 </section>
8701 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8702 <output name="ctd_out" ftype="xml">
8703 <assert_contents>
8704 <is_valid_xml/>
8705 </assert_contents>
8706 </output>
8707 </test>
8708 <test expect_num_outputs="2">
8709 <conditional name="adv_opts_cond">
8710 <param name="adv_opts_selector" value="advanced"/>
8711 <param name="force" value="false"/>
8712 <param name="test" value="true"/>
8713 </conditional>
8714 <param name="in" value="FileFilter_31_34_input.mzML"/>
8715 <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8716 <param name="out_type" value="mzml"/>
8717 <param name="rt" value=":"/>
8718 <param name="mz" value=":"/>
8719 <param name="int" value=":"/>
8720 <param name="sort" value="false"/>
8721 <section name="peak_options">
8722 <param name="sn" value="0.0"/>
8723 <param name="rm_pc_charge" value=""/>
8724 <param name="pc_mz_range" value=":"/>
8725 <param name="pc_mz_list" value=""/>
8726 <param name="level" value="1 2 3"/>
8727 <param name="sort_peaks" value="false"/>
8728 <param name="no_chromatograms" value="false"/>
8729 <param name="remove_chromatograms" value="false"/>
8730 <param name="remove_empty" value="false"/>
8731 <param name="mz_precision" value="64"/>
8732 <param name="int_precision" value="32"/>
8733 <param name="indexed_file" value="true"/>
8734 <param name="zlib_compression" value="false"/>
8735 <section name="numpress">
8736 <param name="masstime" value="none"/>
8737 <param name="lossy_mass_accuracy" value="-1.0"/>
8738 <param name="intensity" value="none"/>
8739 <param name="float_da" value="none"/>
8740 </section>
8741 </section>
8742 <section name="spectra">
8743 <param name="remove_zoom" value="false"/>
8744 <param name="remove_mode" value=""/>
8745 <param name="remove_activation" value=""/>
8746 <param name="remove_collision_energy" value=":"/>
8747 <param name="remove_isolation_window_width" value=":"/>
8748 <param name="select_zoom" value="false"/>
8749 <param name="select_mode" value=""/>
8750 <param name="select_activation" value=""/>
8751 <param name="select_collision_energy" value=":35"/>
8752 <param name="select_isolation_window_width" value=":"/>
8753 <param name="select_polarity" value=""/>
8754 <section name="blackorwhitelist">
8755 <param name="similarity_threshold" value="-1.0"/>
8756 <param name="rt" value="0.01"/>
8757 <param name="mz" value="0.01"/>
8758 <param name="use_ppm_tolerance" value="false"/>
8759 <param name="blacklist" value="true"/>
8760 </section>
8761 </section>
8762 <section name="feature">
8763 <param name="q" value=":"/>
8764 </section>
8765 <section name="consensus">
8766 <param name="map" value=""/>
8767 <param name="map_and" value="false"/>
8768 <section name="blackorwhitelist">
8769 <param name="blacklist" value="true"/>
8770 <param name="maps" value=""/>
8771 <param name="rt" value="60.0"/>
8772 <param name="mz" value="0.01"/>
8773 <param name="use_ppm_tolerance" value="false"/>
8774 </section>
8775 </section>
8776 <section name="f_and_c">
8777 <param name="charge" value=":"/>
8778 <param name="size" value=":"/>
8779 <param name="remove_meta" value=""/>
8780 </section>
8781 <section name="id">
8782 <param name="remove_clashes" value="false"/>
8783 <param name="keep_best_score_id" value="false"/>
8784 <param name="sequences_whitelist" value=""/>
8785 <param name="sequence_comparison_method" value="substring"/>
8786 <param name="accessions_whitelist" value=""/>
8787 <param name="remove_annotated_features" value="false"/>
8788 <param name="remove_unannotated_features" value="false"/>
8789 <param name="remove_unassigned_ids" value="false"/>
8790 <param name="rt" value="0.1"/>
8791 <param name="mz" value="0.001"/>
8792 <param name="blacklist_imperfect" value="false"/>
8793 </section>
8794 <section name="algorithm">
8795 <section name="SignalToNoise">
8796 <param name="max_intensity" value="-1"/>
8797 <param name="auto_max_stdev_factor" value="3.0"/>
8798 <param name="auto_max_percentile" value="95"/>
8799 <param name="auto_mode" value="0"/>
8800 <param name="win_len" value="200.0"/>
8801 <param name="bin_count" value="30"/>
8802 <param name="min_required_elements" value="10"/>
8803 <param name="noise_for_empty_window" value="1e+20"/>
8804 <param name="write_log_messages" value="true"/>
8805 </section>
8806 </section>
8807 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8808 <output name="ctd_out" ftype="xml">
8809 <assert_contents>
8810 <is_valid_xml/>
8811 </assert_contents>
8812 </output>
8813 </test>
8814 <test expect_num_outputs="2">
8815 <conditional name="adv_opts_cond">
8816 <param name="adv_opts_selector" value="advanced"/>
8817 <param name="force" value="false"/>
8818 <param name="test" value="true"/>
8819 </conditional>
8820 <param name="in" value="FileFilter_1_input.mzML"/>
8821 <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8822 <param name="out_type" value="mzML"/>
8823 <param name="rt" value=":"/>
8824 <param name="mz" value=":"/>
8825 <param name="int" value=":"/>
8826 <param name="sort" value="false"/>
8827 <section name="peak_options">
8828 <param name="sn" value="0.0"/>
8829 <param name="rm_pc_charge" value=""/>
8830 <param name="pc_mz_range" value=":"/>
8831 <param name="pc_mz_list" value=""/>
8832 <param name="level" value="1 2 3"/>
8833 <param name="sort_peaks" value="false"/>
8834 <param name="no_chromatograms" value="false"/>
8835 <param name="remove_chromatograms" value="false"/>
8836 <param name="remove_empty" value="false"/>
8837 <param name="mz_precision" value="64"/>
8838 <param name="int_precision" value="32"/>
8839 <param name="indexed_file" value="true"/>
8840 <param name="zlib_compression" value="false"/>
8841 <section name="numpress">
8842 <param name="masstime" value="none"/>
8843 <param name="lossy_mass_accuracy" value="-1.0"/>
8844 <param name="intensity" value="none"/>
8845 <param name="float_da" value="none"/>
8846 </section>
8847 </section>
8848 <section name="spectra">
8849 <param name="remove_zoom" value="false"/>
8850 <param name="remove_mode" value=""/>
8851 <param name="remove_activation" value=""/>
8852 <param name="remove_collision_energy" value=":"/>
8853 <param name="remove_isolation_window_width" value=":"/>
8854 <param name="select_zoom" value="false"/>
8855 <param name="select_mode" value=""/>
8856 <param name="select_activation" value=""/>
8857 <param name="select_collision_energy" value=":"/>
8858 <param name="select_isolation_window_width" value=":"/>
8859 <param name="select_polarity" value=""/>
8860 <section name="blackorwhitelist">
8861 <param name="similarity_threshold" value="-1.0"/>
8862 <param name="rt" value="0.01"/>
8863 <param name="mz" value="0.01"/>
8864 <param name="use_ppm_tolerance" value="false"/>
8865 <param name="blacklist" value="true"/>
8866 </section>
8867 </section>
8868 <section name="feature">
8869 <param name="q" value=":"/>
8870 </section>
8871 <section name="consensus">
8872 <param name="map" value=""/>
8873 <param name="map_and" value="false"/>
8874 <section name="blackorwhitelist">
8875 <param name="blacklist" value="true"/>
8876 <param name="maps" value=""/>
8877 <param name="rt" value="60.0"/>
8878 <param name="mz" value="0.01"/>
8879 <param name="use_ppm_tolerance" value="false"/>
8880 </section>
8881 </section>
8882 <section name="f_and_c">
8883 <param name="charge" value=":"/>
8884 <param name="size" value=":"/>
8885 <param name="remove_meta" value=""/>
8886 </section>
8887 <section name="id">
8888 <param name="remove_clashes" value="false"/>
8889 <param name="keep_best_score_id" value="false"/>
8890 <param name="sequences_whitelist" value=""/>
8891 <param name="sequence_comparison_method" value="substring"/>
8892 <param name="accessions_whitelist" value=""/>
8893 <param name="remove_annotated_features" value="false"/>
8894 <param name="remove_unannotated_features" value="false"/>
8895 <param name="remove_unassigned_ids" value="false"/>
8896 <param name="rt" value="0.1"/>
8897 <param name="mz" value="0.001"/>
8898 <param name="blacklist_imperfect" value="false"/>
8899 </section>
8900 <section name="algorithm">
8901 <section name="SignalToNoise">
8902 <param name="max_intensity" value="-1"/>
8903 <param name="auto_max_stdev_factor" value="3.0"/>
8904 <param name="auto_max_percentile" value="95"/>
8905 <param name="auto_mode" value="0"/>
8906 <param name="win_len" value="200.0"/>
8907 <param name="bin_count" value="30"/>
8908 <param name="min_required_elements" value="10"/>
8909 <param name="noise_for_empty_window" value="1e+20"/>
8910 <param name="write_log_messages" value="true"/>
8911 </section>
8912 </section>
8913 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8914 <output name="ctd_out" ftype="xml">
8915 <assert_contents>
8916 <is_valid_xml/>
8917 </assert_contents>
8918 </output>
8919 </test>
8920 <test expect_num_outputs="2">
8921 <conditional name="adv_opts_cond">
8922 <param name="adv_opts_selector" value="advanced"/>
8923 <param name="force" value="false"/>
8924 <param name="test" value="true"/>
8925 </conditional>
8926 <param name="in" value="FileFilter_1_input.mzML"/>
8927 <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8928 <param name="out_type" value="mzML"/>
8929 <param name="rt" value=":"/>
8930 <param name="mz" value=":"/>
8931 <param name="int" value=":"/>
8932 <param name="sort" value="false"/>
8933 <section name="peak_options">
8934 <param name="sn" value="0.0"/>
8935 <param name="rm_pc_charge" value=""/>
8936 <param name="pc_mz_range" value=":"/>
8937 <param name="pc_mz_list" value=""/>
8938 <param name="level" value="1 2 3"/>
8939 <param name="sort_peaks" value="false"/>
8940 <param name="no_chromatograms" value="false"/>
8941 <param name="remove_chromatograms" value="false"/>
8942 <param name="remove_empty" value="false"/>
8943 <param name="mz_precision" value="64"/>
8944 <param name="int_precision" value="32"/>
8945 <param name="indexed_file" value="false"/>
8946 <param name="zlib_compression" value="false"/>
8947 <section name="numpress">
8948 <param name="masstime" value="none"/>
8949 <param name="lossy_mass_accuracy" value="-1.0"/>
8950 <param name="intensity" value="none"/>
8951 <param name="float_da" value="none"/>
8952 </section>
8953 </section>
8954 <section name="spectra">
8955 <param name="remove_zoom" value="false"/>
8956 <param name="remove_mode" value=""/>
8957 <param name="remove_activation" value=""/>
8958 <param name="remove_collision_energy" value=":"/>
8959 <param name="remove_isolation_window_width" value=":"/>
8960 <param name="select_zoom" value="false"/>
8961 <param name="select_mode" value=""/>
8962 <param name="select_activation" value=""/>
8963 <param name="select_collision_energy" value=":"/>
8964 <param name="select_isolation_window_width" value=":"/>
8965 <param name="select_polarity" value=""/>
8966 <section name="blackorwhitelist">
8967 <param name="similarity_threshold" value="-1.0"/>
8968 <param name="rt" value="0.01"/>
8969 <param name="mz" value="0.01"/>
8970 <param name="use_ppm_tolerance" value="false"/>
8971 <param name="blacklist" value="true"/>
8972 </section>
8973 </section>
8974 <section name="feature">
8975 <param name="q" value=":"/>
8976 </section>
8977 <section name="consensus">
8978 <param name="map" value=""/>
8979 <param name="map_and" value="false"/>
8980 <section name="blackorwhitelist">
8981 <param name="blacklist" value="true"/>
8982 <param name="maps" value=""/>
8983 <param name="rt" value="60.0"/>
8984 <param name="mz" value="0.01"/>
8985 <param name="use_ppm_tolerance" value="false"/>
8986 </section>
8987 </section>
8988 <section name="f_and_c">
8989 <param name="charge" value=":"/>
8990 <param name="size" value=":"/>
8991 <param name="remove_meta" value=""/>
8992 </section>
8993 <section name="id">
8994 <param name="remove_clashes" value="false"/>
8995 <param name="keep_best_score_id" value="false"/>
8996 <param name="sequences_whitelist" value=""/>
8997 <param name="sequence_comparison_method" value="substring"/>
8998 <param name="accessions_whitelist" value=""/>
8999 <param name="remove_annotated_features" value="false"/>
9000 <param name="remove_unannotated_features" value="false"/>
9001 <param name="remove_unassigned_ids" value="false"/>
9002 <param name="rt" value="0.1"/>
9003 <param name="mz" value="0.001"/>
9004 <param name="blacklist_imperfect" value="false"/>
9005 </section>
9006 <section name="algorithm">
9007 <section name="SignalToNoise">
9008 <param name="max_intensity" value="-1"/>
9009 <param name="auto_max_stdev_factor" value="3.0"/>
9010 <param name="auto_max_percentile" value="95"/>
9011 <param name="auto_mode" value="0"/>
9012 <param name="win_len" value="200.0"/>
9013 <param name="bin_count" value="30"/>
9014 <param name="min_required_elements" value="10"/>
9015 <param name="noise_for_empty_window" value="1e+20"/>
9016 <param name="write_log_messages" value="true"/>
9017 </section>
9018 </section>
9019 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9020 <output name="ctd_out" ftype="xml">
9021 <assert_contents>
9022 <is_valid_xml/>
9023 </assert_contents>
9024 </output>
9025 </test>
9026 <test expect_num_outputs="2">
9027 <conditional name="adv_opts_cond">
9028 <param name="adv_opts_selector" value="advanced"/>
9029 <param name="force" value="false"/>
9030 <param name="test" value="true"/>
9031 </conditional>
9032 <param name="in" value="FileFilter_1_input.mzML"/>
9033 <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9034 <param name="out_type" value="mzML"/>
9035 <param name="rt" value=":"/>
9036 <param name="mz" value=":"/>
9037 <param name="int" value=":"/>
9038 <param name="sort" value="false"/>
9039 <section name="peak_options">
9040 <param name="sn" value="0.0"/>
9041 <param name="rm_pc_charge" value=""/>
9042 <param name="pc_mz_range" value=":"/>
9043 <param name="pc_mz_list" value=""/>
9044 <param name="level" value="1 2 3"/>
9045 <param name="sort_peaks" value="false"/>
9046 <param name="no_chromatograms" value="false"/>
9047 <param name="remove_chromatograms" value="false"/>
9048 <param name="remove_empty" value="false"/>
9049 <param name="mz_precision" value="64"/>
9050 <param name="int_precision" value="32"/>
9051 <param name="indexed_file" value="true"/>
9052 <param name="zlib_compression" value="false"/>
9053 <section name="numpress">
9054 <param name="masstime" value="linear"/>
9055 <param name="lossy_mass_accuracy" value="0.0001"/>
9056 <param name="intensity" value="slof"/>
9057 <param name="float_da" value="none"/>
9058 </section>
9059 </section>
9060 <section name="spectra">
9061 <param name="remove_zoom" value="false"/>
9062 <param name="remove_mode" value=""/>
9063 <param name="remove_activation" value=""/>
9064 <param name="remove_collision_energy" value=":"/>
9065 <param name="remove_isolation_window_width" value=":"/>
9066 <param name="select_zoom" value="false"/>
9067 <param name="select_mode" value=""/>
9068 <param name="select_activation" value=""/>
9069 <param name="select_collision_energy" value=":"/>
9070 <param name="select_isolation_window_width" value=":"/>
9071 <param name="select_polarity" value=""/>
9072 <section name="blackorwhitelist">
9073 <param name="similarity_threshold" value="-1.0"/>
9074 <param name="rt" value="0.01"/>
9075 <param name="mz" value="0.01"/>
9076 <param name="use_ppm_tolerance" value="false"/>
9077 <param name="blacklist" value="true"/>
9078 </section>
9079 </section>
9080 <section name="feature">
9081 <param name="q" value=":"/>
9082 </section>
9083 <section name="consensus">
9084 <param name="map" value=""/>
9085 <param name="map_and" value="false"/>
9086 <section name="blackorwhitelist">
9087 <param name="blacklist" value="true"/>
9088 <param name="maps" value=""/>
9089 <param name="rt" value="60.0"/>
9090 <param name="mz" value="0.01"/>
9091 <param name="use_ppm_tolerance" value="false"/>
9092 </section>
9093 </section>
9094 <section name="f_and_c">
9095 <param name="charge" value=":"/>
9096 <param name="size" value=":"/>
9097 <param name="remove_meta" value=""/>
9098 </section>
9099 <section name="id">
9100 <param name="remove_clashes" value="false"/>
9101 <param name="keep_best_score_id" value="false"/>
9102 <param name="sequences_whitelist" value=""/>
9103 <param name="sequence_comparison_method" value="substring"/>
9104 <param name="accessions_whitelist" value=""/>
9105 <param name="remove_annotated_features" value="false"/>
9106 <param name="remove_unannotated_features" value="false"/>
9107 <param name="remove_unassigned_ids" value="false"/>
9108 <param name="rt" value="0.1"/>
9109 <param name="mz" value="0.001"/>
9110 <param name="blacklist_imperfect" value="false"/>
9111 </section>
9112 <section name="algorithm">
9113 <section name="SignalToNoise">
9114 <param name="max_intensity" value="-1"/>
9115 <param name="auto_max_stdev_factor" value="3.0"/>
9116 <param name="auto_max_percentile" value="95"/>
9117 <param name="auto_mode" value="0"/>
9118 <param name="win_len" value="200.0"/>
9119 <param name="bin_count" value="30"/>
9120 <param name="min_required_elements" value="10"/>
9121 <param name="noise_for_empty_window" value="1e+20"/>
9122 <param name="write_log_messages" value="true"/>
9123 </section>
9124 </section>
9125 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9126 <output name="ctd_out" ftype="xml">
9127 <assert_contents>
9128 <is_valid_xml/>
9129 </assert_contents>
9130 </output>
9131 </test>
9132 <test expect_num_outputs="2">
9133 <conditional name="adv_opts_cond">
9134 <param name="adv_opts_selector" value="advanced"/>
9135 <param name="force" value="false"/>
9136 <param name="test" value="true"/>
9137 </conditional>
9138 <param name="in" value="FileFilter_1_input.mzML"/>
9139 <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9140 <param name="out_type" value="mzML"/>
9141 <param name="rt" value=":"/>
9142 <param name="mz" value=":"/>
9143 <param name="int" value=":"/>
9144 <param name="sort" value="false"/>
9145 <section name="peak_options">
9146 <param name="sn" value="0.0"/>
9147 <param name="rm_pc_charge" value=""/>
9148 <param name="pc_mz_range" value=":"/>
9149 <param name="pc_mz_list" value=""/>
9150 <param name="level" value="1 2 3"/>
9151 <param name="sort_peaks" value="false"/>
9152 <param name="no_chromatograms" value="false"/>
9153 <param name="remove_chromatograms" value="false"/>
9154 <param name="remove_empty" value="false"/>
9155 <param name="mz_precision" value="64"/>
9156 <param name="int_precision" value="32"/>
9157 <param name="indexed_file" value="true"/>
9158 <param name="zlib_compression" value="false"/>
9159 <section name="numpress">
9160 <param name="masstime" value="linear"/>
9161 <param name="lossy_mass_accuracy" value="0.0001"/>
9162 <param name="intensity" value="pic"/>
9163 <param name="float_da" value="none"/>
9164 </section>
9165 </section>
9166 <section name="spectra">
9167 <param name="remove_zoom" value="false"/>
9168 <param name="remove_mode" value=""/>
9169 <param name="remove_activation" value=""/>
9170 <param name="remove_collision_energy" value=":"/>
9171 <param name="remove_isolation_window_width" value=":"/>
9172 <param name="select_zoom" value="false"/>
9173 <param name="select_mode" value=""/>
9174 <param name="select_activation" value=""/>
9175 <param name="select_collision_energy" value=":"/>
9176 <param name="select_isolation_window_width" value=":"/>
9177 <param name="select_polarity" value=""/>
9178 <section name="blackorwhitelist">
9179 <param name="similarity_threshold" value="-1.0"/>
9180 <param name="rt" value="0.01"/>
9181 <param name="mz" value="0.01"/>
9182 <param name="use_ppm_tolerance" value="false"/>
9183 <param name="blacklist" value="true"/>
9184 </section>
9185 </section>
9186 <section name="feature">
9187 <param name="q" value=":"/>
9188 </section>
9189 <section name="consensus">
9190 <param name="map" value=""/>
9191 <param name="map_and" value="false"/>
9192 <section name="blackorwhitelist">
9193 <param name="blacklist" value="true"/>
9194 <param name="maps" value=""/>
9195 <param name="rt" value="60.0"/>
9196 <param name="mz" value="0.01"/>
9197 <param name="use_ppm_tolerance" value="false"/>
9198 </section>
9199 </section>
9200 <section name="f_and_c">
9201 <param name="charge" value=":"/>
9202 <param name="size" value=":"/>
9203 <param name="remove_meta" value=""/>
9204 </section>
9205 <section name="id">
9206 <param name="remove_clashes" value="false"/>
9207 <param name="keep_best_score_id" value="false"/>
9208 <param name="sequences_whitelist" value=""/>
9209 <param name="sequence_comparison_method" value="substring"/>
9210 <param name="accessions_whitelist" value=""/>
9211 <param name="remove_annotated_features" value="false"/>
9212 <param name="remove_unannotated_features" value="false"/>
9213 <param name="remove_unassigned_ids" value="false"/>
9214 <param name="rt" value="0.1"/>
9215 <param name="mz" value="0.001"/>
9216 <param name="blacklist_imperfect" value="false"/>
9217 </section>
9218 <section name="algorithm">
9219 <section name="SignalToNoise">
9220 <param name="max_intensity" value="-1"/>
9221 <param name="auto_max_stdev_factor" value="3.0"/>
9222 <param name="auto_max_percentile" value="95"/>
9223 <param name="auto_mode" value="0"/>
9224 <param name="win_len" value="200.0"/>
9225 <param name="bin_count" value="30"/>
9226 <param name="min_required_elements" value="10"/>
9227 <param name="noise_for_empty_window" value="1e+20"/>
9228 <param name="write_log_messages" value="true"/>
9229 </section>
9230 </section>
9231 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9232 <output name="ctd_out" ftype="xml">
9233 <assert_contents>
9234 <is_valid_xml/>
9235 </assert_contents>
9236 </output>
9237 </test>
9238 <test expect_num_outputs="2">
9239 <conditional name="adv_opts_cond">
9240 <param name="adv_opts_selector" value="advanced"/>
9241 <param name="force" value="false"/>
9242 <param name="test" value="true"/>
9243 </conditional>
9244 <param name="in" value="FileFilter_40_input.mzML"/>
9245 <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9246 <param name="out_type" value="mzML"/>
9247 <param name="rt" value=":"/>
9248 <param name="mz" value=":"/>
9249 <param name="int" value=":"/>
9250 <param name="sort" value="false"/>
9251 <section name="peak_options">
9252 <param name="sn" value="0.0"/>
9253 <param name="rm_pc_charge" value=""/>
9254 <param name="pc_mz_range" value=":"/>
9255 <param name="pc_mz_list" value=""/>
9256 <param name="level" value="1 2 3"/>
9257 <param name="sort_peaks" value="false"/>
9258 <param name="no_chromatograms" value="false"/>
9259 <param name="remove_chromatograms" value="false"/>
9260 <param name="remove_empty" value="false"/>
9261 <param name="mz_precision" value="64"/>
9262 <param name="int_precision" value="32"/>
9263 <param name="indexed_file" value="true"/>
9264 <param name="zlib_compression" value="false"/>
9265 <section name="numpress">
9266 <param name="masstime" value="none"/>
9267 <param name="lossy_mass_accuracy" value="-1.0"/>
9268 <param name="intensity" value="none"/>
9269 <param name="float_da" value="none"/>
9270 </section>
9271 </section>
9272 <section name="spectra">
9273 <param name="remove_zoom" value="false"/>
9274 <param name="remove_mode" value=""/>
9275 <param name="remove_activation" value=""/>
9276 <param name="remove_collision_energy" value=":"/>
9277 <param name="remove_isolation_window_width" value=":"/>
9278 <param name="select_zoom" value="false"/>
9279 <param name="select_mode" value=""/>
9280 <param name="select_activation" value=""/>
9281 <param name="select_collision_energy" value=":"/>
9282 <param name="select_isolation_window_width" value=":"/>
9283 <param name="select_polarity" value="positive"/>
9284 <section name="blackorwhitelist">
9285 <param name="similarity_threshold" value="-1.0"/>
9286 <param name="rt" value="0.01"/>
9287 <param name="mz" value="0.01"/>
9288 <param name="use_ppm_tolerance" value="false"/>
9289 <param name="blacklist" value="true"/>
9290 </section>
9291 </section>
9292 <section name="feature">
9293 <param name="q" value=":"/>
9294 </section>
9295 <section name="consensus">
9296 <param name="map" value=""/>
9297 <param name="map_and" value="false"/>
9298 <section name="blackorwhitelist">
9299 <param name="blacklist" value="true"/>
9300 <param name="maps" value=""/>
9301 <param name="rt" value="60.0"/>
9302 <param name="mz" value="0.01"/>
9303 <param name="use_ppm_tolerance" value="false"/>
9304 </section>
9305 </section>
9306 <section name="f_and_c">
9307 <param name="charge" value=":"/>
9308 <param name="size" value=":"/>
9309 <param name="remove_meta" value=""/>
9310 </section>
9311 <section name="id">
9312 <param name="remove_clashes" value="false"/>
9313 <param name="keep_best_score_id" value="false"/>
9314 <param name="sequences_whitelist" value=""/>
9315 <param name="sequence_comparison_method" value="substring"/>
9316 <param name="accessions_whitelist" value=""/>
9317 <param name="remove_annotated_features" value="false"/>
9318 <param name="remove_unannotated_features" value="false"/>
9319 <param name="remove_unassigned_ids" value="false"/>
9320 <param name="rt" value="0.1"/>
9321 <param name="mz" value="0.001"/>
9322 <param name="blacklist_imperfect" value="false"/>
9323 </section>
9324 <section name="algorithm">
9325 <section name="SignalToNoise">
9326 <param name="max_intensity" value="-1"/>
9327 <param name="auto_max_stdev_factor" value="3.0"/>
9328 <param name="auto_max_percentile" value="95"/>
9329 <param name="auto_mode" value="0"/>
9330 <param name="win_len" value="200.0"/>
9331 <param name="bin_count" value="30"/>
9332 <param name="min_required_elements" value="10"/>
9333 <param name="noise_for_empty_window" value="1e+20"/>
9334 <param name="write_log_messages" value="true"/>
9335 </section>
9336 </section>
9337 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9338 <output name="ctd_out" ftype="xml">
9339 <assert_contents>
9340 <is_valid_xml/>
9341 </assert_contents>
9342 </output>
9343 </test>
9344 <test expect_num_outputs="2">
9345 <conditional name="adv_opts_cond">
9346 <param name="adv_opts_selector" value="advanced"/>
9347 <param name="force" value="false"/>
9348 <param name="test" value="true"/>
9349 </conditional>
9350 <param name="in" value="FileFilter_40_input.mzML"/>
9351 <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9352 <param name="out_type" value="mzML"/>
9353 <param name="rt" value=":"/>
9354 <param name="mz" value=":"/>
9355 <param name="int" value=":"/>
9356 <param name="sort" value="false"/>
9357 <section name="peak_options">
9358 <param name="sn" value="0.0"/>
9359 <param name="rm_pc_charge" value=""/>
9360 <param name="pc_mz_range" value=":"/>
9361 <param name="pc_mz_list" value=""/>
9362 <param name="level" value="1 2 3"/>
9363 <param name="sort_peaks" value="false"/>
9364 <param name="no_chromatograms" value="false"/>
9365 <param name="remove_chromatograms" value="false"/>
9366 <param name="remove_empty" value="false"/>
9367 <param name="mz_precision" value="64"/>
9368 <param name="int_precision" value="32"/>
9369 <param name="indexed_file" value="true"/>
9370 <param name="zlib_compression" value="false"/>
9371 <section name="numpress">
9372 <param name="masstime" value="none"/>
9373 <param name="lossy_mass_accuracy" value="-1.0"/>
9374 <param name="intensity" value="none"/>
9375 <param name="float_da" value="none"/>
9376 </section>
9377 </section>
9378 <section name="spectra">
9379 <param name="remove_zoom" value="false"/>
9380 <param name="remove_mode" value=""/>
9381 <param name="remove_activation" value=""/>
9382 <param name="remove_collision_energy" value=":"/>
9383 <param name="remove_isolation_window_width" value=":"/>
9384 <param name="select_zoom" value="false"/>
9385 <param name="select_mode" value=""/>
9386 <param name="select_activation" value=""/>
9387 <param name="select_collision_energy" value=":"/>
9388 <param name="select_isolation_window_width" value=":"/>
9389 <param name="select_polarity" value="negative"/>
9390 <section name="blackorwhitelist">
9391 <param name="similarity_threshold" value="-1.0"/>
9392 <param name="rt" value="0.01"/>
9393 <param name="mz" value="0.01"/>
9394 <param name="use_ppm_tolerance" value="false"/>
9395 <param name="blacklist" value="true"/>
9396 </section>
9397 </section>
9398 <section name="feature">
9399 <param name="q" value=":"/>
9400 </section>
9401 <section name="consensus">
9402 <param name="map" value=""/>
9403 <param name="map_and" value="false"/>
9404 <section name="blackorwhitelist">
9405 <param name="blacklist" value="true"/>
9406 <param name="maps" value=""/>
9407 <param name="rt" value="60.0"/>
9408 <param name="mz" value="0.01"/>
9409 <param name="use_ppm_tolerance" value="false"/>
9410 </section>
9411 </section>
9412 <section name="f_and_c">
9413 <param name="charge" value=":"/>
9414 <param name="size" value=":"/>
9415 <param name="remove_meta" value=""/>
9416 </section>
9417 <section name="id">
9418 <param name="remove_clashes" value="false"/>
9419 <param name="keep_best_score_id" value="false"/>
9420 <param name="sequences_whitelist" value=""/>
9421 <param name="sequence_comparison_method" value="substring"/>
9422 <param name="accessions_whitelist" value=""/>
9423 <param name="remove_annotated_features" value="false"/>
9424 <param name="remove_unannotated_features" value="false"/>
9425 <param name="remove_unassigned_ids" value="false"/>
9426 <param name="rt" value="0.1"/>
9427 <param name="mz" value="0.001"/>
9428 <param name="blacklist_imperfect" value="false"/>
9429 </section>
9430 <section name="algorithm">
9431 <section name="SignalToNoise">
9432 <param name="max_intensity" value="-1"/>
9433 <param name="auto_max_stdev_factor" value="3.0"/>
9434 <param name="auto_max_percentile" value="95"/>
9435 <param name="auto_mode" value="0"/>
9436 <param name="win_len" value="200.0"/>
9437 <param name="bin_count" value="30"/>
9438 <param name="min_required_elements" value="10"/>
9439 <param name="noise_for_empty_window" value="1e+20"/>
9440 <param name="write_log_messages" value="true"/>
9441 </section>
9442 </section>
9443 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9444 <output name="ctd_out" ftype="xml">
9445 <assert_contents>
9446 <is_valid_xml/>
9447 </assert_contents>
9448 </output>
9449 </test>
9450 <test expect_num_outputs="2">
9451 <conditional name="adv_opts_cond">
9452 <param name="adv_opts_selector" value="advanced"/>
9453 <param name="force" value="false"/>
9454 <param name="test" value="true"/>
9455 </conditional>
9456 <param name="in" value="FileFilter_40_input.mzML"/>
9457 <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9458 <param name="out_type" value="mzML"/>
9459 <param name="rt" value=":"/>
9460 <param name="mz" value=":"/>
9461 <param name="int" value=":"/>
9462 <param name="sort" value="false"/>
9463 <section name="peak_options">
9464 <param name="sn" value="0.0"/>
9465 <param name="rm_pc_charge" value=""/>
9466 <param name="pc_mz_range" value=":"/>
9467 <param name="pc_mz_list" value=""/>
9468 <param name="level" value="1 2 3"/>
9469 <param name="sort_peaks" value="false"/>
9470 <param name="no_chromatograms" value="false"/>
9471 <param name="remove_chromatograms" value="false"/>
9472 <param name="remove_empty" value="false"/>
9473 <param name="mz_precision" value="64"/>
9474 <param name="int_precision" value="32"/>
9475 <param name="indexed_file" value="true"/>
9476 <param name="zlib_compression" value="false"/>
9477 <section name="numpress">
9478 <param name="masstime" value="none"/>
9479 <param name="lossy_mass_accuracy" value="-1.0"/>
9480 <param name="intensity" value="none"/>
9481 <param name="float_da" value="none"/>
9482 </section>
9483 </section>
9484 <section name="spectra">
9485 <param name="remove_zoom" value="false"/>
9486 <param name="remove_mode" value=""/>
9487 <param name="remove_activation" value=""/>
9488 <param name="remove_collision_energy" value=":"/>
9489 <param name="remove_isolation_window_width" value=":"/>
9490 <param name="select_zoom" value="false"/>
9491 <param name="select_mode" value=""/>
9492 <param name="select_activation" value=""/>
9493 <param name="select_collision_energy" value=":"/>
9494 <param name="select_isolation_window_width" value=":"/>
9495 <param name="select_polarity" value=""/>
9496 <section name="blackorwhitelist">
9497 <param name="similarity_threshold" value="-1.0"/>
9498 <param name="rt" value="0.01"/>
9499 <param name="mz" value="0.01"/>
9500 <param name="use_ppm_tolerance" value="false"/>
9501 <param name="blacklist" value="true"/>
9502 </section>
9503 </section>
9504 <section name="feature">
9505 <param name="q" value=":"/>
9506 </section>
9507 <section name="consensus">
9508 <param name="map" value=""/>
9509 <param name="map_and" value="false"/>
9510 <section name="blackorwhitelist">
9511 <param name="blacklist" value="true"/>
9512 <param name="maps" value=""/>
9513 <param name="rt" value="60.0"/>
9514 <param name="mz" value="0.01"/>
9515 <param name="use_ppm_tolerance" value="false"/>
9516 </section>
9517 </section>
9518 <section name="f_and_c">
9519 <param name="charge" value=":"/>
9520 <param name="size" value=":"/>
9521 <param name="remove_meta" value=""/>
9522 </section>
9523 <section name="id">
9524 <param name="remove_clashes" value="false"/>
9525 <param name="keep_best_score_id" value="false"/>
9526 <param name="sequences_whitelist" value=""/>
9527 <param name="sequence_comparison_method" value="substring"/>
9528 <param name="accessions_whitelist" value=""/>
9529 <param name="remove_annotated_features" value="false"/>
9530 <param name="remove_unannotated_features" value="false"/>
9531 <param name="remove_unassigned_ids" value="false"/>
9532 <param name="rt" value="0.1"/>
9533 <param name="mz" value="0.001"/>
9534 <param name="blacklist_imperfect" value="false"/>
9535 </section>
9536 <section name="algorithm">
9537 <section name="SignalToNoise">
9538 <param name="max_intensity" value="-1"/>
9539 <param name="auto_max_stdev_factor" value="3.0"/>
9540 <param name="auto_max_percentile" value="95"/>
9541 <param name="auto_mode" value="0"/>
9542 <param name="win_len" value="200.0"/>
9543 <param name="bin_count" value="30"/>
9544 <param name="min_required_elements" value="10"/>
9545 <param name="noise_for_empty_window" value="1e+20"/>
9546 <param name="write_log_messages" value="true"/>
9547 </section>
9548 </section>
9549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9550 <output name="ctd_out" ftype="xml">
9551 <assert_contents>
9552 <is_valid_xml/>
9553 </assert_contents>
9554 </output>
9555 </test>
9556 <test expect_num_outputs="2">
9557 <conditional name="adv_opts_cond">
9558 <param name="adv_opts_selector" value="advanced"/>
9559 <param name="force" value="false"/>
9560 <param name="test" value="true"/>
9561 </conditional>
9562 <param name="in" value="FileFilter_43_input.mzML"/>
9563 <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9564 <param name="out_type" value="mzML"/>
9565 <param name="rt" value=":"/>
9566 <param name="mz" value=":"/>
9567 <param name="int" value=":"/>
9568 <param name="sort" value="false"/>
9569 <section name="peak_options">
9570 <param name="sn" value="0.0"/>
9571 <param name="rm_pc_charge" value=""/>
9572 <param name="pc_mz_range" value=":"/>
9573 <param name="pc_mz_list" value=""/>
9574 <param name="level" value="1 2 3"/>
9575 <param name="sort_peaks" value="false"/>
9576 <param name="no_chromatograms" value="false"/>
9577 <param name="remove_chromatograms" value="false"/>
9578 <param name="remove_empty" value="false"/>
9579 <param name="mz_precision" value="64"/>
9580 <param name="int_precision" value="32"/>
9581 <param name="indexed_file" value="true"/>
9582 <param name="zlib_compression" value="false"/>
9583 <section name="numpress">
9584 <param name="masstime" value="none"/>
9585 <param name="lossy_mass_accuracy" value="-1.0"/>
9586 <param name="intensity" value="none"/>
9587 <param name="float_da" value="none"/>
9588 </section>
9589 </section>
9590 <section name="spectra">
9591 <param name="remove_zoom" value="false"/>
9592 <param name="remove_mode" value=""/>
9593 <param name="remove_activation" value=""/>
9594 <param name="remove_collision_energy" value=":"/>
9595 <param name="remove_isolation_window_width" value=":"/>
9596 <param name="select_zoom" value="false"/>
9597 <param name="select_mode" value=""/>
9598 <param name="select_activation" value=""/>
9599 <param name="select_collision_energy" value=":"/>
9600 <param name="select_isolation_window_width" value=":"/>
9601 <param name="select_polarity" value=""/>
9602 <section name="blackorwhitelist">
9603 <param name="similarity_threshold" value="-1.0"/>
9604 <param name="rt" value="0.01"/>
9605 <param name="mz" value="0.01"/>
9606 <param name="use_ppm_tolerance" value="false"/>
9607 <param name="blacklist" value="true"/>
9608 </section>
9609 </section>
9610 <section name="feature">
9611 <param name="q" value=":"/>
9612 </section>
9613 <section name="consensus">
9614 <param name="map" value=""/>
9615 <param name="map_and" value="false"/>
9616 <section name="blackorwhitelist">
9617 <param name="blacklist" value="true"/>
9618 <param name="maps" value=""/>
9619 <param name="rt" value="60.0"/>
9620 <param name="mz" value="0.01"/>
9621 <param name="use_ppm_tolerance" value="false"/>
9622 </section>
9623 </section>
9624 <section name="f_and_c">
9625 <param name="charge" value=":"/>
9626 <param name="size" value=":"/>
9627 <param name="remove_meta" value=""/>
9628 </section>
9629 <section name="id">
9630 <param name="remove_clashes" value="false"/>
9631 <param name="keep_best_score_id" value="false"/>
9632 <param name="sequences_whitelist" value=""/>
9633 <param name="sequence_comparison_method" value="substring"/>
9634 <param name="accessions_whitelist" value=""/>
9635 <param name="remove_annotated_features" value="false"/>
9636 <param name="remove_unannotated_features" value="false"/>
9637 <param name="remove_unassigned_ids" value="false"/>
9638 <param name="rt" value="0.1"/>
9639 <param name="mz" value="0.001"/>
9640 <param name="blacklist_imperfect" value="false"/>
9641 </section>
9642 <section name="algorithm">
9643 <section name="SignalToNoise">
9644 <param name="max_intensity" value="-1"/>
9645 <param name="auto_max_stdev_factor" value="3.0"/>
9646 <param name="auto_max_percentile" value="95"/>
9647 <param name="auto_mode" value="0"/>
9648 <param name="win_len" value="200.0"/>
9649 <param name="bin_count" value="30"/>
9650 <param name="min_required_elements" value="10"/>
9651 <param name="noise_for_empty_window" value="1e+20"/>
9652 <param name="write_log_messages" value="true"/>
9653 </section>
9654 </section>
9655 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9656 <output name="ctd_out" ftype="xml">
9657 <assert_contents>
9658 <is_valid_xml/>
9659 </assert_contents>
9660 </output>
9661 </test>
9662 <test expect_num_outputs="2">
9663 <conditional name="adv_opts_cond">
9664 <param name="adv_opts_selector" value="advanced"/>
9665 <param name="force" value="false"/>
9666 <param name="test" value="true"/>
9667 </conditional>
9668 <param name="in" value="FileFilter_43.tmp.mzML"/>
9669 <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/>
9670 <param name="out_type" value="mzML"/>
9671 <param name="rt" value=":"/>
9672 <param name="mz" value=":"/>
9673 <param name="int" value=":"/>
9674 <param name="sort" value="false"/>
9675 <section name="peak_options">
9676 <param name="sn" value="0.0"/>
9677 <param name="rm_pc_charge" value=""/>
9678 <param name="pc_mz_range" value=":"/>
9679 <param name="pc_mz_list" value=""/>
9680 <param name="level" value="1 2 3"/>
9681 <param name="sort_peaks" value="false"/>
9682 <param name="no_chromatograms" value="false"/>
9683 <param name="remove_chromatograms" value="false"/>
9684 <param name="remove_empty" value="false"/>
9685 <param name="mz_precision" value="64"/>
9686 <param name="int_precision" value="32"/>
9687 <param name="indexed_file" value="true"/>
9688 <param name="zlib_compression" value="false"/>
9689 <section name="numpress">
9690 <param name="masstime" value="none"/>
9691 <param name="lossy_mass_accuracy" value="-1.0"/>
9692 <param name="intensity" value="none"/>
9693 <param name="float_da" value="none"/>
9694 </section>
9695 </section>
9696 <section name="spectra">
9697 <param name="remove_zoom" value="false"/>
9698 <param name="remove_mode" value=""/>
9699 <param name="remove_activation" value=""/>
9700 <param name="remove_collision_energy" value=":"/>
9701 <param name="remove_isolation_window_width" value=":"/>
9702 <param name="select_zoom" value="false"/>
9703 <param name="select_mode" value=""/>
9704 <param name="select_activation" value=""/>
9705 <param name="select_collision_energy" value=":"/>
9706 <param name="select_isolation_window_width" value=":"/>
9707 <param name="select_polarity" value=""/>
9708 <section name="blackorwhitelist">
9709 <param name="similarity_threshold" value="-1.0"/>
9710 <param name="rt" value="0.01"/>
9711 <param name="mz" value="0.01"/>
9712 <param name="use_ppm_tolerance" value="false"/>
9713 <param name="blacklist" value="true"/>
9714 </section>
9715 </section>
9716 <section name="feature">
9717 <param name="q" value=":"/>
9718 </section>
9719 <section name="consensus">
9720 <param name="map" value=""/>
9721 <param name="map_and" value="false"/>
9722 <section name="blackorwhitelist">
9723 <param name="blacklist" value="true"/>
9724 <param name="maps" value=""/>
9725 <param name="rt" value="60.0"/>
9726 <param name="mz" value="0.01"/>
9727 <param name="use_ppm_tolerance" value="false"/>
9728 </section>
9729 </section>
9730 <section name="f_and_c">
9731 <param name="charge" value=":"/>
9732 <param name="size" value=":"/>
9733 <param name="remove_meta" value=""/>
9734 </section>
9735 <section name="id">
9736 <param name="remove_clashes" value="false"/>
9737 <param name="keep_best_score_id" value="false"/>
9738 <param name="sequences_whitelist" value=""/>
9739 <param name="sequence_comparison_method" value="substring"/>
9740 <param name="accessions_whitelist" value=""/>
9741 <param name="remove_annotated_features" value="false"/>
9742 <param name="remove_unannotated_features" value="false"/>
9743 <param name="remove_unassigned_ids" value="false"/>
9744 <param name="rt" value="0.1"/>
9745 <param name="mz" value="0.001"/>
9746 <param name="blacklist_imperfect" value="false"/>
9747 </section>
9748 <section name="algorithm">
9749 <section name="SignalToNoise">
9750 <param name="max_intensity" value="-1"/>
9751 <param name="auto_max_stdev_factor" value="3.0"/>
9752 <param name="auto_max_percentile" value="95"/>
9753 <param name="auto_mode" value="0"/>
9754 <param name="win_len" value="200.0"/>
9755 <param name="bin_count" value="30"/>
9756 <param name="min_required_elements" value="10"/>
9757 <param name="noise_for_empty_window" value="1e+20"/>
9758 <param name="write_log_messages" value="true"/>
9759 </section>
9760 </section>
9761 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9762 <output name="ctd_out" ftype="xml">
9763 <assert_contents>
9764 <is_valid_xml/>
9765 </assert_contents>
9766 </output>
9767 </test>
9768 <test expect_num_outputs="2">
9769 <conditional name="adv_opts_cond">
9770 <param name="adv_opts_selector" value="advanced"/>
9771 <param name="force" value="false"/>
9772 <param name="test" value="true"/>
9773 </conditional>
9774 <param name="in" value="FileFilter_44_input.mzML"/>
9775 <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9776 <param name="out_type" value="mzML"/>
9777 <param name="rt" value=":"/>
9778 <param name="mz" value=":"/>
9779 <param name="int" value=":"/>
9780 <param name="sort" value="false"/>
9781 <section name="peak_options">
9782 <param name="sn" value="0.0"/>
9783 <param name="rm_pc_charge" value=""/>
9784 <param name="pc_mz_range" value=":"/>
9785 <param name="pc_mz_list" value=""/>
9786 <param name="level" value="1 2 3"/>
9787 <param name="sort_peaks" value="false"/>
9788 <param name="no_chromatograms" value="false"/>
9789 <param name="remove_chromatograms" value="false"/>
9790 <param name="remove_empty" value="false"/>
9791 <param name="mz_precision" value="64"/>
9792 <param name="int_precision" value="32"/>
9793 <param name="indexed_file" value="true"/>
9794 <param name="zlib_compression" value="false"/>
9795 <section name="numpress">
9796 <param name="masstime" value="none"/>
9797 <param name="lossy_mass_accuracy" value="-1.0"/>
9798 <param name="intensity" value="none"/>
9799 <param name="float_da" value="none"/>
9800 </section>
9801 </section>
9802 <section name="spectra">
9803 <param name="remove_zoom" value="false"/>
9804 <param name="remove_mode" value=""/>
9805 <param name="remove_activation" value=""/>
9806 <param name="remove_collision_energy" value=":"/>
9807 <param name="remove_isolation_window_width" value=":"/>
9808 <param name="select_zoom" value="false"/>
9809 <param name="select_mode" value=""/>
9810 <param name="select_activation" value=""/>
9811 <param name="select_collision_energy" value=":"/>
9812 <param name="select_isolation_window_width" value=":"/>
9813 <param name="select_polarity" value=""/>
9814 <section name="blackorwhitelist">
9815 <param name="similarity_threshold" value="-1.0"/>
9816 <param name="rt" value="0.01"/>
9817 <param name="mz" value="0.01"/>
9818 <param name="use_ppm_tolerance" value="false"/>
9819 <param name="blacklist" value="true"/>
9820 </section>
9821 </section>
9822 <section name="feature">
9823 <param name="q" value=":"/>
9824 </section>
9825 <section name="consensus">
9826 <param name="map" value=""/>
9827 <param name="map_and" value="false"/>
9828 <section name="blackorwhitelist">
9829 <param name="blacklist" value="true"/>
9830 <param name="maps" value=""/>
9831 <param name="rt" value="60.0"/>
9832 <param name="mz" value="0.01"/>
9833 <param name="use_ppm_tolerance" value="false"/>
9834 </section>
9835 </section>
9836 <section name="f_and_c">
9837 <param name="charge" value=":"/>
9838 <param name="size" value=":"/>
9839 <param name="remove_meta" value=""/>
9840 </section>
9841 <section name="id">
9842 <param name="remove_clashes" value="false"/>
9843 <param name="keep_best_score_id" value="false"/>
9844 <param name="sequences_whitelist" value=""/>
9845 <param name="sequence_comparison_method" value="substring"/>
9846 <param name="accessions_whitelist" value=""/>
9847 <param name="remove_annotated_features" value="false"/>
9848 <param name="remove_unannotated_features" value="false"/>
9849 <param name="remove_unassigned_ids" value="false"/>
9850 <param name="rt" value="0.1"/>
9851 <param name="mz" value="0.001"/>
9852 <param name="blacklist_imperfect" value="false"/>
9853 </section>
9854 <section name="algorithm">
9855 <section name="SignalToNoise">
9856 <param name="max_intensity" value="-1"/>
9857 <param name="auto_max_stdev_factor" value="3.0"/>
9858 <param name="auto_max_percentile" value="95"/>
9859 <param name="auto_mode" value="0"/>
9860 <param name="win_len" value="200.0"/>
9861 <param name="bin_count" value="30"/>
9862 <param name="min_required_elements" value="10"/>
9863 <param name="noise_for_empty_window" value="1e+20"/>
9864 <param name="write_log_messages" value="true"/>
9865 </section>
9866 </section>
9867 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9868 <output name="ctd_out" ftype="xml">
9869 <assert_contents>
9870 <is_valid_xml/>
9871 </assert_contents>
9872 </output>
9873 </test>
9874 <test expect_num_outputs="2">
9875 <conditional name="adv_opts_cond">
9876 <param name="adv_opts_selector" value="advanced"/>
9877 <param name="force" value="false"/>
9878 <param name="test" value="true"/>
9879 </conditional>
9880 <param name="in" value="FileFilter_45_input.featureXML"/>
9881 <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
9882 <param name="out_type" value="featurexml"/>
9883 <param name="rt" value=":"/>
9884 <param name="mz" value=":"/>
9885 <param name="int" value=":"/>
9886 <param name="sort" value="false"/>
9887 <section name="peak_options">
9888 <param name="sn" value="0.0"/>
9889 <param name="rm_pc_charge" value=""/>
9890 <param name="pc_mz_range" value=":"/>
9891 <param name="pc_mz_list" value=""/>
9892 <param name="level" value="1 2 3"/>
9893 <param name="sort_peaks" value="false"/>
9894 <param name="no_chromatograms" value="false"/>
9895 <param name="remove_chromatograms" value="false"/>
9896 <param name="remove_empty" value="false"/>
9897 <param name="mz_precision" value="64"/>
9898 <param name="int_precision" value="32"/>
9899 <param name="indexed_file" value="true"/>
9900 <param name="zlib_compression" value="false"/>
9901 <section name="numpress">
9902 <param name="masstime" value="none"/>
9903 <param name="lossy_mass_accuracy" value="-1.0"/>
9904 <param name="intensity" value="none"/>
9905 <param name="float_da" value="none"/>
9906 </section>
9907 </section>
9908 <section name="spectra">
9909 <param name="remove_zoom" value="false"/>
9910 <param name="remove_mode" value=""/>
9911 <param name="remove_activation" value=""/>
9912 <param name="remove_collision_energy" value=":"/>
9913 <param name="remove_isolation_window_width" value=":"/>
9914 <param name="select_zoom" value="false"/>
9915 <param name="select_mode" value=""/>
9916 <param name="select_activation" value=""/>
9917 <param name="select_collision_energy" value=":"/>
9918 <param name="select_isolation_window_width" value=":"/>
9919 <param name="select_polarity" value=""/>
9920 <section name="blackorwhitelist">
9921 <param name="similarity_threshold" value="-1.0"/>
9922 <param name="rt" value="0.01"/>
9923 <param name="mz" value="0.01"/>
9924 <param name="use_ppm_tolerance" value="false"/>
9925 <param name="blacklist" value="true"/>
9926 </section>
9927 </section>
9928 <section name="feature">
9929 <param name="q" value=":"/>
9930 </section>
9931 <section name="consensus">
9932 <param name="map" value=""/>
9933 <param name="map_and" value="false"/>
9934 <section name="blackorwhitelist">
9935 <param name="blacklist" value="true"/>
9936 <param name="maps" value=""/>
9937 <param name="rt" value="60.0"/>
9938 <param name="mz" value="0.01"/>
9939 <param name="use_ppm_tolerance" value="false"/>
9940 </section>
9941 </section>
9942 <section name="f_and_c">
9943 <param name="charge" value=":"/>
9944 <param name="size" value=":"/>
9945 <param name="remove_meta" value=""/>
9946 </section>
9947 <section name="id">
9948 <param name="remove_clashes" value="false"/>
9949 <param name="keep_best_score_id" value="false"/>
9950 <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
9951 <param name="sequence_comparison_method" value="substring"/>
9952 <param name="accessions_whitelist" value=""/>
9953 <param name="remove_annotated_features" value="false"/>
9954 <param name="remove_unannotated_features" value="false"/>
9955 <param name="remove_unassigned_ids" value="false"/>
9956 <param name="rt" value="0.1"/>
9957 <param name="mz" value="0.001"/>
9958 <param name="blacklist_imperfect" value="false"/>
9959 </section>
9960 <section name="algorithm">
9961 <section name="SignalToNoise">
9962 <param name="max_intensity" value="-1"/>
9963 <param name="auto_max_stdev_factor" value="3.0"/>
9964 <param name="auto_max_percentile" value="95"/>
9965 <param name="auto_mode" value="0"/>
9966 <param name="win_len" value="200.0"/>
9967 <param name="bin_count" value="30"/>
9968 <param name="min_required_elements" value="10"/>
9969 <param name="noise_for_empty_window" value="1e+20"/>
9970 <param name="write_log_messages" value="true"/>
9971 </section>
9972 </section>
9973 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9974 <output name="ctd_out" ftype="xml">
9975 <assert_contents>
9976 <is_valid_xml/>
9977 </assert_contents>
9978 </output>
9979 </test>
9980 <test expect_num_outputs="2">
9981 <conditional name="adv_opts_cond">
9982 <param name="adv_opts_selector" value="advanced"/>
9983 <param name="force" value="false"/>
9984 <param name="test" value="true"/>
9985 </conditional>
9986 <param name="in" value="FileFilter_46_input.featureXML"/>
9987 <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
9988 <param name="out_type" value="featurexml"/>
9989 <param name="rt" value=":"/>
9990 <param name="mz" value=":"/>
9991 <param name="int" value=":"/>
9992 <param name="sort" value="false"/>
9993 <section name="peak_options">
9994 <param name="sn" value="0.0"/>
9995 <param name="rm_pc_charge" value=""/>
9996 <param name="pc_mz_range" value=":"/>
9997 <param name="pc_mz_list" value=""/>
9998 <param name="level" value="1 2 3"/>
9999 <param name="sort_peaks" value="false"/>
10000 <param name="no_chromatograms" value="false"/>
10001 <param name="remove_chromatograms" value="false"/>
10002 <param name="remove_empty" value="false"/>
10003 <param name="mz_precision" value="64"/>
10004 <param name="int_precision" value="32"/>
10005 <param name="indexed_file" value="true"/>
10006 <param name="zlib_compression" value="false"/>
10007 <section name="numpress">
10008 <param name="masstime" value="none"/>
10009 <param name="lossy_mass_accuracy" value="-1.0"/>
10010 <param name="intensity" value="none"/>
10011 <param name="float_da" value="none"/>
10012 </section>
10013 </section>
10014 <section name="spectra">
10015 <param name="remove_zoom" value="false"/>
10016 <param name="remove_mode" value=""/>
10017 <param name="remove_activation" value=""/>
10018 <param name="remove_collision_energy" value=":"/>
10019 <param name="remove_isolation_window_width" value=":"/>
10020 <param name="select_zoom" value="false"/>
10021 <param name="select_mode" value=""/>
10022 <param name="select_activation" value=""/>
10023 <param name="select_collision_energy" value=":"/>
10024 <param name="select_isolation_window_width" value=":"/>
10025 <param name="select_polarity" value=""/>
10026 <section name="blackorwhitelist">
10027 <param name="similarity_threshold" value="-1.0"/>
10028 <param name="rt" value="0.01"/>
10029 <param name="mz" value="0.01"/>
10030 <param name="use_ppm_tolerance" value="false"/>
10031 <param name="blacklist" value="true"/>
10032 </section>
10033 </section>
10034 <section name="feature">
10035 <param name="q" value=":"/>
10036 </section>
10037 <section name="consensus">
10038 <param name="map" value=""/>
10039 <param name="map_and" value="false"/>
10040 <section name="blackorwhitelist">
10041 <param name="blacklist" value="true"/>
10042 <param name="maps" value=""/>
10043 <param name="rt" value="60.0"/>
10044 <param name="mz" value="0.01"/>
10045 <param name="use_ppm_tolerance" value="false"/>
10046 </section>
10047 </section>
10048 <section name="f_and_c">
10049 <param name="charge" value=":"/>
10050 <param name="size" value=":"/>
10051 <param name="remove_meta" value=""/>
10052 </section>
10053 <section name="id">
10054 <param name="remove_clashes" value="false"/>
10055 <param name="keep_best_score_id" value="false"/>
10056 <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
10057 <param name="sequence_comparison_method" value="exact"/>
10058 <param name="accessions_whitelist" value=""/>
10059 <param name="remove_annotated_features" value="false"/>
10060 <param name="remove_unannotated_features" value="false"/>
10061 <param name="remove_unassigned_ids" value="false"/>
10062 <param name="rt" value="0.1"/>
10063 <param name="mz" value="0.001"/>
10064 <param name="blacklist_imperfect" value="false"/>
10065 </section>
10066 <section name="algorithm">
10067 <section name="SignalToNoise">
10068 <param name="max_intensity" value="-1"/>
10069 <param name="auto_max_stdev_factor" value="3.0"/>
10070 <param name="auto_max_percentile" value="95"/>
10071 <param name="auto_mode" value="0"/>
10072 <param name="win_len" value="200.0"/>
10073 <param name="bin_count" value="30"/>
10074 <param name="min_required_elements" value="10"/>
10075 <param name="noise_for_empty_window" value="1e+20"/>
10076 <param name="write_log_messages" value="true"/>
10077 </section>
10078 </section>
10079 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10080 <output name="ctd_out" ftype="xml">
10081 <assert_contents>
10082 <is_valid_xml/>
10083 </assert_contents>
10084 </output>
10085 </test>
10086 <test expect_num_outputs="2">
10087 <conditional name="adv_opts_cond">
10088 <param name="adv_opts_selector" value="advanced"/>
10089 <param name="force" value="false"/>
10090 <param name="test" value="true"/>
10091 </conditional>
10092 <param name="in" value="FileFilter_47_input.mzML"/>
10093 <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10094 <param name="out_type" value="mzml"/>
10095 <param name="rt" value=":"/>
10096 <param name="mz" value=":"/>
10097 <param name="int" value=":"/>
10098 <param name="sort" value="false"/>
10099 <section name="peak_options">
10100 <param name="sn" value="0.0"/>
10101 <param name="rm_pc_charge" value=""/>
10102 <param name="pc_mz_range" value=":"/>
10103 <param name="pc_mz_list" value=""/>
10104 <param name="level" value="1 2 3"/>
10105 <param name="sort_peaks" value="false"/>
10106 <param name="no_chromatograms" value="false"/>
10107 <param name="remove_chromatograms" value="false"/>
10108 <param name="remove_empty" value="false"/>
10109 <param name="mz_precision" value="64"/>
10110 <param name="int_precision" value="32"/>
10111 <param name="indexed_file" value="true"/>
10112 <param name="zlib_compression" value="false"/>
10113 <section name="numpress">
10114 <param name="masstime" value="none"/>
10115 <param name="lossy_mass_accuracy" value="-1.0"/>
10116 <param name="intensity" value="none"/>
10117 <param name="float_da" value="none"/>
10118 </section>
10119 </section>
10120 <section name="spectra">
10121 <param name="remove_zoom" value="false"/>
10122 <param name="remove_mode" value=""/>
10123 <param name="remove_activation" value=""/>
10124 <param name="remove_collision_energy" value=":"/>
10125 <param name="remove_isolation_window_width" value=":"/>
10126 <param name="select_zoom" value="false"/>
10127 <param name="select_mode" value=""/>
10128 <param name="select_activation" value=""/>
10129 <param name="select_collision_energy" value=":"/>
10130 <param name="select_isolation_window_width" value=":"/>
10131 <param name="select_polarity" value=""/>
10132 <section name="blackorwhitelist">
10133 <param name="file" value="FileFilter_47_input_select.mzML"/>
10134 <param name="similarity_threshold" value="0.9"/>
10135 <param name="rt" value="0.01"/>
10136 <param name="mz" value="0.01"/>
10137 <param name="use_ppm_tolerance" value="false"/>
10138 <param name="blacklist" value="true"/>
10139 </section>
10140 </section>
10141 <section name="feature">
10142 <param name="q" value=":"/>
10143 </section>
10144 <section name="consensus">
10145 <param name="map" value=""/>
10146 <param name="map_and" value="false"/>
10147 <section name="blackorwhitelist">
10148 <param name="blacklist" value="true"/>
10149 <param name="maps" value=""/>
10150 <param name="rt" value="60.0"/>
10151 <param name="mz" value="0.01"/>
10152 <param name="use_ppm_tolerance" value="false"/>
10153 </section>
10154 </section>
10155 <section name="f_and_c">
10156 <param name="charge" value=":"/>
10157 <param name="size" value=":"/>
10158 <param name="remove_meta" value=""/>
10159 </section>
10160 <section name="id">
10161 <param name="remove_clashes" value="false"/>
10162 <param name="keep_best_score_id" value="false"/>
10163 <param name="sequences_whitelist" value=""/>
10164 <param name="sequence_comparison_method" value="substring"/>
10165 <param name="accessions_whitelist" value=""/>
10166 <param name="remove_annotated_features" value="false"/>
10167 <param name="remove_unannotated_features" value="false"/>
10168 <param name="remove_unassigned_ids" value="false"/>
10169 <param name="rt" value="0.1"/>
10170 <param name="mz" value="0.001"/>
10171 <param name="blacklist_imperfect" value="false"/>
10172 </section>
10173 <section name="algorithm">
10174 <section name="SignalToNoise">
10175 <param name="max_intensity" value="-1"/>
10176 <param name="auto_max_stdev_factor" value="3.0"/>
10177 <param name="auto_max_percentile" value="95"/>
10178 <param name="auto_mode" value="0"/>
10179 <param name="win_len" value="200.0"/>
10180 <param name="bin_count" value="30"/>
10181 <param name="min_required_elements" value="10"/>
10182 <param name="noise_for_empty_window" value="1e+20"/>
10183 <param name="write_log_messages" value="true"/>
10184 </section>
10185 </section>
10186 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10187 <output name="ctd_out" ftype="xml">
10188 <assert_contents>
10189 <is_valid_xml/>
10190 </assert_contents>
10191 </output>
10192 </test>
10193 <test expect_num_outputs="2">
10194 <conditional name="adv_opts_cond">
10195 <param name="adv_opts_selector" value="advanced"/>
10196 <param name="force" value="false"/>
10197 <param name="test" value="true"/>
10198 </conditional>
10199 <param name="in" value="FileFilter_47_input.mzML"/>
10200 <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10201 <param name="out_type" value="mzml"/>
10202 <param name="rt" value=":"/>
10203 <param name="mz" value=":"/>
10204 <param name="int" value=":"/>
10205 <param name="sort" value="false"/>
10206 <section name="peak_options">
10207 <param name="sn" value="0.0"/>
10208 <param name="rm_pc_charge" value=""/>
10209 <param name="pc_mz_range" value=":"/>
10210 <param name="pc_mz_list" value=""/>
10211 <param name="level" value="1 2 3"/>
10212 <param name="sort_peaks" value="false"/>
10213 <param name="no_chromatograms" value="false"/>
10214 <param name="remove_chromatograms" value="false"/>
10215 <param name="remove_empty" value="false"/>
10216 <param name="mz_precision" value="64"/>
10217 <param name="int_precision" value="32"/>
10218 <param name="indexed_file" value="true"/>
10219 <param name="zlib_compression" value="false"/>
10220 <section name="numpress">
10221 <param name="masstime" value="none"/>
10222 <param name="lossy_mass_accuracy" value="-1.0"/>
10223 <param name="intensity" value="none"/>
10224 <param name="float_da" value="none"/>
10225 </section>
10226 </section>
10227 <section name="spectra">
10228 <param name="remove_zoom" value="false"/>
10229 <param name="remove_mode" value=""/>
10230 <param name="remove_activation" value=""/>
10231 <param name="remove_collision_energy" value=":"/>
10232 <param name="remove_isolation_window_width" value=":"/>
10233 <param name="select_zoom" value="false"/>
10234 <param name="select_mode" value=""/>
10235 <param name="select_activation" value=""/>
10236 <param name="select_collision_energy" value=":"/>
10237 <param name="select_isolation_window_width" value=":"/>
10238 <param name="select_polarity" value=""/>
10239 <section name="blackorwhitelist">
10240 <param name="file" value="FileFilter_47_input_select.mzML"/>
10241 <param name="similarity_threshold" value="0.9"/>
10242 <param name="rt" value="0.01"/>
10243 <param name="mz" value="0.01"/>
10244 <param name="use_ppm_tolerance" value="false"/>
10245 <param name="blacklist" value="false"/>
10246 </section>
10247 </section>
10248 <section name="feature">
10249 <param name="q" value=":"/>
10250 </section>
10251 <section name="consensus">
10252 <param name="map" value=""/>
10253 <param name="map_and" value="false"/>
10254 <section name="blackorwhitelist">
10255 <param name="blacklist" value="true"/>
10256 <param name="maps" value=""/>
10257 <param name="rt" value="60.0"/>
10258 <param name="mz" value="0.01"/>
10259 <param name="use_ppm_tolerance" value="false"/>
10260 </section>
10261 </section>
10262 <section name="f_and_c">
10263 <param name="charge" value=":"/>
10264 <param name="size" value=":"/>
10265 <param name="remove_meta" value=""/>
10266 </section>
10267 <section name="id">
10268 <param name="remove_clashes" value="false"/>
10269 <param name="keep_best_score_id" value="false"/>
10270 <param name="sequences_whitelist" value=""/>
10271 <param name="sequence_comparison_method" value="substring"/>
10272 <param name="accessions_whitelist" value=""/>
10273 <param name="remove_annotated_features" value="false"/>
10274 <param name="remove_unannotated_features" value="false"/>
10275 <param name="remove_unassigned_ids" value="false"/>
10276 <param name="rt" value="0.1"/>
10277 <param name="mz" value="0.001"/>
10278 <param name="blacklist_imperfect" value="false"/>
10279 </section>
10280 <section name="algorithm">
10281 <section name="SignalToNoise">
10282 <param name="max_intensity" value="-1"/>
10283 <param name="auto_max_stdev_factor" value="3.0"/>
10284 <param name="auto_max_percentile" value="95"/>
10285 <param name="auto_mode" value="0"/>
10286 <param name="win_len" value="200.0"/>
10287 <param name="bin_count" value="30"/>
10288 <param name="min_required_elements" value="10"/>
10289 <param name="noise_for_empty_window" value="1e+20"/>
10290 <param name="write_log_messages" value="true"/>
10291 </section>
10292 </section>
10293 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10294 <output name="ctd_out" ftype="xml">
10295 <assert_contents>
10296 <is_valid_xml/>
10297 </assert_contents>
10298 </output>
10299 </test>
10300 <test expect_num_outputs="2">
10301 <conditional name="adv_opts_cond">
10302 <param name="adv_opts_selector" value="advanced"/>
10303 <param name="force" value="false"/>
10304 <param name="test" value="true"/>
10305 </conditional>
10306 <param name="in" value="FileFilter_49_input.mzML"/>
10307 <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10308 <param name="out_type" value="mzml"/>
10309 <param name="rt" value=":"/>
10310 <param name="mz" value=":"/>
10311 <param name="int" value=":"/>
10312 <param name="sort" value="false"/>
10313 <section name="peak_options">
10314 <param name="sn" value="0.0"/>
10315 <param name="rm_pc_charge" value=""/>
10316 <param name="pc_mz_range" value=":"/>
10317 <param name="pc_mz_list" value=""/>
10318 <param name="level" value="1 2 3"/>
10319 <param name="sort_peaks" value="false"/>
10320 <param name="no_chromatograms" value="false"/>
10321 <param name="remove_chromatograms" value="false"/>
10322 <param name="remove_empty" value="false"/>
10323 <param name="mz_precision" value="64"/>
10324 <param name="int_precision" value="32"/>
10325 <param name="indexed_file" value="true"/>
10326 <param name="zlib_compression" value="true"/>
10327 <section name="numpress">
10328 <param name="masstime" value="linear"/>
10329 <param name="lossy_mass_accuracy" value="-1.0"/>
10330 <param name="intensity" value="pic"/>
10331 <param name="float_da" value="slof"/>
10332 </section>
10333 </section>
10334 <section name="spectra">
10335 <param name="remove_zoom" value="false"/>
10336 <param name="remove_mode" value=""/>
10337 <param name="remove_activation" value=""/>
10338 <param name="remove_collision_energy" value=":"/>
10339 <param name="remove_isolation_window_width" value=":"/>
10340 <param name="select_zoom" value="false"/>
10341 <param name="select_mode" value=""/>
10342 <param name="select_activation" value=""/>
10343 <param name="select_collision_energy" value=":"/>
10344 <param name="select_isolation_window_width" value=":"/>
10345 <param name="select_polarity" value=""/>
10346 <section name="blackorwhitelist">
10347 <param name="similarity_threshold" value="-1.0"/>
10348 <param name="rt" value="0.01"/>
10349 <param name="mz" value="0.01"/>
10350 <param name="use_ppm_tolerance" value="false"/>
10351 <param name="blacklist" value="true"/>
10352 </section>
10353 </section>
10354 <section name="feature">
10355 <param name="q" value=":"/>
10356 </section>
10357 <section name="consensus">
10358 <param name="map" value=""/>
10359 <param name="map_and" value="false"/>
10360 <section name="blackorwhitelist">
10361 <param name="blacklist" value="true"/>
10362 <param name="maps" value=""/>
10363 <param name="rt" value="60.0"/>
10364 <param name="mz" value="0.01"/>
10365 <param name="use_ppm_tolerance" value="false"/>
10366 </section>
10367 </section>
10368 <section name="f_and_c">
10369 <param name="charge" value=":"/>
10370 <param name="size" value=":"/>
10371 <param name="remove_meta" value=""/>
10372 </section>
10373 <section name="id">
10374 <param name="remove_clashes" value="false"/>
10375 <param name="keep_best_score_id" value="false"/>
10376 <param name="sequences_whitelist" value=""/>
10377 <param name="sequence_comparison_method" value="substring"/>
10378 <param name="accessions_whitelist" value=""/>
10379 <param name="remove_annotated_features" value="false"/>
10380 <param name="remove_unannotated_features" value="false"/>
10381 <param name="remove_unassigned_ids" value="false"/>
10382 <param name="rt" value="0.1"/>
10383 <param name="mz" value="0.001"/>
10384 <param name="blacklist_imperfect" value="false"/>
10385 </section>
10386 <section name="algorithm">
10387 <section name="SignalToNoise">
10388 <param name="max_intensity" value="-1"/>
10389 <param name="auto_max_stdev_factor" value="3.0"/>
10390 <param name="auto_max_percentile" value="95"/>
10391 <param name="auto_mode" value="0"/>
10392 <param name="win_len" value="200.0"/>
10393 <param name="bin_count" value="30"/>
10394 <param name="min_required_elements" value="10"/>
10395 <param name="noise_for_empty_window" value="1e+20"/>
10396 <param name="write_log_messages" value="true"/>
10397 </section>
10398 </section>
10399 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10400 <output name="ctd_out" ftype="xml">
10401 <assert_contents>
10402 <is_valid_xml/>
10403 </assert_contents>
10404 </output>
10405 </test>
10406 </xml>
10407 <xml name="autotest_FileInfo">
10408 <test expect_num_outputs="2">
10409 <conditional name="adv_opts_cond">
10410 <param name="adv_opts_selector" value="advanced"/>
10411 <param name="force" value="false"/>
10412 <param name="test" value="true"/>
10413 </conditional>
10414 <param name="in" value="FileInfo_1_input.dta" ftype="dta"/>
10415 <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10416 <param name="m" value="false"/>
10417 <param name="p" value="false"/>
10418 <param name="s" value="false"/>
10419 <param name="d" value="false"/>
10420 <param name="c" value="false"/>
10421 <param name="v" value="false"/>
10422 <param name="i" value="false"/>
10423 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10424 <output name="ctd_out" ftype="xml">
10425 <assert_contents>
10426 <is_valid_xml/>
10427 </assert_contents>
10428 </output>
10429 </test>
10430 <test expect_num_outputs="2">
10431 <conditional name="adv_opts_cond">
10432 <param name="adv_opts_selector" value="advanced"/>
10433 <param name="force" value="false"/>
10434 <param name="test" value="true"/>
10435 </conditional>
10436 <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/>
10437 <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10438 <param name="m" value="false"/>
10439 <param name="p" value="false"/>
10440 <param name="s" value="false"/>
10441 <param name="d" value="false"/>
10442 <param name="c" value="false"/>
10443 <param name="v" value="false"/>
10444 <param name="i" value="false"/>
10445 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10446 <output name="ctd_out" ftype="xml">
10447 <assert_contents>
10448 <is_valid_xml/>
10449 </assert_contents>
10450 </output>
10451 </test>
10452 <test expect_num_outputs="2">
10453 <conditional name="adv_opts_cond">
10454 <param name="adv_opts_selector" value="advanced"/>
10455 <param name="force" value="false"/>
10456 <param name="test" value="true"/>
10457 </conditional>
10458 <param name="in" value="FileInfo_3_input.featureXML"/>
10459 <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10460 <param name="m" value="true"/>
10461 <param name="p" value="true"/>
10462 <param name="s" value="true"/>
10463 <param name="d" value="false"/>
10464 <param name="c" value="false"/>
10465 <param name="v" value="false"/>
10466 <param name="i" value="false"/>
10467 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10468 <output name="ctd_out" ftype="xml">
10469 <assert_contents>
10470 <is_valid_xml/>
10471 </assert_contents>
10472 </output>
10473 </test>
10474 <test expect_num_outputs="2">
10475 <conditional name="adv_opts_cond">
10476 <param name="adv_opts_selector" value="advanced"/>
10477 <param name="force" value="false"/>
10478 <param name="test" value="true"/>
10479 </conditional>
10480 <param name="in" value="FileInfo_4_input.mzXML"/>
10481 <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10482 <param name="m" value="true"/>
10483 <param name="p" value="false"/>
10484 <param name="s" value="false"/>
10485 <param name="d" value="false"/>
10486 <param name="c" value="false"/>
10487 <param name="v" value="false"/>
10488 <param name="i" value="false"/>
10489 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10490 <output name="ctd_out" ftype="xml">
10491 <assert_contents>
10492 <is_valid_xml/>
10493 </assert_contents>
10494 </output>
10495 </test>
10496 <test expect_num_outputs="2">
10497 <conditional name="adv_opts_cond">
10498 <param name="adv_opts_selector" value="advanced"/>
10499 <param name="force" value="false"/>
10500 <param name="test" value="true"/>
10501 </conditional>
10502 <param name="in" value="FileInfo_5_input.mzDat"/>
10503 <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10504 <param name="m" value="true"/>
10505 <param name="p" value="false"/>
10506 <param name="s" value="true"/>
10507 <param name="d" value="false"/>
10508 <param name="c" value="false"/>
10509 <param name="v" value="false"/>
10510 <param name="i" value="false"/>
10511 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10512 <output name="ctd_out" ftype="xml">
10513 <assert_contents>
10514 <is_valid_xml/>
10515 </assert_contents>
10516 </output>
10517 </test>
10518 <test expect_num_outputs="2">
10519 <conditional name="adv_opts_cond">
10520 <param name="adv_opts_selector" value="advanced"/>
10521 <param name="force" value="false"/>
10522 <param name="test" value="true"/>
10523 </conditional>
10524 <param name="in" value="FileInfo_6_input.mzData"/>
10525 <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10526 <param name="m" value="false"/>
10527 <param name="p" value="false"/>
10528 <param name="s" value="true"/>
10529 <param name="d" value="true"/>
10530 <param name="c" value="false"/>
10531 <param name="v" value="false"/>
10532 <param name="i" value="false"/>
10533 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10534 <output name="ctd_out" ftype="xml">
10535 <assert_contents>
10536 <is_valid_xml/>
10537 </assert_contents>
10538 </output>
10539 </test>
10540 <test expect_num_outputs="2">
10541 <conditional name="adv_opts_cond">
10542 <param name="adv_opts_selector" value="advanced"/>
10543 <param name="force" value="false"/>
10544 <param name="test" value="true"/>
10545 </conditional>
10546 <param name="in" value="FileInfo_7_input.consensusXML"/>
10547 <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10548 <param name="m" value="true"/>
10549 <param name="p" value="true"/>
10550 <param name="s" value="true"/>
10551 <param name="d" value="false"/>
10552 <param name="c" value="false"/>
10553 <param name="v" value="false"/>
10554 <param name="i" value="false"/>
10555 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10556 <output name="ctd_out" ftype="xml">
10557 <assert_contents>
10558 <is_valid_xml/>
10559 </assert_contents>
10560 </output>
10561 </test>
10562 <test expect_num_outputs="2">
10563 <conditional name="adv_opts_cond">
10564 <param name="adv_opts_selector" value="advanced"/>
10565 <param name="force" value="false"/>
10566 <param name="test" value="true"/>
10567 </conditional>
10568 <param name="in" value="FileInfo_9_input.mzML"/>
10569 <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10570 <param name="m" value="true"/>
10571 <param name="p" value="true"/>
10572 <param name="s" value="true"/>
10573 <param name="d" value="false"/>
10574 <param name="c" value="false"/>
10575 <param name="v" value="false"/>
10576 <param name="i" value="false"/>
10577 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10578 <output name="ctd_out" ftype="xml">
10579 <assert_contents>
10580 <is_valid_xml/>
10581 </assert_contents>
10582 </output>
10583 </test>
10584 <test expect_num_outputs="2">
10585 <conditional name="adv_opts_cond">
10586 <param name="adv_opts_selector" value="advanced"/>
10587 <param name="force" value="false"/>
10588 <param name="test" value="true"/>
10589 </conditional>
10590 <param name="in" value="FileInfo_10_input.idXML"/>
10591 <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10592 <param name="m" value="false"/>
10593 <param name="p" value="false"/>
10594 <param name="s" value="false"/>
10595 <param name="d" value="false"/>
10596 <param name="c" value="false"/>
10597 <param name="v" value="false"/>
10598 <param name="i" value="false"/>
10599 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10600 <output name="ctd_out" ftype="xml">
10601 <assert_contents>
10602 <is_valid_xml/>
10603 </assert_contents>
10604 </output>
10605 </test>
10606 <test expect_num_outputs="2">
10607 <conditional name="adv_opts_cond">
10608 <param name="adv_opts_selector" value="advanced"/>
10609 <param name="force" value="false"/>
10610 <param name="test" value="true"/>
10611 </conditional>
10612 <param name="in" value="FileInfo_12_input.mzML"/>
10613 <param name="m" value="false"/>
10614 <param name="p" value="false"/>
10615 <param name="s" value="false"/>
10616 <param name="d" value="false"/>
10617 <param name="c" value="false"/>
10618 <param name="v" value="false"/>
10619 <param name="i" value="true"/>
10620 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10621 <output name="ctd_out" ftype="xml">
10622 <assert_contents>
10623 <is_valid_xml/>
10624 </assert_contents>
10625 </output>
10626 </test>
10627 <test expect_num_outputs="2">
10628 <conditional name="adv_opts_cond">
10629 <param name="adv_opts_selector" value="advanced"/>
10630 <param name="force" value="false"/>
10631 <param name="test" value="true"/>
10632 </conditional>
10633 <param name="in" value="FileInfo_13_input.consensusXML"/>
10634 <param name="m" value="false"/>
10635 <param name="p" value="false"/>
10636 <param name="s" value="false"/>
10637 <param name="d" value="false"/>
10638 <param name="c" value="false"/>
10639 <param name="v" value="false"/>
10640 <param name="i" value="false"/>
10641 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10642 <output name="ctd_out" ftype="xml">
10643 <assert_contents>
10644 <is_valid_xml/>
10645 </assert_contents>
10646 </output>
10647 </test>
10648 <test expect_num_outputs="2">
10649 <conditional name="adv_opts_cond">
10650 <param name="adv_opts_selector" value="advanced"/>
10651 <param name="force" value="false"/>
10652 <param name="test" value="true"/>
10653 </conditional>
10654 <param name="in" value="FileInfo_14_input.mzid"/>
10655 <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10656 <param name="m" value="false"/>
10657 <param name="p" value="false"/>
10658 <param name="s" value="false"/>
10659 <param name="d" value="false"/>
10660 <param name="c" value="false"/>
10661 <param name="v" value="true"/>
10662 <param name="i" value="false"/>
10663 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10664 <output name="ctd_out" ftype="xml">
10665 <assert_contents>
10666 <is_valid_xml/>
10667 </assert_contents>
10668 </output>
10669 </test>
10670 <test expect_num_outputs="2">
10671 <conditional name="adv_opts_cond">
10672 <param name="adv_opts_selector" value="advanced"/>
10673 <param name="force" value="false"/>
10674 <param name="test" value="true"/>
10675 </conditional>
10676 <param name="in" value="FileInfo_15_input.mzid"/>
10677 <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10678 <param name="m" value="false"/>
10679 <param name="p" value="false"/>
10680 <param name="s" value="false"/>
10681 <param name="d" value="false"/>
10682 <param name="c" value="false"/>
10683 <param name="v" value="true"/>
10684 <param name="i" value="false"/>
10685 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10686 <output name="ctd_out" ftype="xml">
10687 <assert_contents>
10688 <is_valid_xml/>
10689 </assert_contents>
10690 </output>
10691 </test>
10692 <test expect_num_outputs="2">
10693 <conditional name="adv_opts_cond">
10694 <param name="adv_opts_selector" value="advanced"/>
10695 <param name="force" value="false"/>
10696 <param name="test" value="true"/>
10697 </conditional>
10698 <param name="in" value="FileInfo_16_input.trafoXML"/>
10699 <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10700 <param name="m" value="false"/>
10701 <param name="p" value="false"/>
10702 <param name="s" value="false"/>
10703 <param name="d" value="false"/>
10704 <param name="c" value="false"/>
10705 <param name="v" value="false"/>
10706 <param name="i" value="false"/>
10707 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10708 <output name="ctd_out" ftype="xml">
10709 <assert_contents>
10710 <is_valid_xml/>
10711 </assert_contents>
10712 </output>
10713 </test>
10714 <test expect_num_outputs="2">
10715 <conditional name="adv_opts_cond">
10716 <param name="adv_opts_selector" value="advanced"/>
10717 <param name="force" value="false"/>
10718 <param name="test" value="true"/>
10719 </conditional>
10720 <param name="in" value="FileInfo_17_input.fasta"/>
10721 <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10722 <param name="m" value="false"/>
10723 <param name="p" value="false"/>
10724 <param name="s" value="false"/>
10725 <param name="d" value="false"/>
10726 <param name="c" value="false"/>
10727 <param name="v" value="false"/>
10728 <param name="i" value="false"/>
10729 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10730 <output name="ctd_out" ftype="xml">
10731 <assert_contents>
10732 <is_valid_xml/>
10733 </assert_contents>
10734 </output>
10735 </test>
10736 <test expect_num_outputs="2">
10737 <conditional name="adv_opts_cond">
10738 <param name="adv_opts_selector" value="advanced"/>
10739 <param name="force" value="false"/>
10740 <param name="test" value="true"/>
10741 </conditional>
10742 <param name="in" value="FileInfo_18_input.fasta"/>
10743 <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10744 <param name="m" value="false"/>
10745 <param name="p" value="false"/>
10746 <param name="s" value="false"/>
10747 <param name="d" value="false"/>
10748 <param name="c" value="false"/>
10749 <param name="v" value="false"/>
10750 <param name="i" value="false"/>
10751 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10752 <output name="ctd_out" ftype="xml">
10753 <assert_contents>
10754 <is_valid_xml/>
10755 </assert_contents>
10756 </output>
10757 </test>
10758 </xml>
10759 <xml name="autotest_FileMerger">
10760 <test expect_num_outputs="2">
10761 <conditional name="adv_opts_cond">
10762 <param name="adv_opts_selector" value="advanced"/>
10763 <param name="force" value="false"/>
10764 <param name="test" value="true"/>
10765 </conditional>
10766 <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/>
10767 <param name="out_type" value="mzML"/>
10768 <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10769 <param name="annotate_file_origin" value="false"/>
10770 <param name="append_method" value="append_rows"/>
10771 <section name="rt_concat">
10772 <param name="gap" value="0.0"/>
10773 </section>
10774 <section name="raw">
10775 <param name="rt_auto" value="false"/>
10776 <param name="rt_custom" value="5.0 10.0"/>
10777 <param name="rt_filename" value="false"/>
10778 <param name="ms_level" value="0"/>
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" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/>
10794 <param name="out_type" value="mzML"/>
10795 <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10796 <param name="annotate_file_origin" value="false"/>
10797 <param name="append_method" value="append_rows"/>
10798 <section name="rt_concat">
10799 <param name="gap" value="0.0"/>
10800 </section>
10801 <section name="raw">
10802 <param name="rt_auto" value="true"/>
10803 <param name="rt_custom" value=""/>
10804 <param name="rt_filename" value="false"/>
10805 <param name="ms_level" value="0"/>
10806 </section>
10807 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10808 <output name="ctd_out" ftype="xml">
10809 <assert_contents>
10810 <is_valid_xml/>
10811 </assert_contents>
10812 </output>
10813 </test>
10814 <test expect_num_outputs="2">
10815 <conditional name="adv_opts_cond">
10816 <param name="adv_opts_selector" value="advanced"/>
10817 <param name="force" value="false"/>
10818 <param name="test" value="true"/>
10819 </conditional>
10820 <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/>
10821 <param name="out_type" value="mzML"/>
10822 <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10823 <param name="annotate_file_origin" value="false"/>
10824 <param name="append_method" value="append_rows"/>
10825 <section name="rt_concat">
10826 <param name="gap" value="0.0"/>
10827 </section>
10828 <section name="raw">
10829 <param name="rt_auto" value="false"/>
10830 <param name="rt_custom" value=""/>
10831 <param name="rt_filename" value="false"/>
10832 <param name="ms_level" value="0"/>
10833 </section>
10834 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10835 <output name="ctd_out" ftype="xml">
10836 <assert_contents>
10837 <is_valid_xml/>
10838 </assert_contents>
10839 </output>
10840 </test>
10841 <test expect_num_outputs="2">
10842 <conditional name="adv_opts_cond">
10843 <param name="adv_opts_selector" value="advanced"/>
10844 <param name="force" value="false"/>
10845 <param name="test" value="true"/>
10846 </conditional>
10847 <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/>
10848 <param name="out_type" value="mzML"/>
10849 <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10850 <param name="annotate_file_origin" value="false"/>
10851 <param name="append_method" value="append_rows"/>
10852 <section name="rt_concat">
10853 <param name="gap" value="0.0"/>
10854 </section>
10855 <section name="raw">
10856 <param name="rt_auto" value="false"/>
10857 <param name="rt_custom" value=""/>
10858 <param name="rt_filename" value="true"/>
10859 <param name="ms_level" value="2"/>
10860 </section>
10861 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10862 <output name="ctd_out" ftype="xml">
10863 <assert_contents>
10864 <is_valid_xml/>
10865 </assert_contents>
10866 </output>
10867 </test>
10868 <test expect_num_outputs="2">
10869 <conditional name="adv_opts_cond">
10870 <param name="adv_opts_selector" value="advanced"/>
10871 <param name="force" value="false"/>
10872 <param name="test" value="true"/>
10873 </conditional>
10874 <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/>
10875 <param name="out_type" value="mzML"/>
10876 <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10877 <param name="annotate_file_origin" value="false"/>
10878 <param name="append_method" value="append_rows"/>
10879 <section name="rt_concat">
10880 <param name="gap" value="0.0"/>
10881 </section>
10882 <section name="raw">
10883 <param name="rt_auto" value="false"/>
10884 <param name="rt_custom" value=""/>
10885 <param name="rt_filename" value="false"/>
10886 <param name="ms_level" value="0"/>
10887 </section>
10888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10889 <output name="ctd_out" ftype="xml">
10890 <assert_contents>
10891 <is_valid_xml/>
10892 </assert_contents>
10893 </output>
10894 </test>
10895 <test expect_num_outputs="2">
10896 <conditional name="adv_opts_cond">
10897 <param name="adv_opts_selector" value="advanced"/>
10898 <param name="force" value="false"/>
10899 <param name="test" value="true"/>
10900 </conditional>
10901 <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/>
10902 <param name="out_type" value="featureXML"/>
10903 <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
10904 <param name="annotate_file_origin" value="false"/>
10905 <param name="append_method" value="append_rows"/>
10906 <section name="rt_concat">
10907 <param name="gap" value="0.0"/>
10908 </section>
10909 <section name="raw">
10910 <param name="rt_auto" value="false"/>
10911 <param name="rt_custom" value=""/>
10912 <param name="rt_filename" value="false"/>
10913 <param name="ms_level" value="0"/>
10914 </section>
10915 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10916 <output name="ctd_out" ftype="xml">
10917 <assert_contents>
10918 <is_valid_xml/>
10919 </assert_contents>
10920 </output>
10921 </test>
10922 <test expect_num_outputs="2">
10923 <conditional name="adv_opts_cond">
10924 <param name="adv_opts_selector" value="advanced"/>
10925 <param name="force" value="false"/>
10926 <param name="test" value="true"/>
10927 </conditional>
10928 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
10929 <param name="out_type" value="consensusXML"/>
10930 <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
10931 <param name="annotate_file_origin" value="false"/>
10932 <param name="append_method" value="append_rows"/>
10933 <section name="rt_concat">
10934 <param name="gap" value="0.0"/>
10935 </section>
10936 <section name="raw">
10937 <param name="rt_auto" value="false"/>
10938 <param name="rt_custom" value=""/>
10939 <param name="rt_filename" value="false"/>
10940 <param name="ms_level" value="0"/>
10941 </section>
10942 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10943 <output name="ctd_out" ftype="xml">
10944 <assert_contents>
10945 <is_valid_xml/>
10946 </assert_contents>
10947 </output>
10948 </test>
10949 <test expect_num_outputs="2">
10950 <conditional name="adv_opts_cond">
10951 <param name="adv_opts_selector" value="advanced"/>
10952 <param name="force" value="false"/>
10953 <param name="test" value="true"/>
10954 </conditional>
10955 <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/>
10956 <param name="out_type" value="traML"/>
10957 <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/>
10958 <param name="annotate_file_origin" value="false"/>
10959 <param name="append_method" value="append_rows"/>
10960 <section name="rt_concat">
10961 <param name="gap" value="0.0"/>
10962 </section>
10963 <section name="raw">
10964 <param name="rt_auto" value="false"/>
10965 <param name="rt_custom" value=""/>
10966 <param name="rt_filename" value="false"/>
10967 <param name="ms_level" value="0"/>
10968 </section>
10969 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10970 <output name="ctd_out" ftype="xml">
10971 <assert_contents>
10972 <is_valid_xml/>
10973 </assert_contents>
10974 </output>
10975 </test>
10976 <test expect_num_outputs="3">
10977 <conditional name="adv_opts_cond">
10978 <param name="adv_opts_selector" value="advanced"/>
10979 <param name="force" value="false"/>
10980 <param name="test" value="true"/>
10981 </conditional>
10982 <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/>
10983 <param name="out_type" value="mzML"/>
10984 <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10985 <param name="annotate_file_origin" value="false"/>
10986 <param name="append_method" value="append_rows"/>
10987 <section name="rt_concat">
10988 <param name="gap" value="10.0"/>
10989 </section>
10990 <output_collection name="rt_concat_trafo_out" count="2"/>
10991 <section name="raw">
10992 <param name="rt_auto" value="false"/>
10993 <param name="rt_custom" value=""/>
10994 <param name="rt_filename" value="false"/>
10995 <param name="ms_level" value="0"/>
10996 </section>
10997 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
10998 <output name="ctd_out" ftype="xml">
10999 <assert_contents>
11000 <is_valid_xml/>
11001 </assert_contents>
11002 </output>
11003 </test>
11004 <test expect_num_outputs="2">
11005 <conditional name="adv_opts_cond">
11006 <param name="adv_opts_selector" value="advanced"/>
11007 <param name="force" value="false"/>
11008 <param name="test" value="true"/>
11009 </conditional>
11010 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
11011 <param name="out_type" value="consensusXML"/>
11012 <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
11013 <param name="annotate_file_origin" value="false"/>
11014 <param name="append_method" value="append_cols"/>
11015 <section name="rt_concat">
11016 <param name="gap" value="0.0"/>
11017 </section>
11018 <section name="raw">
11019 <param name="rt_auto" value="false"/>
11020 <param name="rt_custom" value=""/>
11021 <param name="rt_filename" value="false"/>
11022 <param name="ms_level" value="0"/>
11023 </section>
11024 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11025 <output name="ctd_out" ftype="xml">
11026 <assert_contents>
11027 <is_valid_xml/>
11028 </assert_contents>
11029 </output>
11030 </test>
11031 </xml>
11032 <xml name="autotest_FuzzyDiff">
11033 <test expect_num_outputs="1">
11034 <conditional name="adv_opts_cond">
11035 <param name="adv_opts_selector" value="advanced"/>
11036 <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
11037 <param name="matched_whitelist" value=""/>
11038 <param name="force" value="false"/>
11039 <param name="test" value="true"/>
11040 </conditional>
11041 <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
11042 <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
11043 <param name="ratio" value="1.01"/>
11044 <param name="absdiff" value="0.01"/>
11045 <param name="verbose" value="1"/>
11046 <param name="tab_width" value="8"/>
11047 <param name="first_column" value="1"/>
11048 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11049 <output name="ctd_out" ftype="xml">
11050 <assert_contents>
11051 <is_valid_xml/>
11052 </assert_contents>
11053 </output>
11054 </test>
11055 </xml>
11056 <xml name="autotest_GNPSExport">
11057 <test expect_num_outputs="2">
11058 <conditional name="adv_opts_cond">
11059 <param name="adv_opts_selector" value="advanced"/>
11060 <param name="force" value="false"/>
11061 <param name="test" value="true"/>
11062 </conditional>
11063 <param name="in_cm" value="GNPSExport_single.consensusXML"/>
11064 <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
11065 <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
11066 <param name="output_type" value="full_spectra"/>
11067 <param name="precursor_mz_tolerance" value="0.0001"/>
11068 <param name="precursor_rt_tolerance" value="5.0"/>
11069 <section name="merged_spectra">
11070 <param name="cos_similarity" value="0.95"/>
11071 </section>
11072 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11073 <output name="ctd_out" ftype="xml">
11074 <assert_contents>
11075 <is_valid_xml/>
11076 </assert_contents>
11077 </output>
11078 </test>
11079 <test expect_num_outputs="2">
11080 <conditional name="adv_opts_cond">
11081 <param name="adv_opts_selector" value="advanced"/>
11082 <param name="force" value="false"/>
11083 <param name="test" value="true"/>
11084 </conditional>
11085 <param name="in_cm" value="GNPSExport_single.consensusXML"/>
11086 <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
11087 <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
11088 <param name="output_type" value="merged_spectra"/>
11089 <param name="precursor_mz_tolerance" value="0.0001"/>
11090 <param name="precursor_rt_tolerance" value="5.0"/>
11091 <section name="merged_spectra">
11092 <param name="cos_similarity" value="0.95"/>
11093 </section>
11094 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11095 <output name="ctd_out" ftype="xml">
11096 <assert_contents>
11097 <is_valid_xml/>
11098 </assert_contents>
11099 </output>
11100 </test>
11101 <test expect_num_outputs="2">
11102 <conditional name="adv_opts_cond">
11103 <param name="adv_opts_selector" value="advanced"/>
11104 <param name="force" value="false"/>
11105 <param name="test" value="true"/>
11106 </conditional>
11107 <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
11108 <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
11109 <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
11110 <param name="output_type" value="full_spectra"/>
11111 <param name="precursor_mz_tolerance" value="0.0001"/>
11112 <param name="precursor_rt_tolerance" value="5.0"/>
11113 <section name="merged_spectra">
11114 <param name="cos_similarity" value="0.95"/>
11115 </section>
11116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11117 <output name="ctd_out" ftype="xml">
11118 <assert_contents>
11119 <is_valid_xml/>
11120 </assert_contents>
11121 </output>
11122 </test>
11123 <test expect_num_outputs="2">
11124 <conditional name="adv_opts_cond">
11125 <param name="adv_opts_selector" value="advanced"/>
11126 <param name="force" value="false"/>
11127 <param name="test" value="true"/>
11128 </conditional>
11129 <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
11130 <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
11131 <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
11132 <param name="output_type" value="full_spectra"/>
11133 <param name="precursor_mz_tolerance" value="0.0001"/>
11134 <param name="precursor_rt_tolerance" value="5.0"/>
11135 <section name="merged_spectra">
11136 <param name="cos_similarity" value="0.95"/>
11137 </section>
11138 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11139 <output name="ctd_out" ftype="xml">
11140 <assert_contents>
11141 <is_valid_xml/>
11142 </assert_contents>
11143 </output>
11144 </test>
11145 </xml>
11146 <xml name="autotest_HighResPrecursorMassCorrector">
11147 <test expect_num_outputs="2">
11148 <conditional name="adv_opts_cond">
11149 <param name="adv_opts_selector" value="advanced"/>
11150 <param name="force" value="false"/>
11151 <param name="test" value="true"/>
11152 </conditional>
11153 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
11154 <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
11155 <section name="feature">
11156 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
11157 <param name="mz_tolerance" value="5.0"/>
11158 <param name="mz_tolerance_unit" value="ppm"/>
11159 <param name="rt_tolerance" value="0.0"/>
11160 <param name="max_trace" value="2"/>
11161 <param name="believe_charge" value="false"/>
11162 <param name="keep_original" value="false"/>
11163 <param name="assign_all_matching" value="false"/>
11164 </section>
11165 <section name="nearest_peak">
11166 <param name="mz_tolerance" value="0.0"/>
11167 <param name="mz_tolerance_unit" value="ppm"/>
11168 </section>
11169 <section name="highest_intensity_peak">
11170 <param name="mz_tolerance" value="0.0"/>
11171 <param name="mz_tolerance_unit" value="ppm"/>
11172 </section>
11173 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11174 <output name="ctd_out" ftype="xml">
11175 <assert_contents>
11176 <is_valid_xml/>
11177 </assert_contents>
11178 </output>
11179 </test>
11180 <test expect_num_outputs="2">
11181 <conditional name="adv_opts_cond">
11182 <param name="adv_opts_selector" value="advanced"/>
11183 <param name="force" value="false"/>
11184 <param name="test" value="true"/>
11185 </conditional>
11186 <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/>
11187 <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
11188 <section name="feature">
11189 <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/>
11190 <param name="mz_tolerance" value="10.0"/>
11191 <param name="mz_tolerance_unit" value="ppm"/>
11192 <param name="rt_tolerance" value="0.0"/>
11193 <param name="max_trace" value="4"/>
11194 <param name="believe_charge" value="false"/>
11195 <param name="keep_original" value="false"/>
11196 <param name="assign_all_matching" value="false"/>
11197 </section>
11198 <section name="nearest_peak">
11199 <param name="mz_tolerance" value="0.0"/>
11200 <param name="mz_tolerance_unit" value="ppm"/>
11201 </section>
11202 <section name="highest_intensity_peak">
11203 <param name="mz_tolerance" value="0.0"/>
11204 <param name="mz_tolerance_unit" value="ppm"/>
11205 </section>
11206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11207 <output name="ctd_out" ftype="xml">
11208 <assert_contents>
11209 <is_valid_xml/>
11210 </assert_contents>
11211 </output>
11212 </test>
11213 <test expect_num_outputs="2">
11214 <conditional name="adv_opts_cond">
11215 <param name="adv_opts_selector" value="advanced"/>
11216 <param name="force" value="false"/>
11217 <param name="test" value="true"/>
11218 </conditional>
11219 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
11220 <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
11221 <section name="feature">
11222 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
11223 <param name="mz_tolerance" value="5.0"/>
11224 <param name="mz_tolerance_unit" value="ppm"/>
11225 <param name="rt_tolerance" value="0.0"/>
11226 <param name="max_trace" value="2"/>
11227 <param name="believe_charge" value="false"/>
11228 <param name="keep_original" value="false"/>
11229 <param name="assign_all_matching" value="false"/>
11230 </section>
11231 <section name="nearest_peak">
11232 <param name="mz_tolerance" value="0.0"/>
11233 <param name="mz_tolerance_unit" value="ppm"/>
11234 </section>
11235 <section name="highest_intensity_peak">
11236 <param name="mz_tolerance" value="0.0"/>
11237 <param name="mz_tolerance_unit" value="ppm"/>
11238 </section>
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="force" value="false"/>
11250 <param name="test" value="true"/>
11251 </conditional>
11252 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
11253 <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
11254 <section name="feature">
11255 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
11256 <param name="mz_tolerance" value="5.0"/>
11257 <param name="mz_tolerance_unit" value="ppm"/>
11258 <param name="rt_tolerance" value="0.0"/>
11259 <param name="max_trace" value="2"/>
11260 <param name="believe_charge" value="false"/>
11261 <param name="keep_original" value="false"/>
11262 <param name="assign_all_matching" value="false"/>
11263 </section>
11264 <section name="nearest_peak">
11265 <param name="mz_tolerance" value="0.0"/>
11266 <param name="mz_tolerance_unit" value="ppm"/>
11267 </section>
11268 <section name="highest_intensity_peak">
11269 <param name="mz_tolerance" value="0.0"/>
11270 <param name="mz_tolerance_unit" value="ppm"/>
11271 </section>
11272 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11273 <output name="ctd_out" ftype="xml">
11274 <assert_contents>
11275 <is_valid_xml/>
11276 </assert_contents>
11277 </output>
11278 </test>
11279 <test expect_num_outputs="2">
11280 <conditional name="adv_opts_cond">
11281 <param name="adv_opts_selector" value="advanced"/>
11282 <param name="force" value="false"/>
11283 <param name="test" value="true"/>
11284 </conditional>
11285 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
11286 <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
11287 <section name="feature">
11288 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
11289 <param name="mz_tolerance" value="5.0"/>
11290 <param name="mz_tolerance_unit" value="ppm"/>
11291 <param name="rt_tolerance" value="0.0"/>
11292 <param name="max_trace" value="2"/>
11293 <param name="believe_charge" value="false"/>
11294 <param name="keep_original" value="false"/>
11295 <param name="assign_all_matching" value="false"/>
11296 </section>
11297 <section name="nearest_peak">
11298 <param name="mz_tolerance" value="0.0"/>
11299 <param name="mz_tolerance_unit" value="ppm"/>
11300 </section>
11301 <section name="highest_intensity_peak">
11302 <param name="mz_tolerance" value="0.0"/>
11303 <param name="mz_tolerance_unit" value="ppm"/>
11304 </section>
11305 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11306 <output name="ctd_out" ftype="xml">
11307 <assert_contents>
11308 <is_valid_xml/>
11309 </assert_contents>
11310 </output>
11311 </test>
11312 <test expect_num_outputs="2">
11313 <conditional name="adv_opts_cond">
11314 <param name="adv_opts_selector" value="advanced"/>
11315 <param name="force" value="false"/>
11316 <param name="test" value="true"/>
11317 </conditional>
11318 <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
11319 <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
11320 <section name="feature">
11321 <param name="mz_tolerance" value="5.0"/>
11322 <param name="mz_tolerance_unit" value="ppm"/>
11323 <param name="rt_tolerance" value="0.0"/>
11324 <param name="max_trace" value="2"/>
11325 <param name="believe_charge" value="false"/>
11326 <param name="keep_original" value="false"/>
11327 <param name="assign_all_matching" value="false"/>
11328 </section>
11329 <section name="nearest_peak">
11330 <param name="mz_tolerance" value="0.0"/>
11331 <param name="mz_tolerance_unit" value="ppm"/>
11332 </section>
11333 <section name="highest_intensity_peak">
11334 <param name="mz_tolerance" value="0.2"/>
11335 <param name="mz_tolerance_unit" value="ppm"/>
11336 </section>
11337 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11338 <output name="ctd_out" ftype="xml">
11339 <assert_contents>
11340 <is_valid_xml/>
11341 </assert_contents>
11342 </output>
11343 </test>
11344 </xml>
11345 <xml name="autotest_IDConflictResolver">
11346 <test expect_num_outputs="2">
11347 <conditional name="adv_opts_cond">
11348 <param name="adv_opts_selector" value="advanced"/>
11349 <param name="force" value="false"/>
11350 <param name="test" value="true"/>
11351 </conditional>
11352 <param name="in" value="IDConflictResolver_1_input.featureXML"/>
11353 <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
11354 <param name="resolve_between_features" value="off"/>
11355 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11356 <output name="ctd_out" ftype="xml">
11357 <assert_contents>
11358 <is_valid_xml/>
11359 </assert_contents>
11360 </output>
11361 </test>
11362 <test expect_num_outputs="2">
11363 <conditional name="adv_opts_cond">
11364 <param name="adv_opts_selector" value="advanced"/>
11365 <param name="force" value="false"/>
11366 <param name="test" value="true"/>
11367 </conditional>
11368 <param name="in" value="IDConflictResolver_2_input.consensusXML"/>
11369 <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
11370 <param name="resolve_between_features" value="off"/>
11371 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11372 <output name="ctd_out" ftype="xml">
11373 <assert_contents>
11374 <is_valid_xml/>
11375 </assert_contents>
11376 </output>
11377 </test>
11378 <test expect_num_outputs="2">
11379 <conditional name="adv_opts_cond">
11380 <param name="adv_opts_selector" value="advanced"/>
11381 <param name="force" value="false"/>
11382 <param name="test" value="true"/>
11383 </conditional>
11384 <param name="in" value="IDConflictResolver_3_input.consensusXML"/>
11385 <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
11386 <param name="resolve_between_features" value="off"/>
11387 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11388 <output name="ctd_out" ftype="xml">
11389 <assert_contents>
11390 <is_valid_xml/>
11391 </assert_contents>
11392 </output>
11393 </test>
11394 <test expect_num_outputs="2">
11395 <conditional name="adv_opts_cond">
11396 <param name="adv_opts_selector" value="advanced"/>
11397 <param name="force" value="false"/>
11398 <param name="test" value="true"/>
11399 </conditional>
11400 <param name="in" value="IDConflictResolver_4_input.featureXML"/>
11401 <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
11402 <param name="resolve_between_features" value="highest_intensity"/>
11403 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11404 <output name="ctd_out" ftype="xml">
11405 <assert_contents>
11406 <is_valid_xml/>
11407 </assert_contents>
11408 </output>
11409 </test>
11410 </xml>
11411 <xml name="autotest_IDExtractor">
11412 </xml>
11413 <xml name="autotest_IDFileConverter">
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="concatenate_peptides" value="false"/>
11423 <param name="number_of_hits" value="1"/>
11424 <param name="force" value="false"/>
11425 <param name="test" value="true"/>
11426 </conditional>
11427 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
11428 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11429 <param name="out_type" value="idXML"/>
11430 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
11431 <param name="mz_name" value=""/>
11432 <param name="peptideprophet_analyzed" value="false"/>
11433 <param name="score_type" value="qvalue"/>
11434 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11435 <output name="ctd_out" ftype="xml">
11436 <assert_contents>
11437 <is_valid_xml/>
11438 </assert_contents>
11439 </output>
11440 </test>
11441 <test expect_num_outputs="2">
11442 <conditional name="adv_opts_cond">
11443 <param name="adv_opts_selector" value="advanced"/>
11444 <param name="ignore_proteins_per_peptide" value="false"/>
11445 <param name="scan_regex" value=""/>
11446 <param name="no_spectra_data_override" value="false"/>
11447 <param name="no_spectra_references_override" value="false"/>
11448 <param name="add_ionmatch_annotation" value="0.0"/>
11449 <param name="concatenate_peptides" value="false"/>
11450 <param name="number_of_hits" value="1"/>
11451 <param name="force" value="false"/>
11452 <param name="test" value="true"/>
11453 </conditional>
11454 <param name="in" value="PepXMLFile_test.pepxml"/>
11455 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11456 <param name="out_type" value="idXML"/>
11457 <param name="mz_file" value="PepXMLFile_test.mzML"/>
11458 <param name="mz_name" value="PepXMLFile_test"/>
11459 <param name="peptideprophet_analyzed" value="false"/>
11460 <param name="score_type" value="qvalue"/>
11461 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11462 <output name="ctd_out" ftype="xml">
11463 <assert_contents>
11464 <is_valid_xml/>
11465 </assert_contents>
11466 </output>
11467 </test>
11468 <test expect_num_outputs="2">
11469 <conditional name="adv_opts_cond">
11470 <param name="adv_opts_selector" value="advanced"/>
11471 <param name="ignore_proteins_per_peptide" value="false"/>
11472 <param name="scan_regex" value=""/>
11473 <param name="no_spectra_data_override" value="false"/>
11474 <param name="no_spectra_references_override" value="false"/>
11475 <param name="add_ionmatch_annotation" value="0.0"/>
11476 <param name="concatenate_peptides" value="false"/>
11477 <param name="number_of_hits" value="1"/>
11478 <param name="force" value="false"/>
11479 <param name="test" value="true"/>
11480 </conditional>
11481 <param name="in" value="IDFileConverter_3_input.protXML"/>
11482 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11483 <param name="out_type" value="idXML"/>
11484 <param name="mz_name" value=""/>
11485 <param name="peptideprophet_analyzed" value="false"/>
11486 <param name="score_type" value="qvalue"/>
11487 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11488 <output name="ctd_out" ftype="xml">
11489 <assert_contents>
11490 <is_valid_xml/>
11491 </assert_contents>
11492 </output>
11493 </test>
11494 <test expect_num_outputs="2">
11495 <conditional name="adv_opts_cond">
11496 <param name="adv_opts_selector" value="advanced"/>
11497 <param name="ignore_proteins_per_peptide" value="false"/>
11498 <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
11499 <param name="no_spectra_data_override" value="false"/>
11500 <param name="no_spectra_references_override" value="false"/>
11501 <param name="add_ionmatch_annotation" value="0.0"/>
11502 <param name="concatenate_peptides" value="false"/>
11503 <param name="number_of_hits" value="1"/>
11504 <param name="force" value="false"/>
11505 <param name="test" value="true"/>
11506 </conditional>
11507 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
11508 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11509 <param name="out_type" value="idXML"/>
11510 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
11511 <param name="mz_name" value=""/>
11512 <param name="peptideprophet_analyzed" value="false"/>
11513 <param name="score_type" value="qvalue"/>
11514 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11515 <output name="ctd_out" ftype="xml">
11516 <assert_contents>
11517 <is_valid_xml/>
11518 </assert_contents>
11519 </output>
11520 </test>
11521 <test expect_num_outputs="2">
11522 <conditional name="adv_opts_cond">
11523 <param name="adv_opts_selector" value="advanced"/>
11524 <param name="ignore_proteins_per_peptide" value="false"/>
11525 <param name="scan_regex" value=""/>
11526 <param name="no_spectra_data_override" value="false"/>
11527 <param name="no_spectra_references_override" value="false"/>
11528 <param name="add_ionmatch_annotation" value="0.0"/>
11529 <param name="concatenate_peptides" value="false"/>
11530 <param name="number_of_hits" value="1"/>
11531 <param name="force" value="false"/>
11532 <param name="test" value="true"/>
11533 </conditional>
11534 <param name="in" value="IDFileConverter_6_input1.pepXML"/>
11535 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11536 <param name="out_type" value="idXML"/>
11537 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
11538 <param name="mz_name" value="F025589.dat.mzML"/>
11539 <param name="peptideprophet_analyzed" value="false"/>
11540 <param name="score_type" value="qvalue"/>
11541 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11542 <output name="ctd_out" ftype="xml">
11543 <assert_contents>
11544 <is_valid_xml/>
11545 </assert_contents>
11546 </output>
11547 </test>
11548 <test expect_num_outputs="2">
11549 <conditional name="adv_opts_cond">
11550 <param name="adv_opts_selector" value="advanced"/>
11551 <param name="ignore_proteins_per_peptide" value="false"/>
11552 <param name="scan_regex" value=""/>
11553 <param name="no_spectra_data_override" value="false"/>
11554 <param name="no_spectra_references_override" value="false"/>
11555 <param name="add_ionmatch_annotation" value="0.0"/>
11556 <param name="concatenate_peptides" value="false"/>
11557 <param name="number_of_hits" value="1"/>
11558 <param name="force" value="false"/>
11559 <param name="test" value="true"/>
11560 </conditional>
11561 <param name="in" value="IDFileConverter_7_input1.xml"/>
11562 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11563 <param name="out_type" value="idXML"/>
11564 <param name="mz_name" value=""/>
11565 <param name="peptideprophet_analyzed" value="false"/>
11566 <param name="score_type" value="qvalue"/>
11567 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11568 <output name="ctd_out" ftype="xml">
11569 <assert_contents>
11570 <is_valid_xml/>
11571 </assert_contents>
11572 </output>
11573 </test>
11574 <test expect_num_outputs="2">
11575 <conditional name="adv_opts_cond">
11576 <param name="adv_opts_selector" value="advanced"/>
11577 <param name="ignore_proteins_per_peptide" value="false"/>
11578 <param name="scan_regex" value=""/>
11579 <param name="no_spectra_data_override" value="false"/>
11580 <param name="no_spectra_references_override" value="false"/>
11581 <param name="add_ionmatch_annotation" value="0.0"/>
11582 <param name="concatenate_peptides" value="false"/>
11583 <param name="number_of_hits" value="1"/>
11584 <param name="force" value="false"/>
11585 <param name="test" value="true"/>
11586 </conditional>
11587 <param name="in" value="IDFileConverter_8_input.mzid"/>
11588 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11589 <param name="out_type" value="idXML"/>
11590 <param name="mz_name" value=""/>
11591 <param name="peptideprophet_analyzed" value="false"/>
11592 <param name="score_type" value="qvalue"/>
11593 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11594 <output name="ctd_out" ftype="xml">
11595 <assert_contents>
11596 <is_valid_xml/>
11597 </assert_contents>
11598 </output>
11599 </test>
11600 <test expect_num_outputs="2">
11601 <conditional name="adv_opts_cond">
11602 <param name="adv_opts_selector" value="advanced"/>
11603 <param name="ignore_proteins_per_peptide" value="false"/>
11604 <param name="scan_regex" value=""/>
11605 <param name="no_spectra_data_override" value="false"/>
11606 <param name="no_spectra_references_override" value="false"/>
11607 <param name="add_ionmatch_annotation" value="0.0"/>
11608 <param name="concatenate_peptides" value="false"/>
11609 <param name="number_of_hits" value="1"/>
11610 <param name="force" value="false"/>
11611 <param name="test" value="true"/>
11612 </conditional>
11613 <param name="in" value="IDFileConverter_9_input.idXML"/>
11614 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
11615 <param name="out_type" value="mzid"/>
11616 <param name="mz_name" value=""/>
11617 <param name="peptideprophet_analyzed" value="false"/>
11618 <param name="score_type" value="qvalue"/>
11619 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11620 <output name="ctd_out" ftype="xml">
11621 <assert_contents>
11622 <is_valid_xml/>
11623 </assert_contents>
11624 </output>
11625 </test>
11626 <test expect_num_outputs="2">
11627 <conditional name="adv_opts_cond">
11628 <param name="adv_opts_selector" value="advanced"/>
11629 <param name="ignore_proteins_per_peptide" value="false"/>
11630 <param name="scan_regex" value=""/>
11631 <param name="no_spectra_data_override" value="false"/>
11632 <param name="no_spectra_references_override" value="false"/>
11633 <param name="add_ionmatch_annotation" value="0.0"/>
11634 <param name="concatenate_peptides" value="false"/>
11635 <param name="number_of_hits" value="1"/>
11636 <param name="force" value="false"/>
11637 <param name="test" value="true"/>
11638 </conditional>
11639 <param name="in" value="IDFileConverter_10_input.pepXML"/>
11640 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11641 <param name="out_type" value="idXML"/>
11642 <param name="mz_name" value=""/>
11643 <param name="peptideprophet_analyzed" value="false"/>
11644 <param name="score_type" value="qvalue"/>
11645 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11646 <output name="ctd_out" ftype="xml">
11647 <assert_contents>
11648 <is_valid_xml/>
11649 </assert_contents>
11650 </output>
11651 </test>
11652 <test expect_num_outputs="2">
11653 <conditional name="adv_opts_cond">
11654 <param name="adv_opts_selector" value="advanced"/>
11655 <param name="ignore_proteins_per_peptide" value="false"/>
11656 <param name="scan_regex" value=""/>
11657 <param name="no_spectra_data_override" value="false"/>
11658 <param name="no_spectra_references_override" value="false"/>
11659 <param name="add_ionmatch_annotation" value="0.0"/>
11660 <param name="concatenate_peptides" value="false"/>
11661 <param name="number_of_hits" value="1"/>
11662 <param name="force" value="false"/>
11663 <param name="test" value="true"/>
11664 </conditional>
11665 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
11666 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11667 <param name="out_type" value="idXML"/>
11668 <param name="mz_name" value=""/>
11669 <param name="peptideprophet_analyzed" value="false"/>
11670 <param name="score_type" value="qvalue"/>
11671 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11672 <output name="ctd_out" ftype="xml">
11673 <assert_contents>
11674 <is_valid_xml/>
11675 </assert_contents>
11676 </output>
11677 </test>
11678 <test expect_num_outputs="2">
11679 <conditional name="adv_opts_cond">
11680 <param name="adv_opts_selector" value="advanced"/>
11681 <param name="ignore_proteins_per_peptide" value="false"/>
11682 <param name="scan_regex" value=""/>
11683 <param name="no_spectra_data_override" value="false"/>
11684 <param name="no_spectra_references_override" value="false"/>
11685 <param name="add_ionmatch_annotation" value="0.0"/>
11686 <param name="concatenate_peptides" value="false"/>
11687 <param name="number_of_hits" value="1"/>
11688 <param name="force" value="false"/>
11689 <param name="test" value="true"/>
11690 </conditional>
11691 <param name="in" value="IDFileConverter_12_input.psms"/>
11692 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11693 <param name="out_type" value="idXML"/>
11694 <param name="mz_name" value=""/>
11695 <param name="peptideprophet_analyzed" value="false"/>
11696 <param name="score_type" value="qvalue"/>
11697 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11698 <output name="ctd_out" ftype="xml">
11699 <assert_contents>
11700 <is_valid_xml/>
11701 </assert_contents>
11702 </output>
11703 </test>
11704 <test expect_num_outputs="2">
11705 <conditional name="adv_opts_cond">
11706 <param name="adv_opts_selector" value="advanced"/>
11707 <param name="ignore_proteins_per_peptide" value="false"/>
11708 <param name="scan_regex" value=""/>
11709 <param name="no_spectra_data_override" value="false"/>
11710 <param name="no_spectra_references_override" value="false"/>
11711 <param name="add_ionmatch_annotation" value="0.0"/>
11712 <param name="concatenate_peptides" value="false"/>
11713 <param name="number_of_hits" value="1"/>
11714 <param name="force" value="false"/>
11715 <param name="test" value="true"/>
11716 </conditional>
11717 <param name="in" value="IDFileConverter_12_input.psms"/>
11718 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11719 <param name="out_type" value="idXML"/>
11720 <param name="mz_name" value=""/>
11721 <param name="peptideprophet_analyzed" value="false"/>
11722 <param name="score_type" value="PEP"/>
11723 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11724 <output name="ctd_out" ftype="xml">
11725 <assert_contents>
11726 <is_valid_xml/>
11727 </assert_contents>
11728 </output>
11729 </test>
11730 <test expect_num_outputs="2">
11731 <conditional name="adv_opts_cond">
11732 <param name="adv_opts_selector" value="advanced"/>
11733 <param name="ignore_proteins_per_peptide" value="false"/>
11734 <param name="scan_regex" value=""/>
11735 <param name="no_spectra_data_override" value="false"/>
11736 <param name="no_spectra_references_override" value="false"/>
11737 <param name="add_ionmatch_annotation" value="0.0"/>
11738 <param name="concatenate_peptides" value="false"/>
11739 <param name="number_of_hits" value="1"/>
11740 <param name="force" value="false"/>
11741 <param name="test" value="true"/>
11742 </conditional>
11743 <param name="in" value="IDFileConverter_12_input.psms"/>
11744 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11745 <param name="out_type" value="idXML"/>
11746 <param name="mz_name" value=""/>
11747 <param name="peptideprophet_analyzed" value="false"/>
11748 <param name="score_type" value="score"/>
11749 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11750 <output name="ctd_out" ftype="xml">
11751 <assert_contents>
11752 <is_valid_xml/>
11753 </assert_contents>
11754 </output>
11755 </test>
11756 <test expect_num_outputs="2">
11757 <conditional name="adv_opts_cond">
11758 <param name="adv_opts_selector" value="advanced"/>
11759 <param name="ignore_proteins_per_peptide" value="false"/>
11760 <param name="scan_regex" value=""/>
11761 <param name="no_spectra_data_override" value="false"/>
11762 <param name="no_spectra_references_override" value="false"/>
11763 <param name="add_ionmatch_annotation" value="0.0"/>
11764 <param name="concatenate_peptides" value="false"/>
11765 <param name="number_of_hits" value="1"/>
11766 <param name="force" value="false"/>
11767 <param name="test" value="true"/>
11768 </conditional>
11769 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
11770 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11771 <param name="out_type" value="idXML"/>
11772 <param name="mz_file" value="spectra.mzML"/>
11773 <param name="mz_name" value=""/>
11774 <param name="peptideprophet_analyzed" value="false"/>
11775 <param name="score_type" value="qvalue"/>
11776 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11777 <output name="ctd_out" ftype="xml">
11778 <assert_contents>
11779 <is_valid_xml/>
11780 </assert_contents>
11781 </output>
11782 </test>
11783 <test expect_num_outputs="2">
11784 <conditional name="adv_opts_cond">
11785 <param name="adv_opts_selector" value="advanced"/>
11786 <param name="ignore_proteins_per_peptide" value="false"/>
11787 <param name="scan_regex" value=""/>
11788 <param name="no_spectra_data_override" value="false"/>
11789 <param name="no_spectra_references_override" value="false"/>
11790 <param name="add_ionmatch_annotation" value="0.0"/>
11791 <param name="concatenate_peptides" value="false"/>
11792 <param name="number_of_hits" value="1"/>
11793 <param name="force" value="false"/>
11794 <param name="test" value="true"/>
11795 </conditional>
11796 <param name="in" value="IDFileConverter_16_input.pepXML"/>
11797 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11798 <param name="out_type" value="idXML"/>
11799 <param name="mz_name" value=""/>
11800 <param name="peptideprophet_analyzed" value="false"/>
11801 <param name="score_type" value="qvalue"/>
11802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11803 <output name="ctd_out" ftype="xml">
11804 <assert_contents>
11805 <is_valid_xml/>
11806 </assert_contents>
11807 </output>
11808 </test>
11809 <test expect_num_outputs="2">
11810 <conditional name="adv_opts_cond">
11811 <param name="adv_opts_selector" value="advanced"/>
11812 <param name="ignore_proteins_per_peptide" value="false"/>
11813 <param name="scan_regex" value=""/>
11814 <param name="no_spectra_data_override" value="false"/>
11815 <param name="no_spectra_references_override" value="false"/>
11816 <param name="add_ionmatch_annotation" value="0.0"/>
11817 <param name="concatenate_peptides" value="false"/>
11818 <param name="number_of_hits" value="1"/>
11819 <param name="force" value="false"/>
11820 <param name="test" value="true"/>
11821 </conditional>
11822 <param name="in" value="IDFileConverter_17_input.idXML"/>
11823 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11824 <param name="out_type" value="pepXML"/>
11825 <param name="mz_name" value=""/>
11826 <param name="peptideprophet_analyzed" value="false"/>
11827 <param name="score_type" value="qvalue"/>
11828 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11829 <output name="ctd_out" ftype="xml">
11830 <assert_contents>
11831 <is_valid_xml/>
11832 </assert_contents>
11833 </output>
11834 </test>
11835 <test expect_num_outputs="2">
11836 <conditional name="adv_opts_cond">
11837 <param name="adv_opts_selector" value="advanced"/>
11838 <param name="ignore_proteins_per_peptide" value="false"/>
11839 <param name="scan_regex" value=""/>
11840 <param name="no_spectra_data_override" value="false"/>
11841 <param name="no_spectra_references_override" value="false"/>
11842 <param name="add_ionmatch_annotation" value="0.0"/>
11843 <param name="concatenate_peptides" value="false"/>
11844 <param name="number_of_hits" value="1"/>
11845 <param name="force" value="false"/>
11846 <param name="test" value="true"/>
11847 </conditional>
11848 <param name="in" value="IDFileConverter_18_input.idXML"/>
11849 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11850 <param name="out_type" value="pepXML"/>
11851 <param name="mz_name" value=""/>
11852 <param name="peptideprophet_analyzed" value="false"/>
11853 <param name="score_type" value="qvalue"/>
11854 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11855 <output name="ctd_out" ftype="xml">
11856 <assert_contents>
11857 <is_valid_xml/>
11858 </assert_contents>
11859 </output>
11860 </test>
11861 <test expect_num_outputs="2">
11862 <conditional name="adv_opts_cond">
11863 <param name="adv_opts_selector" value="advanced"/>
11864 <param name="ignore_proteins_per_peptide" value="false"/>
11865 <param name="scan_regex" value=""/>
11866 <param name="no_spectra_data_override" value="false"/>
11867 <param name="no_spectra_references_override" value="false"/>
11868 <param name="add_ionmatch_annotation" value="0.0"/>
11869 <param name="concatenate_peptides" value="false"/>
11870 <param name="number_of_hits" value="1"/>
11871 <param name="force" value="false"/>
11872 <param name="test" value="true"/>
11873 </conditional>
11874 <param name="in" value="IDFileConverter_19_input.idXML"/>
11875 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11876 <param name="out_type" value="pepXML"/>
11877 <param name="mz_name" value=""/>
11878 <param name="peptideprophet_analyzed" value="false"/>
11879 <param name="score_type" value="qvalue"/>
11880 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11881 <output name="ctd_out" ftype="xml">
11882 <assert_contents>
11883 <is_valid_xml/>
11884 </assert_contents>
11885 </output>
11886 </test>
11887 <test expect_num_outputs="2">
11888 <conditional name="adv_opts_cond">
11889 <param name="adv_opts_selector" value="advanced"/>
11890 <param name="ignore_proteins_per_peptide" value="false"/>
11891 <param name="scan_regex" value=""/>
11892 <param name="no_spectra_data_override" value="false"/>
11893 <param name="no_spectra_references_override" value="false"/>
11894 <param name="add_ionmatch_annotation" value="0.0"/>
11895 <param name="concatenate_peptides" value="false"/>
11896 <param name="number_of_hits" value="1"/>
11897 <param name="force" value="false"/>
11898 <param name="test" value="true"/>
11899 </conditional>
11900 <param name="in" value="IDFileConverter_20_input.idXML"/>
11901 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11902 <param name="out_type" value="pepXML"/>
11903 <param name="mz_name" value=""/>
11904 <param name="peptideprophet_analyzed" value="false"/>
11905 <param name="score_type" value="qvalue"/>
11906 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11907 <output name="ctd_out" ftype="xml">
11908 <assert_contents>
11909 <is_valid_xml/>
11910 </assert_contents>
11911 </output>
11912 </test>
11913 <test expect_num_outputs="2">
11914 <conditional name="adv_opts_cond">
11915 <param name="adv_opts_selector" value="advanced"/>
11916 <param name="ignore_proteins_per_peptide" value="false"/>
11917 <param name="scan_regex" value=""/>
11918 <param name="no_spectra_data_override" value="false"/>
11919 <param name="no_spectra_references_override" value="false"/>
11920 <param name="add_ionmatch_annotation" value="0.0"/>
11921 <param name="concatenate_peptides" value="false"/>
11922 <param name="number_of_hits" value="1"/>
11923 <param name="force" value="false"/>
11924 <param name="test" value="true"/>
11925 </conditional>
11926 <param name="in" value="IDFileConverter_21_input.idXML"/>
11927 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11928 <param name="out_type" value="idXML"/>
11929 <param name="mz_file" value="IDMapper_4_input.mzML"/>
11930 <param name="mz_name" value=""/>
11931 <param name="peptideprophet_analyzed" value="false"/>
11932 <param name="score_type" value="qvalue"/>
11933 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11934 <output name="ctd_out" ftype="xml">
11935 <assert_contents>
11936 <is_valid_xml/>
11937 </assert_contents>
11938 </output>
11939 </test>
11940 <test expect_num_outputs="2">
11941 <conditional name="adv_opts_cond">
11942 <param name="adv_opts_selector" value="advanced"/>
11943 <param name="ignore_proteins_per_peptide" value="false"/>
11944 <param name="scan_regex" value=""/>
11945 <param name="no_spectra_data_override" value="false"/>
11946 <param name="no_spectra_references_override" value="false"/>
11947 <param name="add_ionmatch_annotation" value="0.01"/>
11948 <param name="concatenate_peptides" value="false"/>
11949 <param name="number_of_hits" value="1"/>
11950 <param name="force" value="false"/>
11951 <param name="test" value="true"/>
11952 </conditional>
11953 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
11954 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11955 <param name="out_type" value="idXML"/>
11956 <param name="mz_file" value="spectra.mzML"/>
11957 <param name="mz_name" value=""/>
11958 <param name="peptideprophet_analyzed" value="false"/>
11959 <param name="score_type" value="qvalue"/>
11960 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11961 <output name="ctd_out" ftype="xml">
11962 <assert_contents>
11963 <is_valid_xml/>
11964 </assert_contents>
11965 </output>
11966 </test>
11967 <test expect_num_outputs="2">
11968 <conditional name="adv_opts_cond">
11969 <param name="adv_opts_selector" value="advanced"/>
11970 <param name="ignore_proteins_per_peptide" value="false"/>
11971 <param name="scan_regex" value=""/>
11972 <param name="no_spectra_data_override" value="false"/>
11973 <param name="no_spectra_references_override" value="false"/>
11974 <param name="add_ionmatch_annotation" value="0.0"/>
11975 <param name="concatenate_peptides" value="false"/>
11976 <param name="number_of_hits" value="1"/>
11977 <param name="force" value="false"/>
11978 <param name="test" value="true"/>
11979 </conditional>
11980 <param name="in" value="IDFileConverter_23_input.mzid"/>
11981 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11982 <param name="out_type" value="idXML"/>
11983 <param name="mz_name" value=""/>
11984 <param name="peptideprophet_analyzed" value="false"/>
11985 <param name="score_type" value="qvalue"/>
11986 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11987 <output name="ctd_out" ftype="xml">
11988 <assert_contents>
11989 <is_valid_xml/>
11990 </assert_contents>
11991 </output>
11992 </test>
11993 <test expect_num_outputs="2">
11994 <conditional name="adv_opts_cond">
11995 <param name="adv_opts_selector" value="advanced"/>
11996 <param name="ignore_proteins_per_peptide" value="false"/>
11997 <param name="scan_regex" value=""/>
11998 <param name="no_spectra_data_override" value="false"/>
11999 <param name="no_spectra_references_override" value="false"/>
12000 <param name="add_ionmatch_annotation" value="0.0"/>
12001 <param name="concatenate_peptides" value="false"/>
12002 <param name="number_of_hits" value="1"/>
12003 <param name="force" value="false"/>
12004 <param name="test" value="true"/>
12005 </conditional>
12006 <param name="in" value="IDFileConverter_24_input.pep.xml"/>
12007 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12008 <param name="out_type" value="idXML"/>
12009 <param name="mz_name" value=""/>
12010 <param name="peptideprophet_analyzed" value="false"/>
12011 <param name="score_type" value="qvalue"/>
12012 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12013 <output name="ctd_out" ftype="xml">
12014 <assert_contents>
12015 <is_valid_xml/>
12016 </assert_contents>
12017 </output>
12018 </test>
12019 <test expect_num_outputs="2">
12020 <conditional name="adv_opts_cond">
12021 <param name="adv_opts_selector" value="advanced"/>
12022 <param name="ignore_proteins_per_peptide" value="false"/>
12023 <param name="scan_regex" value=""/>
12024 <param name="no_spectra_data_override" value="false"/>
12025 <param name="no_spectra_references_override" value="false"/>
12026 <param name="add_ionmatch_annotation" value="0.0"/>
12027 <param name="concatenate_peptides" value="false"/>
12028 <param name="number_of_hits" value="1"/>
12029 <param name="force" value="false"/>
12030 <param name="test" value="true"/>
12031 </conditional>
12032 <param name="in" value="IDFileConverter_25_input.idXML"/>
12033 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/>
12034 <param name="out_type" value="pepXML"/>
12035 <param name="mz_name" value=""/>
12036 <param name="peptideprophet_analyzed" value="false"/>
12037 <param name="score_type" value="qvalue"/>
12038 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12039 <output name="ctd_out" ftype="xml">
12040 <assert_contents>
12041 <is_valid_xml/>
12042 </assert_contents>
12043 </output>
12044 </test>
12045 <test expect_num_outputs="2">
12046 <conditional name="adv_opts_cond">
12047 <param name="adv_opts_selector" value="advanced"/>
12048 <param name="ignore_proteins_per_peptide" value="false"/>
12049 <param name="scan_regex" value=""/>
12050 <param name="no_spectra_data_override" value="false"/>
12051 <param name="no_spectra_references_override" value="false"/>
12052 <param name="add_ionmatch_annotation" value="0.0"/>
12053 <param name="concatenate_peptides" value="false"/>
12054 <param name="number_of_hits" value="1"/>
12055 <param name="force" value="false"/>
12056 <param name="test" value="true"/>
12057 </conditional>
12058 <param name="in" value="IDFileConverter_26_input.mzid"/>
12059 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12060 <param name="out_type" value="idXML"/>
12061 <param name="mz_name" value=""/>
12062 <param name="peptideprophet_analyzed" value="false"/>
12063 <param name="score_type" value="qvalue"/>
12064 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12065 <output name="ctd_out" ftype="xml">
12066 <assert_contents>
12067 <is_valid_xml/>
12068 </assert_contents>
12069 </output>
12070 </test>
12071 <test expect_num_outputs="2">
12072 <conditional name="adv_opts_cond">
12073 <param name="adv_opts_selector" value="advanced"/>
12074 <param name="ignore_proteins_per_peptide" value="false"/>
12075 <param name="scan_regex" value=""/>
12076 <param name="no_spectra_data_override" value="false"/>
12077 <param name="no_spectra_references_override" value="false"/>
12078 <param name="add_ionmatch_annotation" value="0.0"/>
12079 <param name="concatenate_peptides" value="false"/>
12080 <param name="number_of_hits" value="1"/>
12081 <param name="force" value="false"/>
12082 <param name="test" value="true"/>
12083 </conditional>
12084 <param name="in" value="IDFileConverter_27_input.idXML"/>
12085 <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12086 <param name="out_type" value="FASTA"/>
12087 <param name="mz_name" value=""/>
12088 <param name="peptideprophet_analyzed" value="false"/>
12089 <param name="score_type" value="qvalue"/>
12090 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12091 <output name="ctd_out" ftype="xml">
12092 <assert_contents>
12093 <is_valid_xml/>
12094 </assert_contents>
12095 </output>
12096 </test>
12097 <test expect_num_outputs="2">
12098 <conditional name="adv_opts_cond">
12099 <param name="adv_opts_selector" value="advanced"/>
12100 <param name="ignore_proteins_per_peptide" value="false"/>
12101 <param name="scan_regex" value=""/>
12102 <param name="no_spectra_data_override" value="false"/>
12103 <param name="no_spectra_references_override" value="false"/>
12104 <param name="add_ionmatch_annotation" value="0.0"/>
12105 <param name="concatenate_peptides" value="false"/>
12106 <param name="number_of_hits" value="-1"/>
12107 <param name="force" value="false"/>
12108 <param name="test" value="true"/>
12109 </conditional>
12110 <param name="in" value="IDFileConverter_27_input.idXML"/>
12111 <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12112 <param name="out_type" value="FASTA"/>
12113 <param name="mz_name" value=""/>
12114 <param name="peptideprophet_analyzed" value="false"/>
12115 <param name="score_type" value="qvalue"/>
12116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12117 <output name="ctd_out" ftype="xml">
12118 <assert_contents>
12119 <is_valid_xml/>
12120 </assert_contents>
12121 </output>
12122 </test>
12123 <test expect_num_outputs="2">
12124 <conditional name="adv_opts_cond">
12125 <param name="adv_opts_selector" value="advanced"/>
12126 <param name="ignore_proteins_per_peptide" value="false"/>
12127 <param name="scan_regex" value=""/>
12128 <param name="no_spectra_data_override" value="false"/>
12129 <param name="no_spectra_references_override" value="false"/>
12130 <param name="add_ionmatch_annotation" value="0.0"/>
12131 <param name="concatenate_peptides" value="true"/>
12132 <param name="number_of_hits" value="1"/>
12133 <param name="force" value="false"/>
12134 <param name="test" value="true"/>
12135 </conditional>
12136 <param name="in" value="IDFileConverter_27_input.idXML"/>
12137 <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12138 <param name="out_type" value="FASTA"/>
12139 <param name="mz_name" value=""/>
12140 <param name="peptideprophet_analyzed" value="false"/>
12141 <param name="score_type" value="qvalue"/>
12142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12143 <output name="ctd_out" ftype="xml">
12144 <assert_contents>
12145 <is_valid_xml/>
12146 </assert_contents>
12147 </output>
12148 </test>
12149 <test expect_num_outputs="2">
12150 <conditional name="adv_opts_cond">
12151 <param name="adv_opts_selector" value="advanced"/>
12152 <param name="ignore_proteins_per_peptide" value="false"/>
12153 <param name="scan_regex" value=""/>
12154 <param name="no_spectra_data_override" value="false"/>
12155 <param name="no_spectra_references_override" value="false"/>
12156 <param name="add_ionmatch_annotation" value="0.0"/>
12157 <param name="concatenate_peptides" value="true"/>
12158 <param name="number_of_hits" value="2"/>
12159 <param name="force" value="false"/>
12160 <param name="test" value="true"/>
12161 </conditional>
12162 <param name="in" value="IDFileConverter_27_input.idXML"/>
12163 <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12164 <param name="out_type" value="FASTA"/>
12165 <param name="mz_name" value=""/>
12166 <param name="peptideprophet_analyzed" value="false"/>
12167 <param name="score_type" value="qvalue"/>
12168 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12169 <output name="ctd_out" ftype="xml">
12170 <assert_contents>
12171 <is_valid_xml/>
12172 </assert_contents>
12173 </output>
12174 </test>
12175 <test expect_num_outputs="2">
12176 <conditional name="adv_opts_cond">
12177 <param name="adv_opts_selector" value="advanced"/>
12178 <param name="ignore_proteins_per_peptide" value="false"/>
12179 <param name="scan_regex" value=""/>
12180 <param name="no_spectra_data_override" value="false"/>
12181 <param name="no_spectra_references_override" value="false"/>
12182 <param name="add_ionmatch_annotation" value="0.0"/>
12183 <param name="concatenate_peptides" value="false"/>
12184 <param name="number_of_hits" value="1"/>
12185 <param name="force" value="false"/>
12186 <param name="test" value="true"/>
12187 </conditional>
12188 <param name="in" value="IDFileConverter_31_input.mzid"/>
12189 <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12190 <param name="out_type" value="idXML"/>
12191 <param name="mz_name" value=""/>
12192 <param name="peptideprophet_analyzed" value="false"/>
12193 <param name="score_type" value="qvalue"/>
12194 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12195 <output name="ctd_out" ftype="xml">
12196 <assert_contents>
12197 <is_valid_xml/>
12198 </assert_contents>
12199 </output>
12200 </test>
12201 </xml>
12202 <xml name="autotest_IDFilter">
12203 <test expect_num_outputs="2">
12204 <conditional name="adv_opts_cond">
12205 <param name="adv_opts_selector" value="advanced"/>
12206 <param name="remove_duplicate_psm" value="false"/>
12207 <param name="remove_peptide_hits_by_metavalue" value=""/>
12208 <param name="force" value="false"/>
12209 <param name="test" value="true"/>
12210 </conditional>
12211 <param name="in" value="IDFilter_1_input.idXML"/>
12212 <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12213 <param name="var_mods" value="false"/>
12214 <param name="remove_shared_peptides" value="false"/>
12215 <param name="keep_unreferenced_protein_hits" value="false"/>
12216 <param name="remove_decoys" value="false"/>
12217 <param name="delete_unreferenced_peptide_hits" value="false"/>
12218 <section name="precursor">
12219 <param name="rt" value=":"/>
12220 <param name="mz" value=":"/>
12221 <param name="length" value=":"/>
12222 <param name="charge" value=":"/>
12223 </section>
12224 <section name="score">
12225 <param name="pep" value="0.0"/>
12226 <param name="prot" value="0.0"/>
12227 <param name="protgroup" value="0.0"/>
12228 </section>
12229 <section name="whitelist">
12230 <param name="proteins" value="IDFilter_1_input.fas"/>
12231 <param name="protein_accessions" value=""/>
12232 <param name="ignore_modifications" value="false"/>
12233 <param name="modifications" value=""/>
12234 </section>
12235 <section name="blacklist">
12236 <param name="protein_accessions" value=""/>
12237 <param name="ignore_modifications" value="false"/>
12238 <param name="modifications" value=""/>
12239 </section>
12240 <section name="in_silico_digestion">
12241 <param name="enzyme" value="Trypsin"/>
12242 <param name="specificity" value="full"/>
12243 <param name="missed_cleavages" value="-1"/>
12244 <param name="methionine_cleavage" value="false"/>
12245 </section>
12246 <section name="missed_cleavages">
12247 <param name="number_of_missed_cleavages" value=":"/>
12248 <param name="enzyme" value="Trypsin"/>
12249 </section>
12250 <section name="rt">
12251 <param name="p_value" value="0.0"/>
12252 <param name="p_value_1st_dim" value="0.0"/>
12253 </section>
12254 <section name="mz">
12255 <param name="error" value="-1.0"/>
12256 <param name="unit" value="ppm"/>
12257 </section>
12258 <section name="best">
12259 <param name="n_peptide_hits" value="0"/>
12260 <param name="n_protein_hits" value="0"/>
12261 <param name="strict" value="false"/>
12262 <param name="n_to_m_peptide_hits" value=":"/>
12263 </section>
12264 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12265 <output name="ctd_out" ftype="xml">
12266 <assert_contents>
12267 <is_valid_xml/>
12268 </assert_contents>
12269 </output>
12270 </test>
12271 <test expect_num_outputs="2">
12272 <conditional name="adv_opts_cond">
12273 <param name="adv_opts_selector" value="advanced"/>
12274 <param name="remove_duplicate_psm" value="false"/>
12275 <param name="remove_peptide_hits_by_metavalue" value=""/>
12276 <param name="force" value="false"/>
12277 <param name="test" value="true"/>
12278 </conditional>
12279 <param name="in" value="IDFilter_3_input.idXML"/>
12280 <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12281 <param name="var_mods" value="false"/>
12282 <param name="remove_shared_peptides" value="false"/>
12283 <param name="keep_unreferenced_protein_hits" value="false"/>
12284 <param name="remove_decoys" value="false"/>
12285 <param name="delete_unreferenced_peptide_hits" value="false"/>
12286 <section name="precursor">
12287 <param name="rt" value=":"/>
12288 <param name="mz" value=":"/>
12289 <param name="length" value=":"/>
12290 <param name="charge" value=":"/>
12291 </section>
12292 <section name="score">
12293 <param name="pep" value="0.0"/>
12294 <param name="prot" value="0.0"/>
12295 <param name="protgroup" value="0.0"/>
12296 </section>
12297 <section name="whitelist">
12298 <param name="protein_accessions" value=""/>
12299 <param name="ignore_modifications" value="false"/>
12300 <param name="modifications" value=""/>
12301 </section>
12302 <section name="blacklist">
12303 <param name="protein_accessions" value=""/>
12304 <param name="peptides" value="IDFilter_3_2_input.idXML"/>
12305 <param name="ignore_modifications" value="false"/>
12306 <param name="modifications" value=""/>
12307 </section>
12308 <section name="in_silico_digestion">
12309 <param name="enzyme" value="Trypsin"/>
12310 <param name="specificity" value="full"/>
12311 <param name="missed_cleavages" value="-1"/>
12312 <param name="methionine_cleavage" value="false"/>
12313 </section>
12314 <section name="missed_cleavages">
12315 <param name="number_of_missed_cleavages" value=":"/>
12316 <param name="enzyme" value="Trypsin"/>
12317 </section>
12318 <section name="rt">
12319 <param name="p_value" value="0.0"/>
12320 <param name="p_value_1st_dim" value="0.0"/>
12321 </section>
12322 <section name="mz">
12323 <param name="error" value="-1.0"/>
12324 <param name="unit" value="ppm"/>
12325 </section>
12326 <section name="best">
12327 <param name="n_peptide_hits" value="0"/>
12328 <param name="n_protein_hits" value="0"/>
12329 <param name="strict" value="false"/>
12330 <param name="n_to_m_peptide_hits" value=":"/>
12331 </section>
12332 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12333 <output name="ctd_out" ftype="xml">
12334 <assert_contents>
12335 <is_valid_xml/>
12336 </assert_contents>
12337 </output>
12338 </test>
12339 <test expect_num_outputs="2">
12340 <conditional name="adv_opts_cond">
12341 <param name="adv_opts_selector" value="advanced"/>
12342 <param name="remove_duplicate_psm" value="false"/>
12343 <param name="remove_peptide_hits_by_metavalue" value=""/>
12344 <param name="force" value="false"/>
12345 <param name="test" value="true"/>
12346 </conditional>
12347 <param name="in" value="IDFilter_4_input.idXML"/>
12348 <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12349 <param name="var_mods" value="false"/>
12350 <param name="remove_shared_peptides" value="false"/>
12351 <param name="keep_unreferenced_protein_hits" value="false"/>
12352 <param name="remove_decoys" value="false"/>
12353 <param name="delete_unreferenced_peptide_hits" value="false"/>
12354 <section name="precursor">
12355 <param name="rt" value=":"/>
12356 <param name="mz" value=":"/>
12357 <param name="length" value=":"/>
12358 <param name="charge" value=":"/>
12359 </section>
12360 <section name="score">
12361 <param name="pep" value="0.0"/>
12362 <param name="prot" value="0.0"/>
12363 <param name="protgroup" value="0.0"/>
12364 </section>
12365 <section name="whitelist">
12366 <param name="protein_accessions" value=""/>
12367 <param name="ignore_modifications" value="false"/>
12368 <param name="modifications" value=""/>
12369 </section>
12370 <section name="blacklist">
12371 <param name="protein_accessions" value=""/>
12372 <param name="ignore_modifications" value="false"/>
12373 <param name="modifications" value=""/>
12374 </section>
12375 <section name="in_silico_digestion">
12376 <param name="enzyme" value="Trypsin"/>
12377 <param name="specificity" value="full"/>
12378 <param name="missed_cleavages" value="-1"/>
12379 <param name="methionine_cleavage" value="false"/>
12380 </section>
12381 <section name="missed_cleavages">
12382 <param name="number_of_missed_cleavages" value=":"/>
12383 <param name="enzyme" value="Trypsin"/>
12384 </section>
12385 <section name="rt">
12386 <param name="p_value" value="0.08"/>
12387 <param name="p_value_1st_dim" value="0.0"/>
12388 </section>
12389 <section name="mz">
12390 <param name="error" value="-1.0"/>
12391 <param name="unit" value="ppm"/>
12392 </section>
12393 <section name="best">
12394 <param name="n_peptide_hits" value="0"/>
12395 <param name="n_protein_hits" value="0"/>
12396 <param name="strict" value="false"/>
12397 <param name="n_to_m_peptide_hits" value=":"/>
12398 </section>
12399 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12400 <output name="ctd_out" ftype="xml">
12401 <assert_contents>
12402 <is_valid_xml/>
12403 </assert_contents>
12404 </output>
12405 </test>
12406 <test expect_num_outputs="2">
12407 <conditional name="adv_opts_cond">
12408 <param name="adv_opts_selector" value="advanced"/>
12409 <param name="remove_duplicate_psm" value="false"/>
12410 <param name="remove_peptide_hits_by_metavalue" value=""/>
12411 <param name="force" value="false"/>
12412 <param name="test" value="true"/>
12413 </conditional>
12414 <param name="in" value="IDFilter_5_input.idXML"/>
12415 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12416 <param name="var_mods" value="false"/>
12417 <param name="remove_shared_peptides" value="false"/>
12418 <param name="keep_unreferenced_protein_hits" value="false"/>
12419 <param name="remove_decoys" value="false"/>
12420 <param name="delete_unreferenced_peptide_hits" value="false"/>
12421 <section name="precursor">
12422 <param name="rt" value=":"/>
12423 <param name="mz" value=":"/>
12424 <param name="length" value=":"/>
12425 <param name="charge" value=":"/>
12426 </section>
12427 <section name="score">
12428 <param name="pep" value="32.0"/>
12429 <param name="prot" value="25.0"/>
12430 <param name="protgroup" value="0.0"/>
12431 </section>
12432 <section name="whitelist">
12433 <param name="protein_accessions" value=""/>
12434 <param name="ignore_modifications" value="false"/>
12435 <param name="modifications" value=""/>
12436 </section>
12437 <section name="blacklist">
12438 <param name="protein_accessions" value=""/>
12439 <param name="ignore_modifications" value="false"/>
12440 <param name="modifications" value=""/>
12441 </section>
12442 <section name="in_silico_digestion">
12443 <param name="enzyme" value="Trypsin"/>
12444 <param name="specificity" value="full"/>
12445 <param name="missed_cleavages" value="-1"/>
12446 <param name="methionine_cleavage" value="false"/>
12447 </section>
12448 <section name="missed_cleavages">
12449 <param name="number_of_missed_cleavages" value=":"/>
12450 <param name="enzyme" value="Trypsin"/>
12451 </section>
12452 <section name="rt">
12453 <param name="p_value" value="0.0"/>
12454 <param name="p_value_1st_dim" value="0.0"/>
12455 </section>
12456 <section name="mz">
12457 <param name="error" value="-1.0"/>
12458 <param name="unit" value="ppm"/>
12459 </section>
12460 <section name="best">
12461 <param name="n_peptide_hits" value="0"/>
12462 <param name="n_protein_hits" value="0"/>
12463 <param name="strict" value="false"/>
12464 <param name="n_to_m_peptide_hits" value=":"/>
12465 </section>
12466 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12467 <output name="ctd_out" ftype="xml">
12468 <assert_contents>
12469 <is_valid_xml/>
12470 </assert_contents>
12471 </output>
12472 </test>
12473 <test expect_num_outputs="2">
12474 <conditional name="adv_opts_cond">
12475 <param name="adv_opts_selector" value="advanced"/>
12476 <param name="remove_duplicate_psm" value="false"/>
12477 <param name="remove_peptide_hits_by_metavalue" value=""/>
12478 <param name="force" value="false"/>
12479 <param name="test" value="true"/>
12480 </conditional>
12481 <param name="in" value="IDFilter_5_input.idXML"/>
12482 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12483 <param name="var_mods" value="false"/>
12484 <param name="remove_shared_peptides" value="false"/>
12485 <param name="keep_unreferenced_protein_hits" value="false"/>
12486 <param name="remove_decoys" value="false"/>
12487 <param name="delete_unreferenced_peptide_hits" value="false"/>
12488 <section name="precursor">
12489 <param name="rt" value=":"/>
12490 <param name="mz" value=":"/>
12491 <param name="length" value=":"/>
12492 <param name="charge" value=":"/>
12493 </section>
12494 <section name="score">
12495 <param name="pep" value="32.0"/>
12496 <param name="prot" value="0.0"/>
12497 <param name="protgroup" value="0.0"/>
12498 </section>
12499 <section name="whitelist">
12500 <param name="protein_accessions" value=""/>
12501 <param name="ignore_modifications" value="false"/>
12502 <param name="modifications" value=""/>
12503 </section>
12504 <section name="blacklist">
12505 <param name="protein_accessions" value=""/>
12506 <param name="ignore_modifications" value="false"/>
12507 <param name="modifications" value=""/>
12508 </section>
12509 <section name="in_silico_digestion">
12510 <param name="enzyme" value="Trypsin"/>
12511 <param name="specificity" value="full"/>
12512 <param name="missed_cleavages" value="-1"/>
12513 <param name="methionine_cleavage" value="false"/>
12514 </section>
12515 <section name="missed_cleavages">
12516 <param name="number_of_missed_cleavages" value=":"/>
12517 <param name="enzyme" value="Trypsin"/>
12518 </section>
12519 <section name="rt">
12520 <param name="p_value" value="0.0"/>
12521 <param name="p_value_1st_dim" value="0.0"/>
12522 </section>
12523 <section name="mz">
12524 <param name="error" value="-1.0"/>
12525 <param name="unit" value="ppm"/>
12526 </section>
12527 <section name="best">
12528 <param name="n_peptide_hits" value="0"/>
12529 <param name="n_protein_hits" value="0"/>
12530 <param name="strict" value="false"/>
12531 <param name="n_to_m_peptide_hits" value=":"/>
12532 </section>
12533 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12534 <output name="ctd_out" ftype="xml">
12535 <assert_contents>
12536 <is_valid_xml/>
12537 </assert_contents>
12538 </output>
12539 </test>
12540 <test expect_num_outputs="2">
12541 <conditional name="adv_opts_cond">
12542 <param name="adv_opts_selector" value="advanced"/>
12543 <param name="remove_duplicate_psm" value="false"/>
12544 <param name="remove_peptide_hits_by_metavalue" value=""/>
12545 <param name="force" value="false"/>
12546 <param name="test" value="true"/>
12547 </conditional>
12548 <param name="in" value="IDFilter_5_input.idXML"/>
12549 <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12550 <param name="var_mods" value="false"/>
12551 <param name="remove_shared_peptides" value="false"/>
12552 <param name="keep_unreferenced_protein_hits" value="false"/>
12553 <param name="remove_decoys" value="false"/>
12554 <param name="delete_unreferenced_peptide_hits" value="false"/>
12555 <section name="precursor">
12556 <param name="rt" value=":"/>
12557 <param name="mz" value=":"/>
12558 <param name="length" value=":"/>
12559 <param name="charge" value=":"/>
12560 </section>
12561 <section name="score">
12562 <param name="pep" value="0.0"/>
12563 <param name="prot" value="25.0"/>
12564 <param name="protgroup" value="0.0"/>
12565 </section>
12566 <section name="whitelist">
12567 <param name="protein_accessions" value=""/>
12568 <param name="ignore_modifications" value="false"/>
12569 <param name="modifications" value=""/>
12570 </section>
12571 <section name="blacklist">
12572 <param name="protein_accessions" value=""/>
12573 <param name="ignore_modifications" value="false"/>
12574 <param name="modifications" value=""/>
12575 </section>
12576 <section name="in_silico_digestion">
12577 <param name="enzyme" value="Trypsin"/>
12578 <param name="specificity" value="full"/>
12579 <param name="missed_cleavages" value="-1"/>
12580 <param name="methionine_cleavage" value="false"/>
12581 </section>
12582 <section name="missed_cleavages">
12583 <param name="number_of_missed_cleavages" value=":"/>
12584 <param name="enzyme" value="Trypsin"/>
12585 </section>
12586 <section name="rt">
12587 <param name="p_value" value="0.0"/>
12588 <param name="p_value_1st_dim" value="0.0"/>
12589 </section>
12590 <section name="mz">
12591 <param name="error" value="-1.0"/>
12592 <param name="unit" value="ppm"/>
12593 </section>
12594 <section name="best">
12595 <param name="n_peptide_hits" value="0"/>
12596 <param name="n_protein_hits" value="0"/>
12597 <param name="strict" value="false"/>
12598 <param name="n_to_m_peptide_hits" value=":"/>
12599 </section>
12600 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12601 <output name="ctd_out" ftype="xml">
12602 <assert_contents>
12603 <is_valid_xml/>
12604 </assert_contents>
12605 </output>
12606 </test>
12607 <test expect_num_outputs="2">
12608 <conditional name="adv_opts_cond">
12609 <param name="adv_opts_selector" value="advanced"/>
12610 <param name="remove_duplicate_psm" value="false"/>
12611 <param name="remove_peptide_hits_by_metavalue" value=""/>
12612 <param name="force" value="false"/>
12613 <param name="test" value="true"/>
12614 </conditional>
12615 <param name="in" value="IDFilter_5_input.idXML"/>
12616 <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12617 <param name="var_mods" value="false"/>
12618 <param name="remove_shared_peptides" value="false"/>
12619 <param name="keep_unreferenced_protein_hits" value="false"/>
12620 <param name="remove_decoys" value="false"/>
12621 <param name="delete_unreferenced_peptide_hits" value="true"/>
12622 <section name="precursor">
12623 <param name="rt" value=":"/>
12624 <param name="mz" value=":"/>
12625 <param name="length" value=":"/>
12626 <param name="charge" value=":"/>
12627 </section>
12628 <section name="score">
12629 <param name="pep" value="0.0"/>
12630 <param name="prot" value="25.0"/>
12631 <param name="protgroup" value="0.0"/>
12632 </section>
12633 <section name="whitelist">
12634 <param name="protein_accessions" value=""/>
12635 <param name="ignore_modifications" value="false"/>
12636 <param name="modifications" value=""/>
12637 </section>
12638 <section name="blacklist">
12639 <param name="protein_accessions" value=""/>
12640 <param name="ignore_modifications" value="false"/>
12641 <param name="modifications" value=""/>
12642 </section>
12643 <section name="in_silico_digestion">
12644 <param name="enzyme" value="Trypsin"/>
12645 <param name="specificity" value="full"/>
12646 <param name="missed_cleavages" value="-1"/>
12647 <param name="methionine_cleavage" value="false"/>
12648 </section>
12649 <section name="missed_cleavages">
12650 <param name="number_of_missed_cleavages" value=":"/>
12651 <param name="enzyme" value="Trypsin"/>
12652 </section>
12653 <section name="rt">
12654 <param name="p_value" value="0.0"/>
12655 <param name="p_value_1st_dim" value="0.0"/>
12656 </section>
12657 <section name="mz">
12658 <param name="error" value="-1.0"/>
12659 <param name="unit" value="ppm"/>
12660 </section>
12661 <section name="best">
12662 <param name="n_peptide_hits" value="0"/>
12663 <param name="n_protein_hits" value="0"/>
12664 <param name="strict" value="false"/>
12665 <param name="n_to_m_peptide_hits" value=":"/>
12666 </section>
12667 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12668 <output name="ctd_out" ftype="xml">
12669 <assert_contents>
12670 <is_valid_xml/>
12671 </assert_contents>
12672 </output>
12673 </test>
12674 <test expect_num_outputs="2">
12675 <conditional name="adv_opts_cond">
12676 <param name="adv_opts_selector" value="advanced"/>
12677 <param name="remove_duplicate_psm" value="false"/>
12678 <param name="remove_peptide_hits_by_metavalue" value=""/>
12679 <param name="force" value="false"/>
12680 <param name="test" value="true"/>
12681 </conditional>
12682 <param name="in" value="IDFilter_6_input.idXML"/>
12683 <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12684 <param name="var_mods" value="false"/>
12685 <param name="remove_shared_peptides" value="false"/>
12686 <param name="keep_unreferenced_protein_hits" value="false"/>
12687 <param name="remove_decoys" value="false"/>
12688 <param name="delete_unreferenced_peptide_hits" value="false"/>
12689 <section name="precursor">
12690 <param name="rt" value=":"/>
12691 <param name="mz" value=":"/>
12692 <param name="length" value=":"/>
12693 <param name="charge" value=":"/>
12694 </section>
12695 <section name="score">
12696 <param name="pep" value="0.0"/>
12697 <param name="prot" value="0.0"/>
12698 <param name="protgroup" value="0.0"/>
12699 </section>
12700 <section name="whitelist">
12701 <param name="protein_accessions" value=""/>
12702 <param name="ignore_modifications" value="false"/>
12703 <param name="modifications" value=""/>
12704 </section>
12705 <section name="blacklist">
12706 <param name="protein_accessions" value=""/>
12707 <param name="ignore_modifications" value="false"/>
12708 <param name="modifications" value=""/>
12709 </section>
12710 <section name="in_silico_digestion">
12711 <param name="enzyme" value="Trypsin"/>
12712 <param name="specificity" value="full"/>
12713 <param name="missed_cleavages" value="-1"/>
12714 <param name="methionine_cleavage" value="false"/>
12715 </section>
12716 <section name="missed_cleavages">
12717 <param name="number_of_missed_cleavages" value=":"/>
12718 <param name="enzyme" value="Trypsin"/>
12719 </section>
12720 <section name="rt">
12721 <param name="p_value" value="0.0"/>
12722 <param name="p_value_1st_dim" value="0.0"/>
12723 </section>
12724 <section name="mz">
12725 <param name="error" value="-1.0"/>
12726 <param name="unit" value="ppm"/>
12727 </section>
12728 <section name="best">
12729 <param name="n_peptide_hits" value="2"/>
12730 <param name="n_protein_hits" value="10"/>
12731 <param name="strict" value="false"/>
12732 <param name="n_to_m_peptide_hits" value=":"/>
12733 </section>
12734 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12735 <output name="ctd_out" ftype="xml">
12736 <assert_contents>
12737 <is_valid_xml/>
12738 </assert_contents>
12739 </output>
12740 </test>
12741 <test expect_num_outputs="2">
12742 <conditional name="adv_opts_cond">
12743 <param name="adv_opts_selector" value="advanced"/>
12744 <param name="remove_duplicate_psm" value="true"/>
12745 <param name="remove_peptide_hits_by_metavalue" value=""/>
12746 <param name="force" value="false"/>
12747 <param name="test" value="true"/>
12748 </conditional>
12749 <param name="in" value="IDFilter_7_input.idXML"/>
12750 <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12751 <param name="var_mods" value="false"/>
12752 <param name="remove_shared_peptides" value="false"/>
12753 <param name="keep_unreferenced_protein_hits" value="false"/>
12754 <param name="remove_decoys" value="false"/>
12755 <param name="delete_unreferenced_peptide_hits" value="false"/>
12756 <section name="precursor">
12757 <param name="rt" value=":"/>
12758 <param name="mz" value=":"/>
12759 <param name="length" value=":"/>
12760 <param name="charge" value=":"/>
12761 </section>
12762 <section name="score">
12763 <param name="pep" value="0.0"/>
12764 <param name="prot" value="0.0"/>
12765 <param name="protgroup" value="0.0"/>
12766 </section>
12767 <section name="whitelist">
12768 <param name="protein_accessions" value=""/>
12769 <param name="ignore_modifications" value="false"/>
12770 <param name="modifications" value=""/>
12771 </section>
12772 <section name="blacklist">
12773 <param name="protein_accessions" value=""/>
12774 <param name="ignore_modifications" value="false"/>
12775 <param name="modifications" value=""/>
12776 </section>
12777 <section name="in_silico_digestion">
12778 <param name="enzyme" value="Trypsin"/>
12779 <param name="specificity" value="full"/>
12780 <param name="missed_cleavages" value="-1"/>
12781 <param name="methionine_cleavage" value="false"/>
12782 </section>
12783 <section name="missed_cleavages">
12784 <param name="number_of_missed_cleavages" value=":"/>
12785 <param name="enzyme" value="Trypsin"/>
12786 </section>
12787 <section name="rt">
12788 <param name="p_value" value="0.0"/>
12789 <param name="p_value_1st_dim" value="0.0"/>
12790 </section>
12791 <section name="mz">
12792 <param name="error" value="-1.0"/>
12793 <param name="unit" value="ppm"/>
12794 </section>
12795 <section name="best">
12796 <param name="n_peptide_hits" value="0"/>
12797 <param name="n_protein_hits" value="0"/>
12798 <param name="strict" value="false"/>
12799 <param name="n_to_m_peptide_hits" value=":"/>
12800 </section>
12801 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12802 <output name="ctd_out" ftype="xml">
12803 <assert_contents>
12804 <is_valid_xml/>
12805 </assert_contents>
12806 </output>
12807 </test>
12808 <test expect_num_outputs="2">
12809 <conditional name="adv_opts_cond">
12810 <param name="adv_opts_selector" value="advanced"/>
12811 <param name="remove_duplicate_psm" value="false"/>
12812 <param name="remove_peptide_hits_by_metavalue" value=""/>
12813 <param name="force" value="false"/>
12814 <param name="test" value="true"/>
12815 </conditional>
12816 <param name="in" value="IDFilter_8_input.idXML"/>
12817 <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12818 <param name="var_mods" value="false"/>
12819 <param name="remove_shared_peptides" value="false"/>
12820 <param name="keep_unreferenced_protein_hits" value="false"/>
12821 <param name="remove_decoys" value="false"/>
12822 <param name="delete_unreferenced_peptide_hits" value="false"/>
12823 <section name="precursor">
12824 <param name="rt" value="200:350"/>
12825 <param name="mz" value="999:1000"/>
12826 <param name="length" value=":"/>
12827 <param name="charge" value=":"/>
12828 </section>
12829 <section name="score">
12830 <param name="pep" value="0.0"/>
12831 <param name="prot" value="0.0"/>
12832 <param name="protgroup" value="0.0"/>
12833 </section>
12834 <section name="whitelist">
12835 <param name="protein_accessions" value=""/>
12836 <param name="ignore_modifications" value="false"/>
12837 <param name="modifications" value=""/>
12838 </section>
12839 <section name="blacklist">
12840 <param name="protein_accessions" value=""/>
12841 <param name="ignore_modifications" value="false"/>
12842 <param name="modifications" value=""/>
12843 </section>
12844 <section name="in_silico_digestion">
12845 <param name="enzyme" value="Trypsin"/>
12846 <param name="specificity" value="full"/>
12847 <param name="missed_cleavages" value="-1"/>
12848 <param name="methionine_cleavage" value="false"/>
12849 </section>
12850 <section name="missed_cleavages">
12851 <param name="number_of_missed_cleavages" value=":"/>
12852 <param name="enzyme" value="Trypsin"/>
12853 </section>
12854 <section name="rt">
12855 <param name="p_value" value="0.0"/>
12856 <param name="p_value_1st_dim" value="0.0"/>
12857 </section>
12858 <section name="mz">
12859 <param name="error" value="-1.0"/>
12860 <param name="unit" value="ppm"/>
12861 </section>
12862 <section name="best">
12863 <param name="n_peptide_hits" value="0"/>
12864 <param name="n_protein_hits" value="0"/>
12865 <param name="strict" value="false"/>
12866 <param name="n_to_m_peptide_hits" value=":"/>
12867 </section>
12868 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12869 <output name="ctd_out" ftype="xml">
12870 <assert_contents>
12871 <is_valid_xml/>
12872 </assert_contents>
12873 </output>
12874 </test>
12875 <test expect_num_outputs="2">
12876 <conditional name="adv_opts_cond">
12877 <param name="adv_opts_selector" value="advanced"/>
12878 <param name="remove_duplicate_psm" value="false"/>
12879 <param name="remove_peptide_hits_by_metavalue" value=""/>
12880 <param name="force" value="false"/>
12881 <param name="test" value="true"/>
12882 </conditional>
12883 <param name="in" value="IDFilter_9_input.idXML"/>
12884 <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12885 <param name="var_mods" value="false"/>
12886 <param name="remove_shared_peptides" value="false"/>
12887 <param name="keep_unreferenced_protein_hits" value="false"/>
12888 <param name="remove_decoys" value="false"/>
12889 <param name="delete_unreferenced_peptide_hits" value="false"/>
12890 <section name="precursor">
12891 <param name="rt" value=":"/>
12892 <param name="mz" value=":"/>
12893 <param name="length" value=":"/>
12894 <param name="charge" value=":"/>
12895 </section>
12896 <section name="score">
12897 <param name="pep" value="0.05"/>
12898 <param name="prot" value="0.0"/>
12899 <param name="protgroup" value="0.0"/>
12900 </section>
12901 <section name="whitelist">
12902 <param name="protein_accessions" value=""/>
12903 <param name="ignore_modifications" value="false"/>
12904 <param name="modifications" value=""/>
12905 </section>
12906 <section name="blacklist">
12907 <param name="protein_accessions" value=""/>
12908 <param name="ignore_modifications" value="false"/>
12909 <param name="modifications" value=""/>
12910 </section>
12911 <section name="in_silico_digestion">
12912 <param name="enzyme" value="Trypsin"/>
12913 <param name="specificity" value="full"/>
12914 <param name="missed_cleavages" value="-1"/>
12915 <param name="methionine_cleavage" value="false"/>
12916 </section>
12917 <section name="missed_cleavages">
12918 <param name="number_of_missed_cleavages" value=":"/>
12919 <param name="enzyme" value="Trypsin"/>
12920 </section>
12921 <section name="rt">
12922 <param name="p_value" value="0.0"/>
12923 <param name="p_value_1st_dim" value="0.0"/>
12924 </section>
12925 <section name="mz">
12926 <param name="error" value="-1.0"/>
12927 <param name="unit" value="ppm"/>
12928 </section>
12929 <section name="best">
12930 <param name="n_peptide_hits" value="0"/>
12931 <param name="n_protein_hits" value="0"/>
12932 <param name="strict" value="false"/>
12933 <param name="n_to_m_peptide_hits" value=":"/>
12934 </section>
12935 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12936 <output name="ctd_out" ftype="xml">
12937 <assert_contents>
12938 <is_valid_xml/>
12939 </assert_contents>
12940 </output>
12941 </test>
12942 <test expect_num_outputs="2">
12943 <conditional name="adv_opts_cond">
12944 <param name="adv_opts_selector" value="advanced"/>
12945 <param name="remove_duplicate_psm" value="false"/>
12946 <param name="remove_peptide_hits_by_metavalue" value=""/>
12947 <param name="force" value="false"/>
12948 <param name="test" value="true"/>
12949 </conditional>
12950 <param name="in" value="IDFilter_10_input.idXML"/>
12951 <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12952 <param name="var_mods" value="false"/>
12953 <param name="remove_shared_peptides" value="false"/>
12954 <param name="keep_unreferenced_protein_hits" value="false"/>
12955 <param name="remove_decoys" value="false"/>
12956 <param name="delete_unreferenced_peptide_hits" value="true"/>
12957 <section name="precursor">
12958 <param name="rt" value=":"/>
12959 <param name="mz" value=":"/>
12960 <param name="length" value=":"/>
12961 <param name="charge" value=":"/>
12962 </section>
12963 <section name="score">
12964 <param name="pep" value="0.0"/>
12965 <param name="prot" value="0.3"/>
12966 <param name="protgroup" value="0.0"/>
12967 </section>
12968 <section name="whitelist">
12969 <param name="protein_accessions" value=""/>
12970 <param name="ignore_modifications" value="false"/>
12971 <param name="modifications" value=""/>
12972 </section>
12973 <section name="blacklist">
12974 <param name="protein_accessions" value=""/>
12975 <param name="ignore_modifications" value="false"/>
12976 <param name="modifications" value=""/>
12977 </section>
12978 <section name="in_silico_digestion">
12979 <param name="enzyme" value="Trypsin"/>
12980 <param name="specificity" value="full"/>
12981 <param name="missed_cleavages" value="-1"/>
12982 <param name="methionine_cleavage" value="false"/>
12983 </section>
12984 <section name="missed_cleavages">
12985 <param name="number_of_missed_cleavages" value=":"/>
12986 <param name="enzyme" value="Trypsin"/>
12987 </section>
12988 <section name="rt">
12989 <param name="p_value" value="0.0"/>
12990 <param name="p_value_1st_dim" value="0.0"/>
12991 </section>
12992 <section name="mz">
12993 <param name="error" value="-1.0"/>
12994 <param name="unit" value="ppm"/>
12995 </section>
12996 <section name="best">
12997 <param name="n_peptide_hits" value="0"/>
12998 <param name="n_protein_hits" value="0"/>
12999 <param name="strict" value="false"/>
13000 <param name="n_to_m_peptide_hits" value=":"/>
13001 </section>
13002 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13003 <output name="ctd_out" ftype="xml">
13004 <assert_contents>
13005 <is_valid_xml/>
13006 </assert_contents>
13007 </output>
13008 </test>
13009 <test expect_num_outputs="2">
13010 <conditional name="adv_opts_cond">
13011 <param name="adv_opts_selector" value="advanced"/>
13012 <param name="remove_duplicate_psm" value="false"/>
13013 <param name="remove_peptide_hits_by_metavalue" value=""/>
13014 <param name="force" value="false"/>
13015 <param name="test" value="true"/>
13016 </conditional>
13017 <param name="in" value="IDFilter_11_input.idXML"/>
13018 <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13019 <param name="var_mods" value="false"/>
13020 <param name="remove_shared_peptides" value="false"/>
13021 <param name="keep_unreferenced_protein_hits" value="false"/>
13022 <param name="remove_decoys" value="true"/>
13023 <param name="delete_unreferenced_peptide_hits" value="true"/>
13024 <section name="precursor">
13025 <param name="rt" value=":"/>
13026 <param name="mz" value=":"/>
13027 <param name="length" value=":"/>
13028 <param name="charge" value=":"/>
13029 </section>
13030 <section name="score">
13031 <param name="pep" value="0.0"/>
13032 <param name="prot" value="0.0"/>
13033 <param name="protgroup" value="0.0"/>
13034 </section>
13035 <section name="whitelist">
13036 <param name="protein_accessions" value=""/>
13037 <param name="ignore_modifications" value="false"/>
13038 <param name="modifications" value=""/>
13039 </section>
13040 <section name="blacklist">
13041 <param name="protein_accessions" value=""/>
13042 <param name="ignore_modifications" value="false"/>
13043 <param name="modifications" value=""/>
13044 </section>
13045 <section name="in_silico_digestion">
13046 <param name="enzyme" value="Trypsin"/>
13047 <param name="specificity" value="full"/>
13048 <param name="missed_cleavages" value="-1"/>
13049 <param name="methionine_cleavage" value="false"/>
13050 </section>
13051 <section name="missed_cleavages">
13052 <param name="number_of_missed_cleavages" value=":"/>
13053 <param name="enzyme" value="Trypsin"/>
13054 </section>
13055 <section name="rt">
13056 <param name="p_value" value="0.0"/>
13057 <param name="p_value_1st_dim" value="0.0"/>
13058 </section>
13059 <section name="mz">
13060 <param name="error" value="-1.0"/>
13061 <param name="unit" value="ppm"/>
13062 </section>
13063 <section name="best">
13064 <param name="n_peptide_hits" value="0"/>
13065 <param name="n_protein_hits" value="0"/>
13066 <param name="strict" value="false"/>
13067 <param name="n_to_m_peptide_hits" value=":"/>
13068 </section>
13069 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13070 <output name="ctd_out" ftype="xml">
13071 <assert_contents>
13072 <is_valid_xml/>
13073 </assert_contents>
13074 </output>
13075 </test>
13076 <test expect_num_outputs="2">
13077 <conditional name="adv_opts_cond">
13078 <param name="adv_opts_selector" value="advanced"/>
13079 <param name="remove_duplicate_psm" value="false"/>
13080 <param name="remove_peptide_hits_by_metavalue" value=""/>
13081 <param name="force" value="false"/>
13082 <param name="test" value="true"/>
13083 </conditional>
13084 <param name="in" value="IDFilter_12_input.idXML"/>
13085 <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13086 <param name="var_mods" value="false"/>
13087 <param name="remove_shared_peptides" value="false"/>
13088 <param name="keep_unreferenced_protein_hits" value="false"/>
13089 <param name="remove_decoys" value="false"/>
13090 <param name="delete_unreferenced_peptide_hits" value="false"/>
13091 <section name="precursor">
13092 <param name="rt" value=":"/>
13093 <param name="mz" value=":"/>
13094 <param name="length" value=":"/>
13095 <param name="charge" value=":"/>
13096 </section>
13097 <section name="score">
13098 <param name="pep" value="0.0"/>
13099 <param name="prot" value="0.0"/>
13100 <param name="protgroup" value="0.0"/>
13101 </section>
13102 <section name="whitelist">
13103 <param name="protein_accessions" value=""/>
13104 <param name="ignore_modifications" value="false"/>
13105 <param name="modifications" value=""/>
13106 </section>
13107 <section name="blacklist">
13108 <param name="protein_accessions" value=""/>
13109 <param name="ignore_modifications" value="false"/>
13110 <param name="modifications" value=""/>
13111 </section>
13112 <section name="in_silico_digestion">
13113 <param name="fasta" value="IDFilter_12_input.fasta"/>
13114 <param name="enzyme" value="Trypsin"/>
13115 <param name="specificity" value="full"/>
13116 <param name="missed_cleavages" value="-1"/>
13117 <param name="methionine_cleavage" value="false"/>
13118 </section>
13119 <section name="missed_cleavages">
13120 <param name="number_of_missed_cleavages" value=":"/>
13121 <param name="enzyme" value="Trypsin"/>
13122 </section>
13123 <section name="rt">
13124 <param name="p_value" value="0.0"/>
13125 <param name="p_value_1st_dim" value="0.0"/>
13126 </section>
13127 <section name="mz">
13128 <param name="error" value="-1.0"/>
13129 <param name="unit" value="ppm"/>
13130 </section>
13131 <section name="best">
13132 <param name="n_peptide_hits" value="0"/>
13133 <param name="n_protein_hits" value="0"/>
13134 <param name="strict" value="false"/>
13135 <param name="n_to_m_peptide_hits" value=":"/>
13136 </section>
13137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13138 <output name="ctd_out" ftype="xml">
13139 <assert_contents>
13140 <is_valid_xml/>
13141 </assert_contents>
13142 </output>
13143 </test>
13144 <test expect_num_outputs="2">
13145 <conditional name="adv_opts_cond">
13146 <param name="adv_opts_selector" value="advanced"/>
13147 <param name="remove_duplicate_psm" value="false"/>
13148 <param name="remove_peptide_hits_by_metavalue" value=""/>
13149 <param name="force" value="false"/>
13150 <param name="test" value="true"/>
13151 </conditional>
13152 <param name="in" value="IDFilter_13_input.idXML"/>
13153 <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13154 <param name="var_mods" value="false"/>
13155 <param name="remove_shared_peptides" value="false"/>
13156 <param name="keep_unreferenced_protein_hits" value="false"/>
13157 <param name="remove_decoys" value="false"/>
13158 <param name="delete_unreferenced_peptide_hits" value="false"/>
13159 <section name="precursor">
13160 <param name="rt" value=":"/>
13161 <param name="mz" value=":"/>
13162 <param name="length" value=":"/>
13163 <param name="charge" value=":"/>
13164 </section>
13165 <section name="score">
13166 <param name="pep" value="0.0"/>
13167 <param name="prot" value="0.0"/>
13168 <param name="protgroup" value="0.0"/>
13169 </section>
13170 <section name="whitelist">
13171 <param name="protein_accessions" value=""/>
13172 <param name="ignore_modifications" value="false"/>
13173 <param name="modifications" value=""/>
13174 </section>
13175 <section name="blacklist">
13176 <param name="protein_accessions" value=""/>
13177 <param name="ignore_modifications" value="false"/>
13178 <param name="modifications" value=""/>
13179 </section>
13180 <section name="in_silico_digestion">
13181 <param name="fasta" value="IDFilter_13_input.fasta"/>
13182 <param name="enzyme" value="Trypsin"/>
13183 <param name="specificity" value="full"/>
13184 <param name="missed_cleavages" value="1"/>
13185 <param name="methionine_cleavage" value="false"/>
13186 </section>
13187 <section name="missed_cleavages">
13188 <param name="number_of_missed_cleavages" value=":"/>
13189 <param name="enzyme" value="Trypsin"/>
13190 </section>
13191 <section name="rt">
13192 <param name="p_value" value="0.0"/>
13193 <param name="p_value_1st_dim" value="0.0"/>
13194 </section>
13195 <section name="mz">
13196 <param name="error" value="-1.0"/>
13197 <param name="unit" value="ppm"/>
13198 </section>
13199 <section name="best">
13200 <param name="n_peptide_hits" value="0"/>
13201 <param name="n_protein_hits" value="0"/>
13202 <param name="strict" value="false"/>
13203 <param name="n_to_m_peptide_hits" value=":"/>
13204 </section>
13205 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13206 <output name="ctd_out" ftype="xml">
13207 <assert_contents>
13208 <is_valid_xml/>
13209 </assert_contents>
13210 </output>
13211 </test>
13212 <test expect_num_outputs="2">
13213 <conditional name="adv_opts_cond">
13214 <param name="adv_opts_selector" value="advanced"/>
13215 <param name="remove_duplicate_psm" value="false"/>
13216 <param name="remove_peptide_hits_by_metavalue" value=""/>
13217 <param name="force" value="false"/>
13218 <param name="test" value="true"/>
13219 </conditional>
13220 <param name="in" value="IDFilter_14_input.idXML"/>
13221 <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13222 <param name="var_mods" value="false"/>
13223 <param name="remove_shared_peptides" value="false"/>
13224 <param name="keep_unreferenced_protein_hits" value="false"/>
13225 <param name="remove_decoys" value="false"/>
13226 <param name="delete_unreferenced_peptide_hits" value="false"/>
13227 <section name="precursor">
13228 <param name="rt" value=":"/>
13229 <param name="mz" value=":"/>
13230 <param name="length" value=":"/>
13231 <param name="charge" value=":"/>
13232 </section>
13233 <section name="score">
13234 <param name="pep" value="0.0"/>
13235 <param name="prot" value="0.0"/>
13236 <param name="protgroup" value="0.0"/>
13237 </section>
13238 <section name="whitelist">
13239 <param name="protein_accessions" value=""/>
13240 <param name="ignore_modifications" value="false"/>
13241 <param name="modifications" value=""/>
13242 </section>
13243 <section name="blacklist">
13244 <param name="protein_accessions" value=""/>
13245 <param name="ignore_modifications" value="false"/>
13246 <param name="modifications" value=""/>
13247 </section>
13248 <section name="in_silico_digestion">
13249 <param name="fasta" value="IDFilter_14_input.fasta"/>
13250 <param name="enzyme" value="Trypsin/P"/>
13251 <param name="specificity" value="full"/>
13252 <param name="missed_cleavages" value="1"/>
13253 <param name="methionine_cleavage" value="false"/>
13254 </section>
13255 <section name="missed_cleavages">
13256 <param name="number_of_missed_cleavages" value=":"/>
13257 <param name="enzyme" value="Trypsin"/>
13258 </section>
13259 <section name="rt">
13260 <param name="p_value" value="0.0"/>
13261 <param name="p_value_1st_dim" value="0.0"/>
13262 </section>
13263 <section name="mz">
13264 <param name="error" value="-1.0"/>
13265 <param name="unit" value="ppm"/>
13266 </section>
13267 <section name="best">
13268 <param name="n_peptide_hits" value="0"/>
13269 <param name="n_protein_hits" value="0"/>
13270 <param name="strict" value="false"/>
13271 <param name="n_to_m_peptide_hits" value=":"/>
13272 </section>
13273 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13274 <output name="ctd_out" ftype="xml">
13275 <assert_contents>
13276 <is_valid_xml/>
13277 </assert_contents>
13278 </output>
13279 </test>
13280 <test expect_num_outputs="2">
13281 <conditional name="adv_opts_cond">
13282 <param name="adv_opts_selector" value="advanced"/>
13283 <param name="remove_duplicate_psm" value="false"/>
13284 <param name="remove_peptide_hits_by_metavalue" value=""/>
13285 <param name="force" value="false"/>
13286 <param name="test" value="true"/>
13287 </conditional>
13288 <param name="in" value="IDFilter_15_input.idXML"/>
13289 <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13290 <param name="var_mods" value="false"/>
13291 <param name="remove_shared_peptides" value="false"/>
13292 <param name="keep_unreferenced_protein_hits" value="false"/>
13293 <param name="remove_decoys" value="false"/>
13294 <param name="delete_unreferenced_peptide_hits" value="false"/>
13295 <section name="precursor">
13296 <param name="rt" value=":"/>
13297 <param name="mz" value=":"/>
13298 <param name="length" value=":"/>
13299 <param name="charge" value=":"/>
13300 </section>
13301 <section name="score">
13302 <param name="pep" value="0.0"/>
13303 <param name="prot" value="0.0"/>
13304 <param name="protgroup" value="0.0"/>
13305 </section>
13306 <section name="whitelist">
13307 <param name="protein_accessions" value=""/>
13308 <param name="ignore_modifications" value="false"/>
13309 <param name="modifications" value=""/>
13310 </section>
13311 <section name="blacklist">
13312 <param name="protein_accessions" value=""/>
13313 <param name="ignore_modifications" value="false"/>
13314 <param name="modifications" value=""/>
13315 </section>
13316 <section name="in_silico_digestion">
13317 <param name="fasta" value="IDFilter_15_input.fasta"/>
13318 <param name="enzyme" value="Trypsin/P"/>
13319 <param name="specificity" value="semi"/>
13320 <param name="missed_cleavages" value="1"/>
13321 <param name="methionine_cleavage" value="false"/>
13322 </section>
13323 <section name="missed_cleavages">
13324 <param name="number_of_missed_cleavages" value=":"/>
13325 <param name="enzyme" value="Trypsin"/>
13326 </section>
13327 <section name="rt">
13328 <param name="p_value" value="0.0"/>
13329 <param name="p_value_1st_dim" value="0.0"/>
13330 </section>
13331 <section name="mz">
13332 <param name="error" value="-1.0"/>
13333 <param name="unit" value="ppm"/>
13334 </section>
13335 <section name="best">
13336 <param name="n_peptide_hits" value="0"/>
13337 <param name="n_protein_hits" value="0"/>
13338 <param name="strict" value="false"/>
13339 <param name="n_to_m_peptide_hits" value=":"/>
13340 </section>
13341 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13342 <output name="ctd_out" ftype="xml">
13343 <assert_contents>
13344 <is_valid_xml/>
13345 </assert_contents>
13346 </output>
13347 </test>
13348 <test expect_num_outputs="2">
13349 <conditional name="adv_opts_cond">
13350 <param name="adv_opts_selector" value="advanced"/>
13351 <param name="remove_duplicate_psm" value="false"/>
13352 <param name="remove_peptide_hits_by_metavalue" value=""/>
13353 <param name="force" value="false"/>
13354 <param name="test" value="true"/>
13355 </conditional>
13356 <param name="in" value="IDFilter_16_input.idXML"/>
13357 <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13358 <param name="var_mods" value="false"/>
13359 <param name="remove_shared_peptides" value="false"/>
13360 <param name="keep_unreferenced_protein_hits" value="false"/>
13361 <param name="remove_decoys" value="false"/>
13362 <param name="delete_unreferenced_peptide_hits" value="false"/>
13363 <section name="precursor">
13364 <param name="rt" value=":"/>
13365 <param name="mz" value=":"/>
13366 <param name="length" value=":"/>
13367 <param name="charge" value=":"/>
13368 </section>
13369 <section name="score">
13370 <param name="pep" value="0.0"/>
13371 <param name="prot" value="0.0"/>
13372 <param name="protgroup" value="0.0"/>
13373 </section>
13374 <section name="whitelist">
13375 <param name="protein_accessions" value=""/>
13376 <param name="ignore_modifications" value="false"/>
13377 <param name="modifications" value=""/>
13378 </section>
13379 <section name="blacklist">
13380 <param name="protein_accessions" value=""/>
13381 <param name="ignore_modifications" value="false"/>
13382 <param name="modifications" value=""/>
13383 </section>
13384 <section name="in_silico_digestion">
13385 <param name="fasta" value="IDFilter_16_input.fasta"/>
13386 <param name="enzyme" value="Trypsin/P"/>
13387 <param name="specificity" value="full"/>
13388 <param name="missed_cleavages" value="1"/>
13389 <param name="methionine_cleavage" value="true"/>
13390 </section>
13391 <section name="missed_cleavages">
13392 <param name="number_of_missed_cleavages" value=":"/>
13393 <param name="enzyme" value="Trypsin"/>
13394 </section>
13395 <section name="rt">
13396 <param name="p_value" value="0.0"/>
13397 <param name="p_value_1st_dim" value="0.0"/>
13398 </section>
13399 <section name="mz">
13400 <param name="error" value="-1.0"/>
13401 <param name="unit" value="ppm"/>
13402 </section>
13403 <section name="best">
13404 <param name="n_peptide_hits" value="0"/>
13405 <param name="n_protein_hits" value="0"/>
13406 <param name="strict" value="false"/>
13407 <param name="n_to_m_peptide_hits" value=":"/>
13408 </section>
13409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13410 <output name="ctd_out" ftype="xml">
13411 <assert_contents>
13412 <is_valid_xml/>
13413 </assert_contents>
13414 </output>
13415 </test>
13416 <test expect_num_outputs="2">
13417 <conditional name="adv_opts_cond">
13418 <param name="adv_opts_selector" value="advanced"/>
13419 <param name="remove_duplicate_psm" value="false"/>
13420 <param name="remove_peptide_hits_by_metavalue" value=""/>
13421 <param name="force" value="false"/>
13422 <param name="test" value="true"/>
13423 </conditional>
13424 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
13425 <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13426 <param name="var_mods" value="false"/>
13427 <param name="remove_shared_peptides" value="false"/>
13428 <param name="keep_unreferenced_protein_hits" value="false"/>
13429 <param name="remove_decoys" value="false"/>
13430 <param name="delete_unreferenced_peptide_hits" value="false"/>
13431 <section name="precursor">
13432 <param name="rt" value=":"/>
13433 <param name="mz" value=":"/>
13434 <param name="length" value=":"/>
13435 <param name="charge" value=":"/>
13436 </section>
13437 <section name="score">
13438 <param name="pep" value="0.0"/>
13439 <param name="prot" value="0.0"/>
13440 <param name="protgroup" value="0.0"/>
13441 </section>
13442 <section name="whitelist">
13443 <param name="protein_accessions" value=""/>
13444 <param name="ignore_modifications" value="false"/>
13445 <param name="modifications" value=""/>
13446 </section>
13447 <section name="blacklist">
13448 <param name="protein_accessions" value=""/>
13449 <param name="ignore_modifications" value="false"/>
13450 <param name="modifications" value=""/>
13451 </section>
13452 <section name="in_silico_digestion">
13453 <param name="enzyme" value="Trypsin"/>
13454 <param name="specificity" value="full"/>
13455 <param name="missed_cleavages" value="-1"/>
13456 <param name="methionine_cleavage" value="false"/>
13457 </section>
13458 <section name="missed_cleavages">
13459 <param name="number_of_missed_cleavages" value=":2"/>
13460 <param name="enzyme" value="Lys-N"/>
13461 </section>
13462 <section name="rt">
13463 <param name="p_value" value="0.0"/>
13464 <param name="p_value_1st_dim" value="0.0"/>
13465 </section>
13466 <section name="mz">
13467 <param name="error" value="-1.0"/>
13468 <param name="unit" value="ppm"/>
13469 </section>
13470 <section name="best">
13471 <param name="n_peptide_hits" value="0"/>
13472 <param name="n_protein_hits" value="0"/>
13473 <param name="strict" value="false"/>
13474 <param name="n_to_m_peptide_hits" value=":"/>
13475 </section>
13476 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13477 <output name="ctd_out" ftype="xml">
13478 <assert_contents>
13479 <is_valid_xml/>
13480 </assert_contents>
13481 </output>
13482 </test>
13483 <test expect_num_outputs="2">
13484 <conditional name="adv_opts_cond">
13485 <param name="adv_opts_selector" value="advanced"/>
13486 <param name="remove_duplicate_psm" value="false"/>
13487 <param name="remove_peptide_hits_by_metavalue" value=""/>
13488 <param name="force" value="false"/>
13489 <param name="test" value="true"/>
13490 </conditional>
13491 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
13492 <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13493 <param name="var_mods" value="false"/>
13494 <param name="remove_shared_peptides" value="false"/>
13495 <param name="keep_unreferenced_protein_hits" value="false"/>
13496 <param name="remove_decoys" value="false"/>
13497 <param name="delete_unreferenced_peptide_hits" value="false"/>
13498 <section name="precursor">
13499 <param name="rt" value=":"/>
13500 <param name="mz" value=":"/>
13501 <param name="length" value=":"/>
13502 <param name="charge" value=":"/>
13503 </section>
13504 <section name="score">
13505 <param name="pep" value="0.0"/>
13506 <param name="prot" value="0.0"/>
13507 <param name="protgroup" value="0.0"/>
13508 </section>
13509 <section name="whitelist">
13510 <param name="protein_accessions" value=""/>
13511 <param name="ignore_modifications" value="false"/>
13512 <param name="modifications" value=""/>
13513 </section>
13514 <section name="blacklist">
13515 <param name="protein_accessions" value=""/>
13516 <param name="ignore_modifications" value="false"/>
13517 <param name="modifications" value=""/>
13518 </section>
13519 <section name="in_silico_digestion">
13520 <param name="enzyme" value="Trypsin"/>
13521 <param name="specificity" value="full"/>
13522 <param name="missed_cleavages" value="-1"/>
13523 <param name="methionine_cleavage" value="false"/>
13524 </section>
13525 <section name="missed_cleavages">
13526 <param name="number_of_missed_cleavages" value="2:"/>
13527 <param name="enzyme" value="Lys-N"/>
13528 </section>
13529 <section name="rt">
13530 <param name="p_value" value="0.0"/>
13531 <param name="p_value_1st_dim" value="0.0"/>
13532 </section>
13533 <section name="mz">
13534 <param name="error" value="-1.0"/>
13535 <param name="unit" value="ppm"/>
13536 </section>
13537 <section name="best">
13538 <param name="n_peptide_hits" value="0"/>
13539 <param name="n_protein_hits" value="0"/>
13540 <param name="strict" value="false"/>
13541 <param name="n_to_m_peptide_hits" value=":"/>
13542 </section>
13543 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13544 <output name="ctd_out" ftype="xml">
13545 <assert_contents>
13546 <is_valid_xml/>
13547 </assert_contents>
13548 </output>
13549 </test>
13550 <test expect_num_outputs="2">
13551 <conditional name="adv_opts_cond">
13552 <param name="adv_opts_selector" value="advanced"/>
13553 <param name="remove_duplicate_psm" value="false"/>
13554 <param name="remove_peptide_hits_by_metavalue" value=""/>
13555 <param name="force" value="false"/>
13556 <param name="test" value="true"/>
13557 </conditional>
13558 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
13559 <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13560 <param name="var_mods" value="false"/>
13561 <param name="remove_shared_peptides" value="false"/>
13562 <param name="keep_unreferenced_protein_hits" value="false"/>
13563 <param name="remove_decoys" value="false"/>
13564 <param name="delete_unreferenced_peptide_hits" value="false"/>
13565 <section name="precursor">
13566 <param name="rt" value=":"/>
13567 <param name="mz" value=":"/>
13568 <param name="length" value=":"/>
13569 <param name="charge" value=":"/>
13570 </section>
13571 <section name="score">
13572 <param name="pep" value="0.0"/>
13573 <param name="prot" value="0.0"/>
13574 <param name="protgroup" value="0.0"/>
13575 </section>
13576 <section name="whitelist">
13577 <param name="protein_accessions" value=""/>
13578 <param name="ignore_modifications" value="false"/>
13579 <param name="modifications" value=""/>
13580 </section>
13581 <section name="blacklist">
13582 <param name="protein_accessions" value=""/>
13583 <param name="ignore_modifications" value="false"/>
13584 <param name="modifications" value=""/>
13585 </section>
13586 <section name="in_silico_digestion">
13587 <param name="enzyme" value="Trypsin"/>
13588 <param name="specificity" value="full"/>
13589 <param name="missed_cleavages" value="-1"/>
13590 <param name="methionine_cleavage" value="false"/>
13591 </section>
13592 <section name="missed_cleavages">
13593 <param name="number_of_missed_cleavages" value="1:3"/>
13594 <param name="enzyme" value="Lys-N"/>
13595 </section>
13596 <section name="rt">
13597 <param name="p_value" value="0.0"/>
13598 <param name="p_value_1st_dim" value="0.0"/>
13599 </section>
13600 <section name="mz">
13601 <param name="error" value="-1.0"/>
13602 <param name="unit" value="ppm"/>
13603 </section>
13604 <section name="best">
13605 <param name="n_peptide_hits" value="0"/>
13606 <param name="n_protein_hits" value="0"/>
13607 <param name="strict" value="false"/>
13608 <param name="n_to_m_peptide_hits" value=":"/>
13609 </section>
13610 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13611 <output name="ctd_out" ftype="xml">
13612 <assert_contents>
13613 <is_valid_xml/>
13614 </assert_contents>
13615 </output>
13616 </test>
13617 <test expect_num_outputs="2">
13618 <conditional name="adv_opts_cond">
13619 <param name="adv_opts_selector" value="advanced"/>
13620 <param name="remove_duplicate_psm" value="false"/>
13621 <param name="remove_peptide_hits_by_metavalue" value=""/>
13622 <param name="force" value="false"/>
13623 <param name="test" value="true"/>
13624 </conditional>
13625 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
13626 <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13627 <param name="var_mods" value="false"/>
13628 <param name="remove_shared_peptides" value="false"/>
13629 <param name="keep_unreferenced_protein_hits" value="false"/>
13630 <param name="remove_decoys" value="false"/>
13631 <param name="delete_unreferenced_peptide_hits" value="false"/>
13632 <section name="precursor">
13633 <param name="rt" value=":"/>
13634 <param name="mz" value=":"/>
13635 <param name="length" value=":"/>
13636 <param name="charge" value=":"/>
13637 </section>
13638 <section name="score">
13639 <param name="pep" value="0.0"/>
13640 <param name="prot" value="0.0"/>
13641 <param name="protgroup" value="0.0"/>
13642 </section>
13643 <section name="whitelist">
13644 <param name="protein_accessions" value=""/>
13645 <param name="ignore_modifications" value="false"/>
13646 <param name="modifications" value=""/>
13647 </section>
13648 <section name="blacklist">
13649 <param name="protein_accessions" value=""/>
13650 <param name="ignore_modifications" value="false"/>
13651 <param name="modifications" value=""/>
13652 </section>
13653 <section name="in_silico_digestion">
13654 <param name="enzyme" value="Trypsin"/>
13655 <param name="specificity" value="full"/>
13656 <param name="missed_cleavages" value="-1"/>
13657 <param name="methionine_cleavage" value="false"/>
13658 </section>
13659 <section name="missed_cleavages">
13660 <param name="number_of_missed_cleavages" value="1:0"/>
13661 <param name="enzyme" value="Trypsin"/>
13662 </section>
13663 <section name="rt">
13664 <param name="p_value" value="0.0"/>
13665 <param name="p_value_1st_dim" value="0.0"/>
13666 </section>
13667 <section name="mz">
13668 <param name="error" value="-1.0"/>
13669 <param name="unit" value="ppm"/>
13670 </section>
13671 <section name="best">
13672 <param name="n_peptide_hits" value="0"/>
13673 <param name="n_protein_hits" value="0"/>
13674 <param name="strict" value="false"/>
13675 <param name="n_to_m_peptide_hits" value=":"/>
13676 </section>
13677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13678 <output name="ctd_out" ftype="xml">
13679 <assert_contents>
13680 <is_valid_xml/>
13681 </assert_contents>
13682 </output>
13683 </test>
13684 <test expect_num_outputs="2">
13685 <conditional name="adv_opts_cond">
13686 <param name="adv_opts_selector" value="advanced"/>
13687 <param name="remove_duplicate_psm" value="false"/>
13688 <param name="remove_peptide_hits_by_metavalue" value="&quot;calcMZ&quot; &quot;gt&quot; &quot;750.0&quot;"/>
13689 <param name="force" value="false"/>
13690 <param name="test" value="true"/>
13691 </conditional>
13692 <param name="in" value="IDFilter_16_input.idXML"/>
13693 <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13694 <param name="var_mods" value="false"/>
13695 <param name="remove_shared_peptides" value="false"/>
13696 <param name="keep_unreferenced_protein_hits" value="false"/>
13697 <param name="remove_decoys" value="false"/>
13698 <param name="delete_unreferenced_peptide_hits" value="false"/>
13699 <section name="precursor">
13700 <param name="rt" value=":"/>
13701 <param name="mz" value=":"/>
13702 <param name="length" value=":"/>
13703 <param name="charge" value=":"/>
13704 </section>
13705 <section name="score">
13706 <param name="pep" value="0.0"/>
13707 <param name="prot" value="0.0"/>
13708 <param name="protgroup" value="0.0"/>
13709 </section>
13710 <section name="whitelist">
13711 <param name="protein_accessions" value=""/>
13712 <param name="ignore_modifications" value="false"/>
13713 <param name="modifications" value=""/>
13714 </section>
13715 <section name="blacklist">
13716 <param name="protein_accessions" value=""/>
13717 <param name="ignore_modifications" value="false"/>
13718 <param name="modifications" value=""/>
13719 </section>
13720 <section name="in_silico_digestion">
13721 <param name="enzyme" value="Trypsin"/>
13722 <param name="specificity" value="full"/>
13723 <param name="missed_cleavages" value="-1"/>
13724 <param name="methionine_cleavage" value="false"/>
13725 </section>
13726 <section name="missed_cleavages">
13727 <param name="number_of_missed_cleavages" value=":"/>
13728 <param name="enzyme" value="Trypsin"/>
13729 </section>
13730 <section name="rt">
13731 <param name="p_value" value="0.0"/>
13732 <param name="p_value_1st_dim" value="0.0"/>
13733 </section>
13734 <section name="mz">
13735 <param name="error" value="-1.0"/>
13736 <param name="unit" value="ppm"/>
13737 </section>
13738 <section name="best">
13739 <param name="n_peptide_hits" value="0"/>
13740 <param name="n_protein_hits" value="0"/>
13741 <param name="strict" value="false"/>
13742 <param name="n_to_m_peptide_hits" value=":"/>
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="remove_duplicate_psm" value="false"/>
13755 <param name="remove_peptide_hits_by_metavalue" value="&quot;end&quot; &quot;ne&quot; &quot;23&quot;"/>
13756 <param name="force" value="false"/>
13757 <param name="test" value="true"/>
13758 </conditional>
13759 <param name="in" value="IDFilter_16_input.idXML"/>
13760 <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13761 <param name="var_mods" value="false"/>
13762 <param name="remove_shared_peptides" value="false"/>
13763 <param name="keep_unreferenced_protein_hits" value="false"/>
13764 <param name="remove_decoys" value="false"/>
13765 <param name="delete_unreferenced_peptide_hits" value="false"/>
13766 <section name="precursor">
13767 <param name="rt" value=":"/>
13768 <param name="mz" value=":"/>
13769 <param name="length" value=":"/>
13770 <param name="charge" value=":"/>
13771 </section>
13772 <section name="score">
13773 <param name="pep" value="0.0"/>
13774 <param name="prot" value="0.0"/>
13775 <param name="protgroup" value="0.0"/>
13776 </section>
13777 <section name="whitelist">
13778 <param name="protein_accessions" value=""/>
13779 <param name="ignore_modifications" value="false"/>
13780 <param name="modifications" value=""/>
13781 </section>
13782 <section name="blacklist">
13783 <param name="protein_accessions" value=""/>
13784 <param name="ignore_modifications" value="false"/>
13785 <param name="modifications" value=""/>
13786 </section>
13787 <section name="in_silico_digestion">
13788 <param name="enzyme" value="Trypsin"/>
13789 <param name="specificity" value="full"/>
13790 <param name="missed_cleavages" value="-1"/>
13791 <param name="methionine_cleavage" value="false"/>
13792 </section>
13793 <section name="missed_cleavages">
13794 <param name="number_of_missed_cleavages" value=":"/>
13795 <param name="enzyme" value="Trypsin"/>
13796 </section>
13797 <section name="rt">
13798 <param name="p_value" value="0.0"/>
13799 <param name="p_value_1st_dim" value="0.0"/>
13800 </section>
13801 <section name="mz">
13802 <param name="error" value="-1.0"/>
13803 <param name="unit" value="ppm"/>
13804 </section>
13805 <section name="best">
13806 <param name="n_peptide_hits" value="0"/>
13807 <param name="n_protein_hits" value="0"/>
13808 <param name="strict" value="false"/>
13809 <param name="n_to_m_peptide_hits" value=":"/>
13810 </section>
13811 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13812 <output name="ctd_out" ftype="xml">
13813 <assert_contents>
13814 <is_valid_xml/>
13815 </assert_contents>
13816 </output>
13817 </test>
13818 <test expect_num_outputs="2">
13819 <conditional name="adv_opts_cond">
13820 <param name="adv_opts_selector" value="advanced"/>
13821 <param name="remove_duplicate_psm" value="false"/>
13822 <param name="remove_peptide_hits_by_metavalue" value=""/>
13823 <param name="force" value="false"/>
13824 <param name="test" value="true"/>
13825 </conditional>
13826 <param name="in" value="IDMapper_2_output.consensusXML"/>
13827 <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
13828 <param name="var_mods" value="false"/>
13829 <param name="remove_shared_peptides" value="false"/>
13830 <param name="keep_unreferenced_protein_hits" value="false"/>
13831 <param name="remove_decoys" value="false"/>
13832 <param name="delete_unreferenced_peptide_hits" value="false"/>
13833 <section name="precursor">
13834 <param name="rt" value=":"/>
13835 <param name="mz" value=":"/>
13836 <param name="length" value=":"/>
13837 <param name="charge" value=":"/>
13838 </section>
13839 <section name="score">
13840 <param name="pep" value="0.0"/>
13841 <param name="prot" value="0.0"/>
13842 <param name="protgroup" value="0.0"/>
13843 </section>
13844 <section name="whitelist">
13845 <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
13846 <param name="ignore_modifications" value="false"/>
13847 <param name="modifications" value=""/>
13848 </section>
13849 <section name="blacklist">
13850 <param name="protein_accessions" value=""/>
13851 <param name="ignore_modifications" value="false"/>
13852 <param name="modifications" value=""/>
13853 </section>
13854 <section name="in_silico_digestion">
13855 <param name="enzyme" value="Trypsin"/>
13856 <param name="specificity" value="full"/>
13857 <param name="missed_cleavages" value="-1"/>
13858 <param name="methionine_cleavage" value="false"/>
13859 </section>
13860 <section name="missed_cleavages">
13861 <param name="number_of_missed_cleavages" value=":"/>
13862 <param name="enzyme" value="Trypsin"/>
13863 </section>
13864 <section name="rt">
13865 <param name="p_value" value="0.0"/>
13866 <param name="p_value_1st_dim" value="0.0"/>
13867 </section>
13868 <section name="mz">
13869 <param name="error" value="-1.0"/>
13870 <param name="unit" value="ppm"/>
13871 </section>
13872 <section name="best">
13873 <param name="n_peptide_hits" value="0"/>
13874 <param name="n_protein_hits" value="0"/>
13875 <param name="strict" value="false"/>
13876 <param name="n_to_m_peptide_hits" value=":"/>
13877 </section>
13878 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13879 <output name="ctd_out" ftype="xml">
13880 <assert_contents>
13881 <is_valid_xml/>
13882 </assert_contents>
13883 </output>
13884 </test>
13885 <test expect_num_outputs="2">
13886 <conditional name="adv_opts_cond">
13887 <param name="adv_opts_selector" value="advanced"/>
13888 <param name="remove_duplicate_psm" value="false"/>
13889 <param name="remove_peptide_hits_by_metavalue" value=""/>
13890 <param name="force" value="false"/>
13891 <param name="test" value="true"/>
13892 </conditional>
13893 <param name="in" value="Epifany_3_out.consensusXML"/>
13894 <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
13895 <param name="var_mods" value="false"/>
13896 <param name="remove_shared_peptides" value="false"/>
13897 <param name="keep_unreferenced_protein_hits" value="false"/>
13898 <param name="remove_decoys" value="false"/>
13899 <param name="delete_unreferenced_peptide_hits" value="false"/>
13900 <section name="precursor">
13901 <param name="rt" value=":"/>
13902 <param name="mz" value=":"/>
13903 <param name="length" value=":"/>
13904 <param name="charge" value=":"/>
13905 </section>
13906 <section name="score">
13907 <param name="pep" value="0.0"/>
13908 <param name="prot" value="0.0"/>
13909 <param name="protgroup" value="0.99"/>
13910 </section>
13911 <section name="whitelist">
13912 <param name="protein_accessions" value=""/>
13913 <param name="ignore_modifications" value="false"/>
13914 <param name="modifications" value=""/>
13915 </section>
13916 <section name="blacklist">
13917 <param name="protein_accessions" value=""/>
13918 <param name="ignore_modifications" value="false"/>
13919 <param name="modifications" value=""/>
13920 </section>
13921 <section name="in_silico_digestion">
13922 <param name="enzyme" value="Trypsin"/>
13923 <param name="specificity" value="full"/>
13924 <param name="missed_cleavages" value="-1"/>
13925 <param name="methionine_cleavage" value="false"/>
13926 </section>
13927 <section name="missed_cleavages">
13928 <param name="number_of_missed_cleavages" value=":"/>
13929 <param name="enzyme" value="Trypsin"/>
13930 </section>
13931 <section name="rt">
13932 <param name="p_value" value="0.0"/>
13933 <param name="p_value_1st_dim" value="0.0"/>
13934 </section>
13935 <section name="mz">
13936 <param name="error" value="-1.0"/>
13937 <param name="unit" value="ppm"/>
13938 </section>
13939 <section name="best">
13940 <param name="n_peptide_hits" value="0"/>
13941 <param name="n_protein_hits" value="0"/>
13942 <param name="strict" value="false"/>
13943 <param name="n_to_m_peptide_hits" value=":"/>
13944 </section>
13945 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13946 <output name="ctd_out" ftype="xml">
13947 <assert_contents>
13948 <is_valid_xml/>
13949 </assert_contents>
13950 </output>
13951 </test>
13952 </xml>
13953 <xml name="autotest_IDMapper">
13954 <test expect_num_outputs="2">
13955 <conditional name="adv_opts_cond">
13956 <param name="adv_opts_selector" value="advanced"/>
13957 <param name="ignore_charge" value="true"/>
13958 <param name="force" value="false"/>
13959 <param name="test" value="true"/>
13960 </conditional>
13961 <param name="id" value="IDMapper_1_input.idXML"/>
13962 <param name="in" value="IDMapper_1_input.featureXML"/>
13963 <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
13964 <param name="rt_tolerance" value="5.0"/>
13965 <param name="mz_tolerance" value="1.0"/>
13966 <param name="mz_measure" value="Da"/>
13967 <param name="mz_reference" value="precursor"/>
13968 <section name="feature">
13969 <param name="use_centroid_rt" value="false"/>
13970 <param name="use_centroid_mz" value="false"/>
13971 </section>
13972 <section name="consensus">
13973 <param name="use_subelements" value="false"/>
13974 <param name="annotate_ids_with_subelements" value="false"/>
13975 </section>
13976 <section name="spectra"/>
13977 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13978 <output name="ctd_out" ftype="xml">
13979 <assert_contents>
13980 <is_valid_xml/>
13981 </assert_contents>
13982 </output>
13983 </test>
13984 <test expect_num_outputs="2">
13985 <conditional name="adv_opts_cond">
13986 <param name="adv_opts_selector" value="advanced"/>
13987 <param name="ignore_charge" value="false"/>
13988 <param name="force" value="false"/>
13989 <param name="test" value="true"/>
13990 </conditional>
13991 <param name="id" value="IDMapper_2_input.idXML"/>
13992 <param name="in" value="IDMapper_2_input.consensusXML"/>
13993 <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
13994 <param name="rt_tolerance" value="5.0"/>
13995 <param name="mz_tolerance" value="1.0"/>
13996 <param name="mz_measure" value="Da"/>
13997 <param name="mz_reference" value="precursor"/>
13998 <section name="feature">
13999 <param name="use_centroid_rt" value="false"/>
14000 <param name="use_centroid_mz" value="true"/>
14001 </section>
14002 <section name="consensus">
14003 <param name="use_subelements" value="false"/>
14004 <param name="annotate_ids_with_subelements" value="false"/>
14005 </section>
14006 <section name="spectra"/>
14007 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14008 <output name="ctd_out" ftype="xml">
14009 <assert_contents>
14010 <is_valid_xml/>
14011 </assert_contents>
14012 </output>
14013 </test>
14014 <test expect_num_outputs="2">
14015 <conditional name="adv_opts_cond">
14016 <param name="adv_opts_selector" value="advanced"/>
14017 <param name="ignore_charge" value="true"/>
14018 <param name="force" value="false"/>
14019 <param name="test" value="true"/>
14020 </conditional>
14021 <param name="id" value="IDMapper_3_input.idXML"/>
14022 <param name="in" value="IDMapper_3_input.featureXML"/>
14023 <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
14024 <param name="rt_tolerance" value="4.0"/>
14025 <param name="mz_tolerance" value="3.0"/>
14026 <param name="mz_measure" value="ppm"/>
14027 <param name="mz_reference" value="precursor"/>
14028 <section name="feature">
14029 <param name="use_centroid_rt" value="false"/>
14030 <param name="use_centroid_mz" value="true"/>
14031 </section>
14032 <section name="consensus">
14033 <param name="use_subelements" value="false"/>
14034 <param name="annotate_ids_with_subelements" value="false"/>
14035 </section>
14036 <section name="spectra"/>
14037 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14038 <output name="ctd_out" ftype="xml">
14039 <assert_contents>
14040 <is_valid_xml/>
14041 </assert_contents>
14042 </output>
14043 </test>
14044 <test expect_num_outputs="2">
14045 <conditional name="adv_opts_cond">
14046 <param name="adv_opts_selector" value="advanced"/>
14047 <param name="ignore_charge" value="false"/>
14048 <param name="force" value="false"/>
14049 <param name="test" value="true"/>
14050 </conditional>
14051 <param name="id" value="IDMapper_4_input.idXML"/>
14052 <param name="in" value="IDMapper_4_input.featureXML"/>
14053 <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
14054 <param name="rt_tolerance" value="10.0"/>
14055 <param name="mz_tolerance" value="20.0"/>
14056 <param name="mz_measure" value="ppm"/>
14057 <param name="mz_reference" value="peptide"/>
14058 <section name="feature">
14059 <param name="use_centroid_rt" value="false"/>
14060 <param name="use_centroid_mz" value="true"/>
14061 </section>
14062 <section name="consensus">
14063 <param name="use_subelements" value="false"/>
14064 <param name="annotate_ids_with_subelements" value="false"/>
14065 </section>
14066 <section name="spectra">
14067 <param name="_in" value="IDMapper_4_input.mzML"/>
14068 </section>
14069 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14070 <output name="ctd_out" ftype="xml">
14071 <assert_contents>
14072 <is_valid_xml/>
14073 </assert_contents>
14074 </output>
14075 </test>
14076 <test expect_num_outputs="2">
14077 <conditional name="adv_opts_cond">
14078 <param name="adv_opts_selector" value="advanced"/>
14079 <param name="ignore_charge" value="false"/>
14080 <param name="force" value="false"/>
14081 <param name="test" value="true"/>
14082 </conditional>
14083 <param name="id" value="IDMapper_5_input.idXML"/>
14084 <param name="in" value="IDMapper_5_input.featureXML"/>
14085 <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
14086 <param name="rt_tolerance" value="20.0"/>
14087 <param name="mz_tolerance" value="10.0"/>
14088 <param name="mz_measure" value="ppm"/>
14089 <param name="mz_reference" value="peptide"/>
14090 <section name="feature">
14091 <param name="use_centroid_rt" value="false"/>
14092 <param name="use_centroid_mz" value="false"/>
14093 </section>
14094 <section name="consensus">
14095 <param name="use_subelements" value="false"/>
14096 <param name="annotate_ids_with_subelements" value="false"/>
14097 </section>
14098 <section name="spectra">
14099 <param name="_in" value="IDMapper_5_input.mzML"/>
14100 </section>
14101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14102 <output name="ctd_out" ftype="xml">
14103 <assert_contents>
14104 <is_valid_xml/>
14105 </assert_contents>
14106 </output>
14107 </test>
14108 </xml>
14109 <xml name="autotest_IDMassAccuracy">
14110 <test expect_num_outputs="5">
14111 <conditional name="adv_opts_cond">
14112 <param name="adv_opts_selector" value="advanced"/>
14113 <param name="number_of_bins" value="10"/>
14114 <param name="force" value="false"/>
14115 <param name="test" value="true"/>
14116 </conditional>
14117 <param name="in" value="spectra.mzML"/>
14118 <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
14119 <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
14120 <param name="precursor_error_ppm" value="false"/>
14121 <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
14122 <param name="fragment_error_ppm" value="false"/>
14123 <param name="fragment_mass_tolerance" value="0.5"/>
14124 <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
14125 <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
14126 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
14127 <output name="ctd_out" ftype="xml">
14128 <assert_contents>
14129 <is_valid_xml/>
14130 </assert_contents>
14131 </output>
14132 </test>
14133 </xml>
14134 <xml name="autotest_IDMerger">
14135 <test expect_num_outputs="2">
14136 <conditional name="adv_opts_cond">
14137 <param name="adv_opts_selector" value="advanced"/>
14138 <param name="force" value="false"/>
14139 <param name="test" value="true"/>
14140 </conditional>
14141 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
14142 <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14143 <param name="annotate_file_origin" value="true"/>
14144 <param name="pepxml_protxml" value="false"/>
14145 <param name="merge_proteins_add_PSMs" value="false"/>
14146 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14147 <output name="ctd_out" ftype="xml">
14148 <assert_contents>
14149 <is_valid_xml/>
14150 </assert_contents>
14151 </output>
14152 </test>
14153 <test expect_num_outputs="2">
14154 <conditional name="adv_opts_cond">
14155 <param name="adv_opts_selector" value="advanced"/>
14156 <param name="force" value="false"/>
14157 <param name="test" value="true"/>
14158 </conditional>
14159 <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
14160 <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14161 <param name="annotate_file_origin" value="false"/>
14162 <param name="pepxml_protxml" value="true"/>
14163 <param name="merge_proteins_add_PSMs" value="false"/>
14164 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14165 <output name="ctd_out" ftype="xml">
14166 <assert_contents>
14167 <is_valid_xml/>
14168 </assert_contents>
14169 </output>
14170 </test>
14171 <test expect_num_outputs="2">
14172 <conditional name="adv_opts_cond">
14173 <param name="adv_opts_selector" value="advanced"/>
14174 <param name="force" value="false"/>
14175 <param name="test" value="true"/>
14176 </conditional>
14177 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
14178 <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14179 <param name="annotate_file_origin" value="false"/>
14180 <param name="pepxml_protxml" value="false"/>
14181 <param name="merge_proteins_add_PSMs" value="false"/>
14182 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14183 <output name="ctd_out" ftype="xml">
14184 <assert_contents>
14185 <is_valid_xml/>
14186 </assert_contents>
14187 </output>
14188 </test>
14189 <test expect_num_outputs="2">
14190 <conditional name="adv_opts_cond">
14191 <param name="adv_opts_selector" value="advanced"/>
14192 <param name="force" value="false"/>
14193 <param name="test" value="true"/>
14194 </conditional>
14195 <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
14196 <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14197 <param name="annotate_file_origin" value="false"/>
14198 <param name="pepxml_protxml" value="false"/>
14199 <param name="merge_proteins_add_PSMs" value="false"/>
14200 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14201 <output name="ctd_out" ftype="xml">
14202 <assert_contents>
14203 <is_valid_xml/>
14204 </assert_contents>
14205 </output>
14206 </test>
14207 <test expect_num_outputs="2">
14208 <conditional name="adv_opts_cond">
14209 <param name="adv_opts_selector" value="advanced"/>
14210 <param name="force" value="false"/>
14211 <param name="test" value="true"/>
14212 </conditional>
14213 <param name="in" value="IDMerger_2_input1.idXML"/>
14214 <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14215 <param name="add_to" value="IDMerger_5_input1.idXML"/>
14216 <param name="annotate_file_origin" value="false"/>
14217 <param name="pepxml_protxml" value="false"/>
14218 <param name="merge_proteins_add_PSMs" value="false"/>
14219 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14220 <output name="ctd_out" ftype="xml">
14221 <assert_contents>
14222 <is_valid_xml/>
14223 </assert_contents>
14224 </output>
14225 </test>
14226 <test expect_num_outputs="2">
14227 <conditional name="adv_opts_cond">
14228 <param name="adv_opts_selector" value="advanced"/>
14229 <param name="force" value="false"/>
14230 <param name="test" value="true"/>
14231 </conditional>
14232 <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
14233 <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14234 <param name="annotate_file_origin" value="true"/>
14235 <param name="pepxml_protxml" value="false"/>
14236 <param name="merge_proteins_add_PSMs" value="false"/>
14237 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14238 <output name="ctd_out" ftype="xml">
14239 <assert_contents>
14240 <is_valid_xml/>
14241 </assert_contents>
14242 </output>
14243 </test>
14244 </xml>
14245 <xml name="autotest_IDPosteriorErrorProbability">
14246 <test expect_num_outputs="2">
14247 <conditional name="adv_opts_cond">
14248 <param name="adv_opts_selector" value="advanced"/>
14249 <param name="fdr_for_targets_smaller" value="0.05"/>
14250 <param name="force" value="false"/>
14251 <param name="test" value="true"/>
14252 </conditional>
14253 <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
14254 <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14255 <param name="split_charge" value="false"/>
14256 <param name="top_hits_only" value="false"/>
14257 <param name="ignore_bad_data" value="false"/>
14258 <param name="prob_correct" value="false"/>
14259 <section name="fit_algorithm">
14260 <param name="number_of_bins" value="100"/>
14261 <param name="incorrectly_assigned" value="Gumbel"/>
14262 <param name="max_nr_iterations" value="1000"/>
14263 <param name="neg_log_delta" value="6"/>
14264 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14265 </section>
14266 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14267 <output name="ctd_out" ftype="xml">
14268 <assert_contents>
14269 <is_valid_xml/>
14270 </assert_contents>
14271 </output>
14272 </test>
14273 <test expect_num_outputs="2">
14274 <conditional name="adv_opts_cond">
14275 <param name="adv_opts_selector" value="advanced"/>
14276 <param name="fdr_for_targets_smaller" value="0.05"/>
14277 <param name="force" value="false"/>
14278 <param name="test" value="true"/>
14279 </conditional>
14280 <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
14281 <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14282 <param name="split_charge" value="false"/>
14283 <param name="top_hits_only" value="false"/>
14284 <param name="ignore_bad_data" value="false"/>
14285 <param name="prob_correct" value="false"/>
14286 <section name="fit_algorithm">
14287 <param name="number_of_bins" value="100"/>
14288 <param name="incorrectly_assigned" value="Gumbel"/>
14289 <param name="max_nr_iterations" value="1000"/>
14290 <param name="neg_log_delta" value="6"/>
14291 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14292 </section>
14293 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14294 <output name="ctd_out" ftype="xml">
14295 <assert_contents>
14296 <is_valid_xml/>
14297 </assert_contents>
14298 </output>
14299 </test>
14300 <test expect_num_outputs="2">
14301 <conditional name="adv_opts_cond">
14302 <param name="adv_opts_selector" value="advanced"/>
14303 <param name="fdr_for_targets_smaller" value="0.05"/>
14304 <param name="force" value="false"/>
14305 <param name="test" value="true"/>
14306 </conditional>
14307 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
14308 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14309 <param name="split_charge" value="false"/>
14310 <param name="top_hits_only" value="false"/>
14311 <param name="ignore_bad_data" value="false"/>
14312 <param name="prob_correct" value="false"/>
14313 <section name="fit_algorithm">
14314 <param name="number_of_bins" value="100"/>
14315 <param name="incorrectly_assigned" value="Gumbel"/>
14316 <param name="max_nr_iterations" value="1000"/>
14317 <param name="neg_log_delta" value="6"/>
14318 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14319 </section>
14320 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14321 <output name="ctd_out" ftype="xml">
14322 <assert_contents>
14323 <is_valid_xml/>
14324 </assert_contents>
14325 </output>
14326 </test>
14327 <test expect_num_outputs="2">
14328 <conditional name="adv_opts_cond">
14329 <param name="adv_opts_selector" value="advanced"/>
14330 <param name="fdr_for_targets_smaller" value="0.05"/>
14331 <param name="force" value="false"/>
14332 <param name="test" value="true"/>
14333 </conditional>
14334 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
14335 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14336 <param name="split_charge" value="true"/>
14337 <param name="top_hits_only" value="false"/>
14338 <param name="ignore_bad_data" value="false"/>
14339 <param name="prob_correct" value="false"/>
14340 <section name="fit_algorithm">
14341 <param name="number_of_bins" value="100"/>
14342 <param name="incorrectly_assigned" value="Gumbel"/>
14343 <param name="max_nr_iterations" value="1000"/>
14344 <param name="neg_log_delta" value="6"/>
14345 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14346 </section>
14347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14348 <output name="ctd_out" ftype="xml">
14349 <assert_contents>
14350 <is_valid_xml/>
14351 </assert_contents>
14352 </output>
14353 </test>
14354 <test expect_num_outputs="2">
14355 <conditional name="adv_opts_cond">
14356 <param name="adv_opts_selector" value="advanced"/>
14357 <param name="fdr_for_targets_smaller" value="0.05"/>
14358 <param name="force" value="false"/>
14359 <param name="test" value="true"/>
14360 </conditional>
14361 <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
14362 <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14363 <param name="split_charge" value="true"/>
14364 <param name="top_hits_only" value="false"/>
14365 <param name="ignore_bad_data" value="false"/>
14366 <param name="prob_correct" value="false"/>
14367 <section name="fit_algorithm">
14368 <param name="number_of_bins" value="100"/>
14369 <param name="incorrectly_assigned" value="Gumbel"/>
14370 <param name="max_nr_iterations" value="1000"/>
14371 <param name="neg_log_delta" value="6"/>
14372 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14373 </section>
14374 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14375 <output name="ctd_out" ftype="xml">
14376 <assert_contents>
14377 <is_valid_xml/>
14378 </assert_contents>
14379 </output>
14380 </test>
14381 <test expect_num_outputs="2">
14382 <conditional name="adv_opts_cond">
14383 <param name="adv_opts_selector" value="advanced"/>
14384 <param name="fdr_for_targets_smaller" value="0.05"/>
14385 <param name="force" value="false"/>
14386 <param name="test" value="true"/>
14387 </conditional>
14388 <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
14389 <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14390 <param name="split_charge" value="true"/>
14391 <param name="top_hits_only" value="false"/>
14392 <param name="ignore_bad_data" value="false"/>
14393 <param name="prob_correct" value="false"/>
14394 <section name="fit_algorithm">
14395 <param name="number_of_bins" value="100"/>
14396 <param name="incorrectly_assigned" value="Gumbel"/>
14397 <param name="max_nr_iterations" value="1000"/>
14398 <param name="neg_log_delta" value="6"/>
14399 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14400 </section>
14401 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14402 <output name="ctd_out" ftype="xml">
14403 <assert_contents>
14404 <is_valid_xml/>
14405 </assert_contents>
14406 </output>
14407 </test>
14408 <test expect_num_outputs="2">
14409 <conditional name="adv_opts_cond">
14410 <param name="adv_opts_selector" value="advanced"/>
14411 <param name="fdr_for_targets_smaller" value="0.05"/>
14412 <param name="force" value="false"/>
14413 <param name="test" value="true"/>
14414 </conditional>
14415 <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
14416 <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14417 <param name="split_charge" value="false"/>
14418 <param name="top_hits_only" value="false"/>
14419 <param name="ignore_bad_data" value="true"/>
14420 <param name="prob_correct" value="false"/>
14421 <section name="fit_algorithm">
14422 <param name="number_of_bins" value="100"/>
14423 <param name="incorrectly_assigned" value="Gumbel"/>
14424 <param name="max_nr_iterations" value="1000"/>
14425 <param name="neg_log_delta" value="6"/>
14426 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14427 </section>
14428 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14429 <output name="ctd_out" ftype="xml">
14430 <assert_contents>
14431 <is_valid_xml/>
14432 </assert_contents>
14433 </output>
14434 </test>
14435 <test expect_num_outputs="2">
14436 <conditional name="adv_opts_cond">
14437 <param name="adv_opts_selector" value="advanced"/>
14438 <param name="fdr_for_targets_smaller" value="0.05"/>
14439 <param name="force" value="false"/>
14440 <param name="test" value="true"/>
14441 </conditional>
14442 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
14443 <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14444 <param name="split_charge" value="false"/>
14445 <param name="top_hits_only" value="false"/>
14446 <param name="ignore_bad_data" value="false"/>
14447 <param name="prob_correct" value="true"/>
14448 <section name="fit_algorithm">
14449 <param name="number_of_bins" value="100"/>
14450 <param name="incorrectly_assigned" value="Gumbel"/>
14451 <param name="max_nr_iterations" value="1000"/>
14452 <param name="neg_log_delta" value="6"/>
14453 <param name="outlier_handling" value="ignore_iqr_outliers"/>
14454 </section>
14455 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14456 <output name="ctd_out" ftype="xml">
14457 <assert_contents>
14458 <is_valid_xml/>
14459 </assert_contents>
14460 </output>
14461 </test>
14462 </xml>
14463 <xml name="autotest_IDRipper"/>
14464 <xml name="autotest_IDRTCalibration">
14465 <test expect_num_outputs="2">
14466 <conditional name="adv_opts_cond">
14467 <param name="adv_opts_selector" value="advanced"/>
14468 <param name="force" value="false"/>
14469 <param name="test" value="true"/>
14470 </conditional>
14471 <param name="in" value="IDRTCalibration_1_input.idXML"/>
14472 <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14473 <param name="calibrant_1_reference" value="0.1"/>
14474 <param name="calibrant_2_reference" value="0.9"/>
14475 <param name="calibrant_1_input" value="10.0"/>
14476 <param name="calibrant_2_input" value="90.0"/>
14477 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14478 <output name="ctd_out" ftype="xml">
14479 <assert_contents>
14480 <is_valid_xml/>
14481 </assert_contents>
14482 </output>
14483 </test>
14484 <test expect_num_outputs="2">
14485 <conditional name="adv_opts_cond">
14486 <param name="adv_opts_selector" value="advanced"/>
14487 <param name="force" value="false"/>
14488 <param name="test" value="true"/>
14489 </conditional>
14490 <param name="in" value="degenerated_empty.idXML"/>
14491 <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14492 <param name="calibrant_1_reference" value="0.1"/>
14493 <param name="calibrant_2_reference" value="0.9"/>
14494 <param name="calibrant_1_input" value="10.0"/>
14495 <param name="calibrant_2_input" value="90.0"/>
14496 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14497 <output name="ctd_out" ftype="xml">
14498 <assert_contents>
14499 <is_valid_xml/>
14500 </assert_contents>
14501 </output>
14502 </test>
14503 </xml>
14504 <xml name="autotest_IDScoreSwitcher">
14505 <test expect_num_outputs="2">
14506 <conditional name="adv_opts_cond">
14507 <param name="adv_opts_selector" value="advanced"/>
14508 <param name="force" value="false"/>
14509 <param name="test" value="true"/>
14510 </conditional>
14511 <param name="in" value="IDFileConverter_12_output.idXML"/>
14512 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14513 <param name="proteins" value="false"/>
14514 <param name="new_score" value="Percolator_PEP"/>
14515 <param name="new_score_orientation" value="lower_better"/>
14516 <param name="new_score_type" value="Posterior Error Probability"/>
14517 <param name="old_score" value="Percolator_qvalue"/>
14518 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14519 <output name="ctd_out" ftype="xml">
14520 <assert_contents>
14521 <is_valid_xml/>
14522 </assert_contents>
14523 </output>
14524 </test>
14525 <test expect_num_outputs="2">
14526 <conditional name="adv_opts_cond">
14527 <param name="adv_opts_selector" value="advanced"/>
14528 <param name="force" value="false"/>
14529 <param name="test" value="true"/>
14530 </conditional>
14531 <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
14532 <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14533 <param name="proteins" value="true"/>
14534 <param name="new_score" value="Posterior Probability_score"/>
14535 <param name="new_score_orientation" value="higher_better"/>
14536 <param name="new_score_type" value="Posterior Probability"/>
14537 <param name="old_score" value=""/>
14538 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14539 <output name="ctd_out" ftype="xml">
14540 <assert_contents>
14541 <is_valid_xml/>
14542 </assert_contents>
14543 </output>
14544 </test>
14545 </xml>
14546 <xml name="autotest_IDSplitter">
14547 <test expect_num_outputs="3">
14548 <conditional name="adv_opts_cond">
14549 <param name="adv_opts_selector" value="advanced"/>
14550 <param name="force" value="false"/>
14551 <param name="test" value="true"/>
14552 </conditional>
14553 <param name="in" value="IDMapper_1_output.featureXML"/>
14554 <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
14555 <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14556 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/>
14557 <output name="ctd_out" ftype="xml">
14558 <assert_contents>
14559 <is_valid_xml/>
14560 </assert_contents>
14561 </output>
14562 </test>
14563 </xml>
14564 <xml name="autotest_InternalCalibration">
14565 <test expect_num_outputs="4">
14566 <conditional name="adv_opts_cond">
14567 <param name="adv_opts_selector" value="advanced"/>
14568 <param name="force" value="false"/>
14569 <param name="test" value="true"/>
14570 </conditional>
14571 <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
14572 <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
14573 <param name="ppm_match_tolerance" value="25.0"/>
14574 <param name="ms_level" value="1"/>
14575 <param name="RT_chunking" value="-1.0"/>
14576 <section name="cal">
14577 <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
14578 <param name="lock_require_mono" value="false"/>
14579 <param name="lock_require_iso" value="false"/>
14580 <param name="model_type" value="linear"/>
14581 </section>
14582 <section name="RANSAC">
14583 <param name="enabled" value="true"/>
14584 <param name="threshold" value="1.0"/>
14585 <param name="pc_inliers" value="30"/>
14586 <param name="iter" value="500"/>
14587 </section>
14588 <section name="goodness">
14589 <param name="median" value="4.0"/>
14590 <param name="MAD" value="2.0"/>
14591 </section>
14592 <section name="quality_control"/>
14593 <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
14594 <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
14595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
14596 <output name="ctd_out" ftype="xml">
14597 <assert_contents>
14598 <is_valid_xml/>
14599 </assert_contents>
14600 </output>
14601 </test>
14602 <test expect_num_outputs="4">
14603 <conditional name="adv_opts_cond">
14604 <param name="adv_opts_selector" value="advanced"/>
14605 <param name="force" value="false"/>
14606 <param name="test" value="true"/>
14607 </conditional>
14608 <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
14609 <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
14610 <param name="ppm_match_tolerance" value="25.0"/>
14611 <param name="ms_level" value="1 2 3"/>
14612 <param name="RT_chunking" value="60.0"/>
14613 <section name="cal">
14614 <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
14615 <param name="lock_require_mono" value="true"/>
14616 <param name="lock_require_iso" value="false"/>
14617 <param name="model_type" value="linear"/>
14618 </section>
14619 <section name="RANSAC">
14620 <param name="enabled" value="false"/>
14621 <param name="threshold" value="10.0"/>
14622 <param name="pc_inliers" value="30"/>
14623 <param name="iter" value="70"/>
14624 </section>
14625 <section name="goodness">
14626 <param name="median" value="4.0"/>
14627 <param name="MAD" value="2.0"/>
14628 </section>
14629 <section name="quality_control"/>
14630 <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
14631 <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
14632 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
14633 <output name="ctd_out" ftype="xml">
14634 <assert_contents>
14635 <is_valid_xml/>
14636 </assert_contents>
14637 </output>
14638 </test>
14639 </xml>
14640 <xml name="autotest_IsobaricAnalyzer">
14641 <test expect_num_outputs="2">
14642 <conditional name="adv_opts_cond">
14643 <param name="adv_opts_selector" value="advanced"/>
14644 <param name="force" value="false"/>
14645 <param name="test" value="true"/>
14646 </conditional>
14647 <param name="type" value="itraq4plex"/>
14648 <param name="in" value="IsobaricAnalyzer_input_1.mzML"/>
14649 <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14650 <section name="extraction">
14651 <param name="select_activation" value=""/>
14652 <param name="reporter_mass_shift" value="0.1"/>
14653 <param name="min_precursor_intensity" value="1.0"/>
14654 <param name="keep_unannotated_precursor" value="true"/>
14655 <param name="min_reporter_intensity" value="0.0"/>
14656 <param name="discard_low_intensity_quantifications" value="false"/>
14657 <param name="min_precursor_purity" value="0.0"/>
14658 <param name="precursor_isotope_deviation" value="10.0"/>
14659 <param name="purity_interpolation" value="true"/>
14660 </section>
14661 <section name="itraq4plex">
14662 <param name="channel_114_description" value="l1"/>
14663 <param name="channel_115_description" value="l2"/>
14664 <param name="channel_116_description" value="l3"/>
14665 <param name="channel_117_description" value="lung"/>
14666 <param name="reference_channel" value="114"/>
14667 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14668 </section>
14669 <section name="itraq8plex">
14670 <param name="channel_113_description" value=""/>
14671 <param name="channel_114_description" value=""/>
14672 <param name="channel_115_description" value=""/>
14673 <param name="channel_116_description" value=""/>
14674 <param name="channel_117_description" value=""/>
14675 <param name="channel_118_description" value=""/>
14676 <param name="channel_119_description" value=""/>
14677 <param name="channel_121_description" value=""/>
14678 <param name="reference_channel" value="113"/>
14679 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
14680 </section>
14681 <section name="quantification">
14682 <param name="isotope_correction" value="true"/>
14683 <param name="normalization" value="false"/>
14684 </section>
14685 <section name="tmt10plex">
14686 <param name="channel_126_description" value=""/>
14687 <param name="channel_127N_description" value=""/>
14688 <param name="channel_127C_description" value=""/>
14689 <param name="channel_128N_description" value=""/>
14690 <param name="channel_128C_description" value=""/>
14691 <param name="channel_129N_description" value=""/>
14692 <param name="channel_129C_description" value=""/>
14693 <param name="channel_130N_description" value=""/>
14694 <param name="channel_130C_description" value=""/>
14695 <param name="channel_131_description" value=""/>
14696 <param name="reference_channel" value="126"/>
14697 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14698 </section>
14699 <section name="tmt11plex">
14700 <param name="channel_126_description" value=""/>
14701 <param name="channel_127N_description" value=""/>
14702 <param name="channel_127C_description" value=""/>
14703 <param name="channel_128N_description" value=""/>
14704 <param name="channel_128C_description" value=""/>
14705 <param name="channel_129N_description" value=""/>
14706 <param name="channel_129C_description" value=""/>
14707 <param name="channel_130N_description" value=""/>
14708 <param name="channel_130C_description" value=""/>
14709 <param name="channel_131N_description" value=""/>
14710 <param name="channel_131C_description" value=""/>
14711 <param name="reference_channel" value="126"/>
14712 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14713 </section>
14714 <section name="tmt16plex">
14715 <param name="channel_126_description" value=""/>
14716 <param name="channel_127N_description" value=""/>
14717 <param name="channel_127C_description" value=""/>
14718 <param name="channel_128N_description" value=""/>
14719 <param name="channel_128C_description" value=""/>
14720 <param name="channel_129N_description" value=""/>
14721 <param name="channel_129C_description" value=""/>
14722 <param name="channel_130N_description" value=""/>
14723 <param name="channel_130C_description" value=""/>
14724 <param name="channel_131N_description" value=""/>
14725 <param name="channel_131C_description" value=""/>
14726 <param name="channel_132N_description" value=""/>
14727 <param name="channel_132C_description" value=""/>
14728 <param name="channel_133N_description" value=""/>
14729 <param name="channel_133C_description" value=""/>
14730 <param name="channel_134N_description" value=""/>
14731 <param name="reference_channel" value="126"/>
14732 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
14733 </section>
14734 <section name="tmt6plex">
14735 <param name="channel_126_description" value=""/>
14736 <param name="channel_127_description" value=""/>
14737 <param name="channel_128_description" value=""/>
14738 <param name="channel_129_description" value=""/>
14739 <param name="channel_130_description" value=""/>
14740 <param name="channel_131_description" value=""/>
14741 <param name="reference_channel" value="126"/>
14742 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14743 </section>
14744 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14745 <output name="ctd_out" ftype="xml">
14746 <assert_contents>
14747 <is_valid_xml/>
14748 </assert_contents>
14749 </output>
14750 </test>
14751 <test expect_num_outputs="2">
14752 <conditional name="adv_opts_cond">
14753 <param name="adv_opts_selector" value="advanced"/>
14754 <param name="force" value="false"/>
14755 <param name="test" value="true"/>
14756 </conditional>
14757 <param name="type" value="itraq4plex"/>
14758 <param name="in" value="TMTTenPlexMethod_test.mzML"/>
14759 <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14760 <section name="extraction">
14761 <param name="select_activation" value="High-energy collision-induced dissociation"/>
14762 <param name="reporter_mass_shift" value="0.002"/>
14763 <param name="min_precursor_intensity" value="1.0"/>
14764 <param name="keep_unannotated_precursor" value="true"/>
14765 <param name="min_reporter_intensity" value="0.0"/>
14766 <param name="discard_low_intensity_quantifications" value="false"/>
14767 <param name="min_precursor_purity" value="0.0"/>
14768 <param name="precursor_isotope_deviation" value="10.0"/>
14769 <param name="purity_interpolation" value="true"/>
14770 </section>
14771 <section name="itraq4plex">
14772 <param name="channel_114_description" value=""/>
14773 <param name="channel_115_description" value=""/>
14774 <param name="channel_116_description" value=""/>
14775 <param name="channel_117_description" value=""/>
14776 <param name="reference_channel" value="114"/>
14777 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14778 </section>
14779 <section name="itraq8plex">
14780 <param name="channel_113_description" value=""/>
14781 <param name="channel_114_description" value=""/>
14782 <param name="channel_115_description" value=""/>
14783 <param name="channel_116_description" value=""/>
14784 <param name="channel_117_description" value=""/>
14785 <param name="channel_118_description" value=""/>
14786 <param name="channel_119_description" value=""/>
14787 <param name="channel_121_description" value=""/>
14788 <param name="reference_channel" value="113"/>
14789 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
14790 </section>
14791 <section name="quantification">
14792 <param name="isotope_correction" value="true"/>
14793 <param name="normalization" value="false"/>
14794 </section>
14795 <section name="tmt10plex">
14796 <param name="channel_126_description" value=""/>
14797 <param name="channel_127N_description" value=""/>
14798 <param name="channel_127C_description" value=""/>
14799 <param name="channel_128N_description" value=""/>
14800 <param name="channel_128C_description" value=""/>
14801 <param name="channel_129N_description" value=""/>
14802 <param name="channel_129C_description" value=""/>
14803 <param name="channel_130N_description" value=""/>
14804 <param name="channel_130C_description" value=""/>
14805 <param name="channel_131_description" value=""/>
14806 <param name="reference_channel" value="126"/>
14807 <param name="correction_matrix" value="&quot;0.0/0.0/5.0/0.0&quot; &quot;0.0/0.2/4.6/0.0&quot; &quot;0.0/0.2/4.6/0.3&quot; &quot;0.0/0.9/4.7/0.2&quot; &quot;0.0/0.5/3.2/0.0&quot; &quot;0.0/0.7/3.3/0.0&quot; &quot;0.0/1.3/2.5/0.0&quot; &quot;0.0/1.2/2.8/2.7&quot; &quot;0.0/1.5/2.0/0.0&quot; &quot;0.0/1.5/1.9/0.0&quot;"/>
14808 </section>
14809 <section name="tmt11plex">
14810 <param name="channel_126_description" value=""/>
14811 <param name="channel_127N_description" value=""/>
14812 <param name="channel_127C_description" value=""/>
14813 <param name="channel_128N_description" value=""/>
14814 <param name="channel_128C_description" value=""/>
14815 <param name="channel_129N_description" value=""/>
14816 <param name="channel_129C_description" value=""/>
14817 <param name="channel_130N_description" value=""/>
14818 <param name="channel_130C_description" value=""/>
14819 <param name="channel_131N_description" value=""/>
14820 <param name="channel_131C_description" value=""/>
14821 <param name="reference_channel" value="126"/>
14822 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14823 </section>
14824 <section name="tmt16plex">
14825 <param name="channel_126_description" value=""/>
14826 <param name="channel_127N_description" value=""/>
14827 <param name="channel_127C_description" value=""/>
14828 <param name="channel_128N_description" value=""/>
14829 <param name="channel_128C_description" value=""/>
14830 <param name="channel_129N_description" value=""/>
14831 <param name="channel_129C_description" value=""/>
14832 <param name="channel_130N_description" value=""/>
14833 <param name="channel_130C_description" value=""/>
14834 <param name="channel_131N_description" value=""/>
14835 <param name="channel_131C_description" value=""/>
14836 <param name="channel_132N_description" value=""/>
14837 <param name="channel_132C_description" value=""/>
14838 <param name="channel_133N_description" value=""/>
14839 <param name="channel_133C_description" value=""/>
14840 <param name="channel_134N_description" value=""/>
14841 <param name="reference_channel" value="126"/>
14842 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
14843 </section>
14844 <section name="tmt6plex">
14845 <param name="channel_126_description" value=""/>
14846 <param name="channel_127_description" value=""/>
14847 <param name="channel_128_description" value=""/>
14848 <param name="channel_129_description" value=""/>
14849 <param name="channel_130_description" value=""/>
14850 <param name="channel_131_description" value=""/>
14851 <param name="reference_channel" value="126"/>
14852 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14853 </section>
14854 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14855 <output name="ctd_out" ftype="xml">
14856 <assert_contents>
14857 <is_valid_xml/>
14858 </assert_contents>
14859 </output>
14860 </test>
14861 <test expect_num_outputs="2">
14862 <conditional name="adv_opts_cond">
14863 <param name="adv_opts_selector" value="advanced"/>
14864 <param name="force" value="false"/>
14865 <param name="test" value="true"/>
14866 </conditional>
14867 <param name="type" value="itraq4plex"/>
14868 <param name="in" value="TMTTenPlexMethod_test.mzML"/>
14869 <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14870 <section name="extraction">
14871 <param name="select_activation" value="High-energy collision-induced dissociation"/>
14872 <param name="reporter_mass_shift" value="0.002"/>
14873 <param name="min_precursor_intensity" value="1.0"/>
14874 <param name="keep_unannotated_precursor" value="true"/>
14875 <param name="min_reporter_intensity" value="0.0"/>
14876 <param name="discard_low_intensity_quantifications" value="false"/>
14877 <param name="min_precursor_purity" value="0.0"/>
14878 <param name="precursor_isotope_deviation" value="10.0"/>
14879 <param name="purity_interpolation" value="true"/>
14880 </section>
14881 <section name="itraq4plex">
14882 <param name="channel_114_description" value=""/>
14883 <param name="channel_115_description" value=""/>
14884 <param name="channel_116_description" value=""/>
14885 <param name="channel_117_description" value=""/>
14886 <param name="reference_channel" value="114"/>
14887 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14888 </section>
14889 <section name="itraq8plex">
14890 <param name="channel_113_description" value=""/>
14891 <param name="channel_114_description" value=""/>
14892 <param name="channel_115_description" value=""/>
14893 <param name="channel_116_description" value=""/>
14894 <param name="channel_117_description" value=""/>
14895 <param name="channel_118_description" value=""/>
14896 <param name="channel_119_description" value=""/>
14897 <param name="channel_121_description" value=""/>
14898 <param name="reference_channel" value="113"/>
14899 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
14900 </section>
14901 <section name="quantification">
14902 <param name="isotope_correction" value="true"/>
14903 <param name="normalization" value="false"/>
14904 </section>
14905 <section name="tmt10plex">
14906 <param name="channel_126_description" value=""/>
14907 <param name="channel_127N_description" value=""/>
14908 <param name="channel_127C_description" value=""/>
14909 <param name="channel_128N_description" value=""/>
14910 <param name="channel_128C_description" value=""/>
14911 <param name="channel_129N_description" value=""/>
14912 <param name="channel_129C_description" value=""/>
14913 <param name="channel_130N_description" value=""/>
14914 <param name="channel_130C_description" value=""/>
14915 <param name="channel_131_description" value=""/>
14916 <param name="reference_channel" value="126"/>
14917 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14918 </section>
14919 <section name="tmt11plex">
14920 <param name="channel_126_description" value=""/>
14921 <param name="channel_127N_description" value=""/>
14922 <param name="channel_127C_description" value=""/>
14923 <param name="channel_128N_description" value=""/>
14924 <param name="channel_128C_description" value=""/>
14925 <param name="channel_129N_description" value=""/>
14926 <param name="channel_129C_description" value=""/>
14927 <param name="channel_130N_description" value=""/>
14928 <param name="channel_130C_description" value=""/>
14929 <param name="channel_131N_description" value=""/>
14930 <param name="channel_131C_description" value=""/>
14931 <param name="reference_channel" value="126"/>
14932 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14933 </section>
14934 <section name="tmt16plex">
14935 <param name="channel_126_description" value=""/>
14936 <param name="channel_127N_description" value=""/>
14937 <param name="channel_127C_description" value=""/>
14938 <param name="channel_128N_description" value=""/>
14939 <param name="channel_128C_description" value=""/>
14940 <param name="channel_129N_description" value=""/>
14941 <param name="channel_129C_description" value=""/>
14942 <param name="channel_130N_description" value=""/>
14943 <param name="channel_130C_description" value=""/>
14944 <param name="channel_131N_description" value=""/>
14945 <param name="channel_131C_description" value=""/>
14946 <param name="channel_132N_description" value=""/>
14947 <param name="channel_132C_description" value=""/>
14948 <param name="channel_133N_description" value=""/>
14949 <param name="channel_133C_description" value=""/>
14950 <param name="channel_134N_description" value=""/>
14951 <param name="reference_channel" value="126"/>
14952 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
14953 </section>
14954 <section name="tmt6plex">
14955 <param name="channel_126_description" value=""/>
14956 <param name="channel_127_description" value=""/>
14957 <param name="channel_128_description" value=""/>
14958 <param name="channel_129_description" value=""/>
14959 <param name="channel_130_description" value=""/>
14960 <param name="channel_131_description" value=""/>
14961 <param name="reference_channel" value="126"/>
14962 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14963 </section>
14964 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14965 <output name="ctd_out" ftype="xml">
14966 <assert_contents>
14967 <is_valid_xml/>
14968 </assert_contents>
14969 </output>
14970 </test>
14971 <test expect_num_outputs="2">
14972 <conditional name="adv_opts_cond">
14973 <param name="adv_opts_selector" value="advanced"/>
14974 <param name="force" value="false"/>
14975 <param name="test" value="true"/>
14976 </conditional>
14977 <param name="type" value="tmt10plex"/>
14978 <param name="in" value="MS3_nonHierarchical.mzML"/>
14979 <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14980 <section name="extraction">
14981 <param name="select_activation" value="Collision-induced dissociation"/>
14982 <param name="reporter_mass_shift" value="0.002"/>
14983 <param name="min_precursor_intensity" value="1.0"/>
14984 <param name="keep_unannotated_precursor" value="true"/>
14985 <param name="min_reporter_intensity" value="0.0"/>
14986 <param name="discard_low_intensity_quantifications" value="false"/>
14987 <param name="min_precursor_purity" value="0.0"/>
14988 <param name="precursor_isotope_deviation" value="10.0"/>
14989 <param name="purity_interpolation" value="true"/>
14990 </section>
14991 <section name="itraq4plex">
14992 <param name="channel_114_description" value=""/>
14993 <param name="channel_115_description" value=""/>
14994 <param name="channel_116_description" value=""/>
14995 <param name="channel_117_description" value=""/>
14996 <param name="reference_channel" value="114"/>
14997 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14998 </section>
14999 <section name="itraq8plex">
15000 <param name="channel_113_description" value=""/>
15001 <param name="channel_114_description" value=""/>
15002 <param name="channel_115_description" value=""/>
15003 <param name="channel_116_description" value=""/>
15004 <param name="channel_117_description" value=""/>
15005 <param name="channel_118_description" value=""/>
15006 <param name="channel_119_description" value=""/>
15007 <param name="channel_121_description" value=""/>
15008 <param name="reference_channel" value="113"/>
15009 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
15010 </section>
15011 <section name="quantification">
15012 <param name="isotope_correction" value="true"/>
15013 <param name="normalization" value="false"/>
15014 </section>
15015 <section name="tmt10plex">
15016 <param name="channel_126_description" value=""/>
15017 <param name="channel_127N_description" value=""/>
15018 <param name="channel_127C_description" value=""/>
15019 <param name="channel_128N_description" value=""/>
15020 <param name="channel_128C_description" value=""/>
15021 <param name="channel_129N_description" value=""/>
15022 <param name="channel_129C_description" value=""/>
15023 <param name="channel_130N_description" value=""/>
15024 <param name="channel_130C_description" value=""/>
15025 <param name="channel_131_description" value=""/>
15026 <param name="reference_channel" value="126"/>
15027 <param name="correction_matrix" value="&quot;0.0/0.0/5.09/0.0&quot; &quot;0.0/0.25/5.27/0.0&quot; &quot;0.0/0.37/5.36/0.15&quot; &quot;0.0/0.65/4.17/0.1&quot; &quot;0.08/0.49/3.06/0.0&quot; &quot;0.01/0.71/3.07/0.0&quot; &quot;0.0/1.32/2.62/0.0&quot; &quot;0.02/1.28/2.75/2.53&quot; &quot;0.03/2.08/2.23/0.0&quot; &quot;0.08/1.99/1.65/0.0&quot;"/>
15028 </section>
15029 <section name="tmt11plex">
15030 <param name="channel_126_description" value=""/>
15031 <param name="channel_127N_description" value=""/>
15032 <param name="channel_127C_description" value=""/>
15033 <param name="channel_128N_description" value=""/>
15034 <param name="channel_128C_description" value=""/>
15035 <param name="channel_129N_description" value=""/>
15036 <param name="channel_129C_description" value=""/>
15037 <param name="channel_130N_description" value=""/>
15038 <param name="channel_130C_description" value=""/>
15039 <param name="channel_131N_description" value=""/>
15040 <param name="channel_131C_description" value=""/>
15041 <param name="reference_channel" value="126"/>
15042 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
15043 </section>
15044 <section name="tmt16plex">
15045 <param name="channel_126_description" value=""/>
15046 <param name="channel_127N_description" value=""/>
15047 <param name="channel_127C_description" value=""/>
15048 <param name="channel_128N_description" value=""/>
15049 <param name="channel_128C_description" value=""/>
15050 <param name="channel_129N_description" value=""/>
15051 <param name="channel_129C_description" value=""/>
15052 <param name="channel_130N_description" value=""/>
15053 <param name="channel_130C_description" value=""/>
15054 <param name="channel_131N_description" value=""/>
15055 <param name="channel_131C_description" value=""/>
15056 <param name="channel_132N_description" value=""/>
15057 <param name="channel_132C_description" value=""/>
15058 <param name="channel_133N_description" value=""/>
15059 <param name="channel_133C_description" value=""/>
15060 <param name="channel_134N_description" value=""/>
15061 <param name="reference_channel" value="126"/>
15062 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
15063 </section>
15064 <section name="tmt6plex">
15065 <param name="channel_126_description" value=""/>
15066 <param name="channel_127_description" value=""/>
15067 <param name="channel_128_description" value=""/>
15068 <param name="channel_129_description" value=""/>
15069 <param name="channel_130_description" value=""/>
15070 <param name="channel_131_description" value=""/>
15071 <param name="reference_channel" value="126"/>
15072 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
15073 </section>
15074 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15075 <output name="ctd_out" ftype="xml">
15076 <assert_contents>
15077 <is_valid_xml/>
15078 </assert_contents>
15079 </output>
15080 </test>
15081 </xml>
15082 <xml name="autotest_LabeledEval">
15083 </xml>
15084 <xml name="autotest_LuciphorAdapter">
15085 <test expect_num_outputs="2">
15086 <conditional name="adv_opts_cond">
15087 <param name="adv_opts_selector" value="advanced"/>
15088 <param name="force" value="false"/>
15089 <param name="test" value="true"/>
15090 </conditional>
15091 <param name="in" value="LuciphorAdapter_1_input.mzML"/>
15092 <param name="id" value="LuciphorAdapter_1_input.idXML"/>
15093 <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
15094 <param name="fragment_method" value="CID"/>
15095 <param name="fragment_mass_tolerance" value="0.5"/>
15096 <param name="fragment_error_units" value="Da"/>
15097 <param name="min_mz" value="150.0"/>
15098 <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/>
15099 <param name="neutral_losses" value="&quot;sty -H3PO4 -97.97690&quot;"/>
15100 <param name="decoy_mass" value="79.966331"/>
15101 <param name="decoy_neutral_losses" value="&quot;X -H3PO4 -97.97690&quot;"/>
15102 <param name="max_charge_state" value="5"/>
15103 <param name="max_peptide_length" value="40"/>
15104 <param name="max_num_perm" value="16384"/>
15105 <param name="modeling_score_threshold" value="0.95"/>
15106 <param name="scoring_threshold" value="0.0"/>
15107 <param name="min_num_psms_model" value="1"/>
15108 <param name="run_mode" value="0"/>
15109 <param name="rt_tolerance" value="0.01"/>
15110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15111 <output name="ctd_out" ftype="xml">
15112 <assert_contents>
15113 <is_valid_xml/>
15114 </assert_contents>
15115 </output>
15116 </test>
15117 </xml>
15118 <xml name="autotest_MapAlignerIdentification">
15119 <test expect_num_outputs="2">
15120 <conditional name="adv_opts_cond">
15121 <param name="adv_opts_selector" value="advanced"/>
15122 <param name="force" value="false"/>
15123 <param name="test" value="true"/>
15124 </conditional>
15125 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
15126 <output_collection name="out" count="2"/>
15127 <section name="reference">
15128 <param name="index" value="0"/>
15129 </section>
15130 <section name="algorithm">
15131 <param name="score_cutoff" value="false"/>
15132 <param name="min_score" value="0.05"/>
15133 <param name="min_run_occur" value="2"/>
15134 <param name="max_rt_shift" value="0.0"/>
15135 <param name="use_unassigned_peptides" value="true"/>
15136 <param name="use_feature_rt" value="false"/>
15137 </section>
15138 <section name="model">
15139 <param name="type" value="b_spline"/>
15140 <section name="linear">
15141 <param name="symmetric_regression" value="false"/>
15142 <param name="x_weight" value=""/>
15143 <param name="y_weight" value=""/>
15144 <param name="x_datum_min" value="1e-15"/>
15145 <param name="x_datum_max" value="1000000000000000.0"/>
15146 <param name="y_datum_min" value="1e-15"/>
15147 <param name="y_datum_max" value="1000000000000000.0"/>
15148 </section>
15149 <section name="b_spline">
15150 <param name="wavelength" value="0.0"/>
15151 <param name="num_nodes" value="5"/>
15152 <param name="extrapolate" value="linear"/>
15153 <param name="boundary_condition" value="2"/>
15154 </section>
15155 <section name="lowess">
15156 <param name="span" value="0.666666666666667"/>
15157 <param name="num_iterations" value="3"/>
15158 <param name="delta" value="-1.0"/>
15159 <param name="interpolation_type" value="cspline"/>
15160 <param name="extrapolation_type" value="four-point-linear"/>
15161 </section>
15162 <section name="interpolated">
15163 <param name="interpolation_type" value="cspline"/>
15164 <param name="extrapolation_type" value="two-point-linear"/>
15165 </section>
15166 </section>
15167 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15168 <output name="ctd_out" ftype="xml">
15169 <assert_contents>
15170 <is_valid_xml/>
15171 </assert_contents>
15172 </output>
15173 </test>
15174 <test expect_num_outputs="2">
15175 <conditional name="adv_opts_cond">
15176 <param name="adv_opts_selector" value="advanced"/>
15177 <param name="force" value="false"/>
15178 <param name="test" value="true"/>
15179 </conditional>
15180 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
15181 <output_collection name="out" count="1"/>
15182 <section name="reference">
15183 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
15184 <param name="index" value="0"/>
15185 </section>
15186 <section name="algorithm">
15187 <param name="score_cutoff" value="false"/>
15188 <param name="min_score" value="0.05"/>
15189 <param name="min_run_occur" value="2"/>
15190 <param name="max_rt_shift" value="0.0"/>
15191 <param name="use_unassigned_peptides" value="true"/>
15192 <param name="use_feature_rt" value="false"/>
15193 </section>
15194 <section name="model">
15195 <param name="type" value="b_spline"/>
15196 <section name="linear">
15197 <param name="symmetric_regression" value="false"/>
15198 <param name="x_weight" value=""/>
15199 <param name="y_weight" value=""/>
15200 <param name="x_datum_min" value="1e-15"/>
15201 <param name="x_datum_max" value="1000000000000000.0"/>
15202 <param name="y_datum_min" value="1e-15"/>
15203 <param name="y_datum_max" value="1000000000000000.0"/>
15204 </section>
15205 <section name="b_spline">
15206 <param name="wavelength" value="0.0"/>
15207 <param name="num_nodes" value="5"/>
15208 <param name="extrapolate" value="linear"/>
15209 <param name="boundary_condition" value="2"/>
15210 </section>
15211 <section name="lowess">
15212 <param name="span" value="0.666666666666667"/>
15213 <param name="num_iterations" value="3"/>
15214 <param name="delta" value="-1.0"/>
15215 <param name="interpolation_type" value="cspline"/>
15216 <param name="extrapolation_type" value="four-point-linear"/>
15217 </section>
15218 <section name="interpolated">
15219 <param name="interpolation_type" value="cspline"/>
15220 <param name="extrapolation_type" value="two-point-linear"/>
15221 </section>
15222 </section>
15223 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15224 <output name="ctd_out" ftype="xml">
15225 <assert_contents>
15226 <is_valid_xml/>
15227 </assert_contents>
15228 </output>
15229 </test>
15230 <test expect_num_outputs="2">
15231 <conditional name="adv_opts_cond">
15232 <param name="adv_opts_selector" value="advanced"/>
15233 <param name="force" value="false"/>
15234 <param name="test" value="true"/>
15235 </conditional>
15236 <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/>
15237 <output_collection name="out" count="2"/>
15238 <section name="reference">
15239 <param name="index" value="1"/>
15240 </section>
15241 <section name="algorithm">
15242 <param name="score_cutoff" value="false"/>
15243 <param name="min_score" value="0.05"/>
15244 <param name="min_run_occur" value="2"/>
15245 <param name="max_rt_shift" value="0.0"/>
15246 <param name="use_unassigned_peptides" value="true"/>
15247 <param name="use_feature_rt" value="false"/>
15248 </section>
15249 <section name="model">
15250 <param name="type" value="b_spline"/>
15251 <section name="linear">
15252 <param name="symmetric_regression" value="false"/>
15253 <param name="x_weight" value=""/>
15254 <param name="y_weight" value=""/>
15255 <param name="x_datum_min" value="1e-15"/>
15256 <param name="x_datum_max" value="1000000000000000.0"/>
15257 <param name="y_datum_min" value="1e-15"/>
15258 <param name="y_datum_max" value="1000000000000000.0"/>
15259 </section>
15260 <section name="b_spline">
15261 <param name="wavelength" value="0.0"/>
15262 <param name="num_nodes" value="5"/>
15263 <param name="extrapolate" value="linear"/>
15264 <param name="boundary_condition" value="2"/>
15265 </section>
15266 <section name="lowess">
15267 <param name="span" value="0.666666666666667"/>
15268 <param name="num_iterations" value="3"/>
15269 <param name="delta" value="-1.0"/>
15270 <param name="interpolation_type" value="cspline"/>
15271 <param name="extrapolation_type" value="four-point-linear"/>
15272 </section>
15273 <section name="interpolated">
15274 <param name="interpolation_type" value="cspline"/>
15275 <param name="extrapolation_type" value="two-point-linear"/>
15276 </section>
15277 </section>
15278 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15279 <output name="ctd_out" ftype="xml">
15280 <assert_contents>
15281 <is_valid_xml/>
15282 </assert_contents>
15283 </output>
15284 </test>
15285 <test expect_num_outputs="2">
15286 <conditional name="adv_opts_cond">
15287 <param name="adv_opts_selector" value="advanced"/>
15288 <param name="force" value="false"/>
15289 <param name="test" value="true"/>
15290 </conditional>
15291 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
15292 <output_collection name="out" count="2"/>
15293 <section name="reference">
15294 <param name="index" value="2"/>
15295 </section>
15296 <section name="algorithm">
15297 <param name="score_cutoff" value="false"/>
15298 <param name="min_score" value="0.05"/>
15299 <param name="min_run_occur" value="2"/>
15300 <param name="max_rt_shift" value="0.0"/>
15301 <param name="use_unassigned_peptides" value="true"/>
15302 <param name="use_feature_rt" value="false"/>
15303 </section>
15304 <section name="model">
15305 <param name="type" value="b_spline"/>
15306 <section name="linear">
15307 <param name="symmetric_regression" value="false"/>
15308 <param name="x_weight" value=""/>
15309 <param name="y_weight" value=""/>
15310 <param name="x_datum_min" value="1e-15"/>
15311 <param name="x_datum_max" value="1000000000000000.0"/>
15312 <param name="y_datum_min" value="1e-15"/>
15313 <param name="y_datum_max" value="1000000000000000.0"/>
15314 </section>
15315 <section name="b_spline">
15316 <param name="wavelength" value="0.0"/>
15317 <param name="num_nodes" value="5"/>
15318 <param name="extrapolate" value="linear"/>
15319 <param name="boundary_condition" value="2"/>
15320 </section>
15321 <section name="lowess">
15322 <param name="span" value="0.666666666666667"/>
15323 <param name="num_iterations" value="3"/>
15324 <param name="delta" value="-1.0"/>
15325 <param name="interpolation_type" value="cspline"/>
15326 <param name="extrapolation_type" value="four-point-linear"/>
15327 </section>
15328 <section name="interpolated">
15329 <param name="interpolation_type" value="cspline"/>
15330 <param name="extrapolation_type" value="two-point-linear"/>
15331 </section>
15332 </section>
15333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15334 <output name="ctd_out" ftype="xml">
15335 <assert_contents>
15336 <is_valid_xml/>
15337 </assert_contents>
15338 </output>
15339 </test>
15340 <test expect_num_outputs="2">
15341 <conditional name="adv_opts_cond">
15342 <param name="adv_opts_selector" value="advanced"/>
15343 <param name="force" value="false"/>
15344 <param name="test" value="true"/>
15345 </conditional>
15346 <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/>
15347 <output_collection name="out" count="2"/>
15348 <section name="reference">
15349 <param name="index" value="0"/>
15350 </section>
15351 <section name="algorithm">
15352 <param name="score_cutoff" value="false"/>
15353 <param name="min_score" value="0.05"/>
15354 <param name="min_run_occur" value="2"/>
15355 <param name="max_rt_shift" value="0.0"/>
15356 <param name="use_unassigned_peptides" value="true"/>
15357 <param name="use_feature_rt" value="false"/>
15358 </section>
15359 <section name="model">
15360 <param name="type" value="b_spline"/>
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="in" value="MapAlignerIdentification_1_input1.featureXML"/>
15402 <output_collection name="trafo_out" count="1"/>
15403 <section name="reference">
15404 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
15405 <param name="index" value="0"/>
15406 </section>
15407 <section name="algorithm">
15408 <param name="score_cutoff" value="false"/>
15409 <param name="min_score" value="0.05"/>
15410 <param name="min_run_occur" value="2"/>
15411 <param name="max_rt_shift" value="0.0"/>
15412 <param name="use_unassigned_peptides" value="true"/>
15413 <param name="use_feature_rt" value="false"/>
15414 </section>
15415 <section name="model">
15416 <param name="type" value="b_spline"/>
15417 <section name="linear">
15418 <param name="symmetric_regression" value="false"/>
15419 <param name="x_weight" value=""/>
15420 <param name="y_weight" value=""/>
15421 <param name="x_datum_min" value="1e-15"/>
15422 <param name="x_datum_max" value="1000000000000000.0"/>
15423 <param name="y_datum_min" value="1e-15"/>
15424 <param name="y_datum_max" value="1000000000000000.0"/>
15425 </section>
15426 <section name="b_spline">
15427 <param name="wavelength" value="0.0"/>
15428 <param name="num_nodes" value="5"/>
15429 <param name="extrapolate" value="linear"/>
15430 <param name="boundary_condition" value="2"/>
15431 </section>
15432 <section name="lowess">
15433 <param name="span" value="0.666666666666667"/>
15434 <param name="num_iterations" value="3"/>
15435 <param name="delta" value="-1.0"/>
15436 <param name="interpolation_type" value="cspline"/>
15437 <param name="extrapolation_type" value="four-point-linear"/>
15438 </section>
15439 <section name="interpolated">
15440 <param name="interpolation_type" value="cspline"/>
15441 <param name="extrapolation_type" value="two-point-linear"/>
15442 </section>
15443 </section>
15444 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
15445 <output name="ctd_out" ftype="xml">
15446 <assert_contents>
15447 <is_valid_xml/>
15448 </assert_contents>
15449 </output>
15450 </test>
15451 <test expect_num_outputs="3">
15452 <conditional name="adv_opts_cond">
15453 <param name="adv_opts_selector" value="advanced"/>
15454 <param name="force" value="true"/>
15455 <param name="test" value="true"/>
15456 </conditional>
15457 <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
15458 <output_collection name="out" count="1"/>
15459 <output_collection name="trafo_out" count="1"/>
15460 <section name="reference">
15461 <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
15462 <param name="index" value="0"/>
15463 </section>
15464 <section name="algorithm">
15465 <param name="score_cutoff" value="false"/>
15466 <param name="min_score" value="0.05"/>
15467 <param name="min_run_occur" value="2"/>
15468 <param name="max_rt_shift" value="0.5"/>
15469 <param name="use_unassigned_peptides" value="true"/>
15470 <param name="use_feature_rt" value="false"/>
15471 </section>
15472 <section name="model">
15473 <param name="type" value="b_spline"/>
15474 <section name="linear">
15475 <param name="symmetric_regression" value="false"/>
15476 <param name="x_weight" value=""/>
15477 <param name="y_weight" value=""/>
15478 <param name="x_datum_min" value="1e-15"/>
15479 <param name="x_datum_max" value="1000000000000000.0"/>
15480 <param name="y_datum_min" value="1e-15"/>
15481 <param name="y_datum_max" value="1000000000000000.0"/>
15482 </section>
15483 <section name="b_spline">
15484 <param name="wavelength" value="0.0"/>
15485 <param name="num_nodes" value="5"/>
15486 <param name="extrapolate" value="linear"/>
15487 <param name="boundary_condition" value="2"/>
15488 </section>
15489 <section name="lowess">
15490 <param name="span" value="0.666666666666667"/>
15491 <param name="num_iterations" value="3"/>
15492 <param name="delta" value="-1.0"/>
15493 <param name="interpolation_type" value="cspline"/>
15494 <param name="extrapolation_type" value="four-point-linear"/>
15495 </section>
15496 <section name="interpolated">
15497 <param name="interpolation_type" value="cspline"/>
15498 <param name="extrapolation_type" value="two-point-linear"/>
15499 </section>
15500 </section>
15501 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
15502 <output name="ctd_out" ftype="xml">
15503 <assert_contents>
15504 <is_valid_xml/>
15505 </assert_contents>
15506 </output>
15507 </test>
15508 </xml>
15509 <xml name="autotest_MapAlignerPoseClustering">
15510 <test expect_num_outputs="3">
15511 <conditional name="adv_opts_cond">
15512 <param name="adv_opts_selector" value="advanced"/>
15513 <param name="force" value="false"/>
15514 <param name="test" value="true"/>
15515 </conditional>
15516 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
15517 <output_collection name="out" count="3"/>
15518 <output_collection name="trafo_out" count="3"/>
15519 <section name="reference">
15520 <param name="index" value="0"/>
15521 </section>
15522 <section name="algorithm">
15523 <param name="max_num_peaks_considered" value="400"/>
15524 <section name="superimposer">
15525 <param name="mz_pair_max_distance" value="0.5"/>
15526 <param name="rt_pair_distance_fraction" value="0.1"/>
15527 <param name="num_used_points" value="2000"/>
15528 <param name="scaling_bucket_size" value="0.005"/>
15529 <param name="shift_bucket_size" value="3.0"/>
15530 <param name="max_shift" value="1000.0"/>
15531 <param name="max_scaling" value="2.0"/>
15532 <param name="dump_buckets" value=""/>
15533 <param name="dump_pairs" value=""/>
15534 </section>
15535 <section name="pairfinder">
15536 <param name="second_nearest_gap" value="2.0"/>
15537 <param name="use_identifications" value="false"/>
15538 <param name="ignore_charge" value="true"/>
15539 <param name="ignore_adduct" value="true"/>
15540 <section name="distance_RT">
15541 <param name="max_difference" value="30.0"/>
15542 <param name="exponent" value="1.0"/>
15543 <param name="weight" value="1.0"/>
15544 </section>
15545 <section name="distance_MZ">
15546 <param name="max_difference" value="0.3"/>
15547 <param name="unit" value="Da"/>
15548 <param name="exponent" value="2.0"/>
15549 <param name="weight" value="1.0"/>
15550 </section>
15551 <section name="distance_intensity">
15552 <param name="exponent" value="1.0"/>
15553 <param name="weight" value="0.0"/>
15554 <param name="log_transform" value="disabled"/>
15555 </section>
15556 </section>
15557 </section>
15558 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
15559 <output name="ctd_out" ftype="xml">
15560 <assert_contents>
15561 <is_valid_xml/>
15562 </assert_contents>
15563 </output>
15564 </test>
15565 <test expect_num_outputs="2">
15566 <conditional name="adv_opts_cond">
15567 <param name="adv_opts_selector" value="advanced"/>
15568 <param name="force" value="false"/>
15569 <param name="test" value="true"/>
15570 </conditional>
15571 <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/>
15572 <output_collection name="out" count="3"/>
15573 <section name="reference">
15574 <param name="index" value="0"/>
15575 </section>
15576 <section name="algorithm">
15577 <param name="max_num_peaks_considered" value="400"/>
15578 <section name="superimposer">
15579 <param name="mz_pair_max_distance" value="0.5"/>
15580 <param name="rt_pair_distance_fraction" value="0.1"/>
15581 <param name="num_used_points" value="2000"/>
15582 <param name="scaling_bucket_size" value="0.005"/>
15583 <param name="shift_bucket_size" value="3.0"/>
15584 <param name="max_shift" value="1000.0"/>
15585 <param name="max_scaling" value="2.0"/>
15586 <param name="dump_buckets" value=""/>
15587 <param name="dump_pairs" value=""/>
15588 </section>
15589 <section name="pairfinder">
15590 <param name="second_nearest_gap" value="2.0"/>
15591 <param name="use_identifications" value="false"/>
15592 <param name="ignore_charge" value="false"/>
15593 <param name="ignore_adduct" value="true"/>
15594 <section name="distance_RT">
15595 <param name="max_difference" value="100.0"/>
15596 <param name="exponent" value="1.0"/>
15597 <param name="weight" value="1.0"/>
15598 </section>
15599 <section name="distance_MZ">
15600 <param name="max_difference" value="0.3"/>
15601 <param name="unit" value="Da"/>
15602 <param name="exponent" value="2.0"/>
15603 <param name="weight" value="1.0"/>
15604 </section>
15605 <section name="distance_intensity">
15606 <param name="exponent" value="1.0"/>
15607 <param name="weight" value="0.0"/>
15608 <param name="log_transform" value="disabled"/>
15609 </section>
15610 </section>
15611 </section>
15612 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15613 <output name="ctd_out" ftype="xml">
15614 <assert_contents>
15615 <is_valid_xml/>
15616 </assert_contents>
15617 </output>
15618 </test>
15619 <test expect_num_outputs="2">
15620 <conditional name="adv_opts_cond">
15621 <param name="adv_opts_selector" value="advanced"/>
15622 <param name="force" value="false"/>
15623 <param name="test" value="true"/>
15624 </conditional>
15625 <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
15626 <output_collection name="out" count="2"/>
15627 <section name="reference">
15628 <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/>
15629 <param name="index" value="0"/>
15630 </section>
15631 <section name="algorithm">
15632 <param name="max_num_peaks_considered" value="400"/>
15633 <section name="superimposer">
15634 <param name="mz_pair_max_distance" value="0.5"/>
15635 <param name="rt_pair_distance_fraction" value="0.1"/>
15636 <param name="num_used_points" value="2000"/>
15637 <param name="scaling_bucket_size" value="0.005"/>
15638 <param name="shift_bucket_size" value="3.0"/>
15639 <param name="max_shift" value="1000.0"/>
15640 <param name="max_scaling" value="2.0"/>
15641 <param name="dump_buckets" value=""/>
15642 <param name="dump_pairs" value=""/>
15643 </section>
15644 <section name="pairfinder">
15645 <param name="second_nearest_gap" value="2.0"/>
15646 <param name="use_identifications" value="false"/>
15647 <param name="ignore_charge" value="true"/>
15648 <param name="ignore_adduct" value="true"/>
15649 <section name="distance_RT">
15650 <param name="max_difference" value="30.0"/>
15651 <param name="exponent" value="1.0"/>
15652 <param name="weight" value="1.0"/>
15653 </section>
15654 <section name="distance_MZ">
15655 <param name="max_difference" value="0.3"/>
15656 <param name="unit" value="Da"/>
15657 <param name="exponent" value="2.0"/>
15658 <param name="weight" value="1.0"/>
15659 </section>
15660 <section name="distance_intensity">
15661 <param name="exponent" value="1.0"/>
15662 <param name="weight" value="0.0"/>
15663 <param name="log_transform" value="disabled"/>
15664 </section>
15665 </section>
15666 </section>
15667 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15668 <output name="ctd_out" ftype="xml">
15669 <assert_contents>
15670 <is_valid_xml/>
15671 </assert_contents>
15672 </output>
15673 </test>
15674 <test expect_num_outputs="2">
15675 <conditional name="adv_opts_cond">
15676 <param name="adv_opts_selector" value="advanced"/>
15677 <param name="force" value="false"/>
15678 <param name="test" value="true"/>
15679 </conditional>
15680 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/>
15681 <output_collection name="trafo_out" count="2"/>
15682 <section name="reference">
15683 <param name="index" value="2"/>
15684 </section>
15685 <section name="algorithm">
15686 <param name="max_num_peaks_considered" value="400"/>
15687 <section name="superimposer">
15688 <param name="mz_pair_max_distance" value="0.5"/>
15689 <param name="rt_pair_distance_fraction" value="0.1"/>
15690 <param name="num_used_points" value="2000"/>
15691 <param name="scaling_bucket_size" value="0.005"/>
15692 <param name="shift_bucket_size" value="3.0"/>
15693 <param name="max_shift" value="1000.0"/>
15694 <param name="max_scaling" value="2.0"/>
15695 <param name="dump_buckets" value=""/>
15696 <param name="dump_pairs" value=""/>
15697 </section>
15698 <section name="pairfinder">
15699 <param name="second_nearest_gap" value="2.0"/>
15700 <param name="use_identifications" value="false"/>
15701 <param name="ignore_charge" value="true"/>
15702 <param name="ignore_adduct" value="true"/>
15703 <section name="distance_RT">
15704 <param name="max_difference" value="30.0"/>
15705 <param name="exponent" value="1.0"/>
15706 <param name="weight" value="1.0"/>
15707 </section>
15708 <section name="distance_MZ">
15709 <param name="max_difference" value="0.3"/>
15710 <param name="unit" value="Da"/>
15711 <param name="exponent" value="2.0"/>
15712 <param name="weight" value="1.0"/>
15713 </section>
15714 <section name="distance_intensity">
15715 <param name="exponent" value="1.0"/>
15716 <param name="weight" value="0.0"/>
15717 <param name="log_transform" value="disabled"/>
15718 </section>
15719 </section>
15720 </section>
15721 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
15722 <output name="ctd_out" ftype="xml">
15723 <assert_contents>
15724 <is_valid_xml/>
15725 </assert_contents>
15726 </output>
15727 </test>
15728 </xml>
15729 <xml name="autotest_MapAlignerSpectrum">
15730 <test expect_num_outputs="2">
15731 <conditional name="adv_opts_cond">
15732 <param name="adv_opts_selector" value="advanced"/>
15733 <param name="force" value="false"/>
15734 <param name="test" value="true"/>
15735 </conditional>
15736 <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/>
15737 <output_collection name="out" count="3"/>
15738 <section name="algorithm">
15739 <param name="gapcost" value="1.0"/>
15740 <param name="affinegapcost" value="0.5"/>
15741 <param name="cutoff_score" value="0.7"/>
15742 <param name="bucketsize" value="100"/>
15743 <param name="anchorpoints" value="100"/>
15744 <param name="mismatchscore" value="-5.0"/>
15745 <param name="scorefunction" value="SteinScottImproveScore"/>
15746 </section>
15747 <section name="model">
15748 <param name="type" value="interpolated"/>
15749 <section name="linear">
15750 <param name="symmetric_regression" value="false"/>
15751 <param name="x_weight" value=""/>
15752 <param name="y_weight" value=""/>
15753 <param name="x_datum_min" value="1e-15"/>
15754 <param name="x_datum_max" value="1000000000000000.0"/>
15755 <param name="y_datum_min" value="1e-15"/>
15756 <param name="y_datum_max" value="1000000000000000.0"/>
15757 </section>
15758 <section name="b_spline">
15759 <param name="wavelength" value="0.0"/>
15760 <param name="num_nodes" value="5"/>
15761 <param name="extrapolate" value="linear"/>
15762 <param name="boundary_condition" value="2"/>
15763 </section>
15764 <section name="lowess">
15765 <param name="span" value="0.666666666666667"/>
15766 <param name="num_iterations" value="3"/>
15767 <param name="delta" value="-1.0"/>
15768 <param name="interpolation_type" value="cspline"/>
15769 <param name="extrapolation_type" value="four-point-linear"/>
15770 </section>
15771 <section name="interpolated">
15772 <param name="interpolation_type" value="cspline"/>
15773 <param name="extrapolation_type" value="two-point-linear"/>
15774 </section>
15775 </section>
15776 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15777 <output name="ctd_out" ftype="xml">
15778 <assert_contents>
15779 <is_valid_xml/>
15780 </assert_contents>
15781 </output>
15782 </test>
15783 </xml>
15784 <xml name="autotest_MapAlignerTreeGuided">
15785 <test expect_num_outputs="2">
15786 <conditional name="adv_opts_cond">
15787 <param name="adv_opts_selector" value="advanced"/>
15788 <param name="force" value="false"/>
15789 <param name="test" value="true"/>
15790 </conditional>
15791 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
15792 <output_collection name="out" count="3"/>
15793 <section name="algorithm">
15794 <param name="model_type" value="b_spline"/>
15795 <section name="model">
15796 <param name="type" value="b_spline"/>
15797 <section name="linear">
15798 <param name="symmetric_regression" value="false"/>
15799 <param name="x_weight" value=""/>
15800 <param name="y_weight" value=""/>
15801 <param name="x_datum_min" value="1e-15"/>
15802 <param name="x_datum_max" value="1000000000000000.0"/>
15803 <param name="y_datum_min" value="1e-15"/>
15804 <param name="y_datum_max" value="1000000000000000.0"/>
15805 </section>
15806 <section name="b_spline">
15807 <param name="wavelength" value="0.0"/>
15808 <param name="num_nodes" value="5"/>
15809 <param name="extrapolate" value="linear"/>
15810 <param name="boundary_condition" value="2"/>
15811 </section>
15812 <section name="lowess">
15813 <param name="span" value="0.666666666666667"/>
15814 <param name="num_iterations" value="3"/>
15815 <param name="delta" value="-1.0"/>
15816 <param name="interpolation_type" value="cspline"/>
15817 <param name="extrapolation_type" value="four-point-linear"/>
15818 </section>
15819 <section name="interpolated">
15820 <param name="interpolation_type" value="cspline"/>
15821 <param name="extrapolation_type" value="two-point-linear"/>
15822 </section>
15823 </section>
15824 <section name="align_algorithm">
15825 <param name="score_cutoff" value="false"/>
15826 <param name="min_score" value="0.05"/>
15827 <param name="min_run_occur" value="2"/>
15828 <param name="max_rt_shift" value="0.5"/>
15829 <param name="use_unassigned_peptides" value="true"/>
15830 <param name="use_feature_rt" value="true"/>
15831 </section>
15832 </section>
15833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15834 <output name="ctd_out" ftype="xml">
15835 <assert_contents>
15836 <is_valid_xml/>
15837 </assert_contents>
15838 </output>
15839 </test>
15840 <test expect_num_outputs="2">
15841 <conditional name="adv_opts_cond">
15842 <param name="adv_opts_selector" value="advanced"/>
15843 <param name="force" value="false"/>
15844 <param name="test" value="true"/>
15845 </conditional>
15846 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
15847 <output_collection name="trafo_out" count="3"/>
15848 <section name="algorithm">
15849 <param name="model_type" value="b_spline"/>
15850 <section name="model">
15851 <param name="type" value="b_spline"/>
15852 <section name="linear">
15853 <param name="symmetric_regression" value="false"/>
15854 <param name="x_weight" value=""/>
15855 <param name="y_weight" value=""/>
15856 <param name="x_datum_min" value="1e-15"/>
15857 <param name="x_datum_max" value="1000000000000000.0"/>
15858 <param name="y_datum_min" value="1e-15"/>
15859 <param name="y_datum_max" value="1000000000000000.0"/>
15860 </section>
15861 <section name="b_spline">
15862 <param name="wavelength" value="0.0"/>
15863 <param name="num_nodes" value="5"/>
15864 <param name="extrapolate" value="linear"/>
15865 <param name="boundary_condition" value="2"/>
15866 </section>
15867 <section name="lowess">
15868 <param name="span" value="0.666666666666667"/>
15869 <param name="num_iterations" value="3"/>
15870 <param name="delta" value="-1.0"/>
15871 <param name="interpolation_type" value="cspline"/>
15872 <param name="extrapolation_type" value="four-point-linear"/>
15873 </section>
15874 <section name="interpolated">
15875 <param name="interpolation_type" value="cspline"/>
15876 <param name="extrapolation_type" value="two-point-linear"/>
15877 </section>
15878 </section>
15879 <section name="align_algorithm">
15880 <param name="score_cutoff" value="false"/>
15881 <param name="min_score" value="0.05"/>
15882 <param name="min_run_occur" value="2"/>
15883 <param name="max_rt_shift" value="0.5"/>
15884 <param name="use_unassigned_peptides" value="true"/>
15885 <param name="use_feature_rt" value="true"/>
15886 </section>
15887 </section>
15888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
15889 <output name="ctd_out" ftype="xml">
15890 <assert_contents>
15891 <is_valid_xml/>
15892 </assert_contents>
15893 </output>
15894 </test>
15895 <test expect_num_outputs="2">
15896 <conditional name="adv_opts_cond">
15897 <param name="adv_opts_selector" value="advanced"/>
15898 <param name="force" value="false"/>
15899 <param name="test" value="true"/>
15900 </conditional>
15901 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
15902 <output_collection name="out" count="3"/>
15903 <section name="algorithm">
15904 <param name="model_type" value="b_spline"/>
15905 <section name="model">
15906 <param name="type" value="b_spline"/>
15907 <section name="linear">
15908 <param name="symmetric_regression" value="false"/>
15909 <param name="x_weight" value=""/>
15910 <param name="y_weight" value=""/>
15911 <param name="x_datum_min" value="1e-15"/>
15912 <param name="x_datum_max" value="1000000000000000.0"/>
15913 <param name="y_datum_min" value="1e-15"/>
15914 <param name="y_datum_max" value="1000000000000000.0"/>
15915 </section>
15916 <section name="b_spline">
15917 <param name="wavelength" value="0.0"/>
15918 <param name="num_nodes" value="5"/>
15919 <param name="extrapolate" value="linear"/>
15920 <param name="boundary_condition" value="2"/>
15921 </section>
15922 <section name="lowess">
15923 <param name="span" value="0.666666666666667"/>
15924 <param name="num_iterations" value="3"/>
15925 <param name="delta" value="-1.0"/>
15926 <param name="interpolation_type" value="cspline"/>
15927 <param name="extrapolation_type" value="four-point-linear"/>
15928 </section>
15929 <section name="interpolated">
15930 <param name="interpolation_type" value="cspline"/>
15931 <param name="extrapolation_type" value="two-point-linear"/>
15932 </section>
15933 </section>
15934 <section name="align_algorithm">
15935 <param name="score_cutoff" value="false"/>
15936 <param name="min_score" value="0.05"/>
15937 <param name="min_run_occur" value="2"/>
15938 <param name="max_rt_shift" value="0.5"/>
15939 <param name="use_unassigned_peptides" value="true"/>
15940 <param name="use_feature_rt" value="true"/>
15941 </section>
15942 </section>
15943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15944 <output name="ctd_out" ftype="xml">
15945 <assert_contents>
15946 <is_valid_xml/>
15947 </assert_contents>
15948 </output>
15949 </test>
15950 </xml>
15951 <xml name="autotest_MapNormalizer">
15952 <test expect_num_outputs="2">
15953 <conditional name="adv_opts_cond">
15954 <param name="adv_opts_selector" value="advanced"/>
15955 <param name="force" value="false"/>
15956 <param name="test" value="true"/>
15957 </conditional>
15958 <param name="in" value="MapNormalizer_input.mzML"/>
15959 <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
15960 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15961 <output name="ctd_out" ftype="xml">
15962 <assert_contents>
15963 <is_valid_xml/>
15964 </assert_contents>
15965 </output>
15966 </test>
15967 </xml>
15968 <xml name="autotest_MapRTTransformer">
15969 <test expect_num_outputs="2">
15970 <conditional name="adv_opts_cond">
15971 <param name="adv_opts_selector" value="advanced"/>
15972 <param name="force" value="false"/>
15973 <param name="test" value="true"/>
15974 </conditional>
15975 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
15976 <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
15977 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
15978 <param name="invert" value="false"/>
15979 <param name="store_original_rt" value="false"/>
15980 <section name="model">
15981 <param name="type" value="none"/>
15982 <section name="linear">
15983 <param name="symmetric_regression" value="false"/>
15984 <param name="x_weight" value=""/>
15985 <param name="y_weight" value=""/>
15986 <param name="x_datum_min" value="1e-15"/>
15987 <param name="x_datum_max" value="1000000000000000.0"/>
15988 <param name="y_datum_min" value="1e-15"/>
15989 <param name="y_datum_max" value="1000000000000000.0"/>
15990 </section>
15991 <section name="b_spline">
15992 <param name="wavelength" value="0.0"/>
15993 <param name="num_nodes" value="5"/>
15994 <param name="extrapolate" value="linear"/>
15995 <param name="boundary_condition" value="2"/>
15996 </section>
15997 <section name="lowess">
15998 <param name="span" value="0.666666666666667"/>
15999 <param name="num_iterations" value="3"/>
16000 <param name="delta" value="-1.0"/>
16001 <param name="interpolation_type" value="cspline"/>
16002 <param name="extrapolation_type" value="four-point-linear"/>
16003 </section>
16004 <section name="interpolated">
16005 <param name="interpolation_type" value="cspline"/>
16006 <param name="extrapolation_type" value="two-point-linear"/>
16007 </section>
16008 </section>
16009 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
16010 <output name="ctd_out" ftype="xml">
16011 <assert_contents>
16012 <is_valid_xml/>
16013 </assert_contents>
16014 </output>
16015 </test>
16016 <test expect_num_outputs="2">
16017 <conditional name="adv_opts_cond">
16018 <param name="adv_opts_selector" value="advanced"/>
16019 <param name="force" value="false"/>
16020 <param name="test" value="true"/>
16021 </conditional>
16022 <param name="in" value="MapRTTransformer_2_input.mzML"/>
16023 <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16024 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
16025 <param name="invert" value="false"/>
16026 <param name="store_original_rt" value="false"/>
16027 <section name="model">
16028 <param name="type" value="none"/>
16029 <section name="linear">
16030 <param name="symmetric_regression" value="false"/>
16031 <param name="x_weight" value=""/>
16032 <param name="y_weight" value=""/>
16033 <param name="x_datum_min" value="1e-15"/>
16034 <param name="x_datum_max" value="1000000000000000.0"/>
16035 <param name="y_datum_min" value="1e-15"/>
16036 <param name="y_datum_max" value="1000000000000000.0"/>
16037 </section>
16038 <section name="b_spline">
16039 <param name="wavelength" value="0.0"/>
16040 <param name="num_nodes" value="5"/>
16041 <param name="extrapolate" value="linear"/>
16042 <param name="boundary_condition" value="2"/>
16043 </section>
16044 <section name="lowess">
16045 <param name="span" value="0.666666666666667"/>
16046 <param name="num_iterations" value="3"/>
16047 <param name="delta" value="-1.0"/>
16048 <param name="interpolation_type" value="cspline"/>
16049 <param name="extrapolation_type" value="four-point-linear"/>
16050 </section>
16051 <section name="interpolated">
16052 <param name="interpolation_type" value="cspline"/>
16053 <param name="extrapolation_type" value="two-point-linear"/>
16054 </section>
16055 </section>
16056 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
16057 <output name="ctd_out" ftype="xml">
16058 <assert_contents>
16059 <is_valid_xml/>
16060 </assert_contents>
16061 </output>
16062 </test>
16063 <test expect_num_outputs="2">
16064 <conditional name="adv_opts_cond">
16065 <param name="adv_opts_selector" value="advanced"/>
16066 <param name="force" value="false"/>
16067 <param name="test" value="true"/>
16068 </conditional>
16069 <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
16070 <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
16071 <param name="invert" value="true"/>
16072 <param name="store_original_rt" value="false"/>
16073 <section name="model">
16074 <param name="type" value="none"/>
16075 <section name="linear">
16076 <param name="symmetric_regression" value="false"/>
16077 <param name="x_weight" value=""/>
16078 <param name="y_weight" value=""/>
16079 <param name="x_datum_min" value="1e-15"/>
16080 <param name="x_datum_max" value="1000000000000000.0"/>
16081 <param name="y_datum_min" value="1e-15"/>
16082 <param name="y_datum_max" value="1000000000000000.0"/>
16083 </section>
16084 <section name="b_spline">
16085 <param name="wavelength" value="0.0"/>
16086 <param name="num_nodes" value="5"/>
16087 <param name="extrapolate" value="linear"/>
16088 <param name="boundary_condition" value="2"/>
16089 </section>
16090 <section name="lowess">
16091 <param name="span" value="0.666666666666667"/>
16092 <param name="num_iterations" value="3"/>
16093 <param name="delta" value="-1.0"/>
16094 <param name="interpolation_type" value="cspline"/>
16095 <param name="extrapolation_type" value="four-point-linear"/>
16096 </section>
16097 <section name="interpolated">
16098 <param name="interpolation_type" value="cspline"/>
16099 <param name="extrapolation_type" value="two-point-linear"/>
16100 </section>
16101 </section>
16102 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
16103 <output name="ctd_out" ftype="xml">
16104 <assert_contents>
16105 <is_valid_xml/>
16106 </assert_contents>
16107 </output>
16108 </test>
16109 <test expect_num_outputs="2">
16110 <conditional name="adv_opts_cond">
16111 <param name="adv_opts_selector" value="advanced"/>
16112 <param name="force" value="false"/>
16113 <param name="test" value="true"/>
16114 </conditional>
16115 <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
16116 <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16117 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
16118 <param name="invert" value="false"/>
16119 <param name="store_original_rt" value="false"/>
16120 <section name="model">
16121 <param name="type" value="none"/>
16122 <section name="linear">
16123 <param name="symmetric_regression" value="false"/>
16124 <param name="x_weight" value=""/>
16125 <param name="y_weight" value=""/>
16126 <param name="x_datum_min" value="1e-15"/>
16127 <param name="x_datum_max" value="1000000000000000.0"/>
16128 <param name="y_datum_min" value="1e-15"/>
16129 <param name="y_datum_max" value="1000000000000000.0"/>
16130 </section>
16131 <section name="b_spline">
16132 <param name="wavelength" value="0.0"/>
16133 <param name="num_nodes" value="5"/>
16134 <param name="extrapolate" value="linear"/>
16135 <param name="boundary_condition" value="2"/>
16136 </section>
16137 <section name="lowess">
16138 <param name="span" value="0.666666666666667"/>
16139 <param name="num_iterations" value="3"/>
16140 <param name="delta" value="-1.0"/>
16141 <param name="interpolation_type" value="cspline"/>
16142 <param name="extrapolation_type" value="four-point-linear"/>
16143 </section>
16144 <section name="interpolated">
16145 <param name="interpolation_type" value="cspline"/>
16146 <param name="extrapolation_type" value="two-point-linear"/>
16147 </section>
16148 </section>
16149 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
16150 <output name="ctd_out" ftype="xml">
16151 <assert_contents>
16152 <is_valid_xml/>
16153 </assert_contents>
16154 </output>
16155 </test>
16156 <test expect_num_outputs="2">
16157 <conditional name="adv_opts_cond">
16158 <param name="adv_opts_selector" value="advanced"/>
16159 <param name="force" value="false"/>
16160 <param name="test" value="true"/>
16161 </conditional>
16162 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
16163 <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16164 <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
16165 <param name="invert" value="false"/>
16166 <param name="store_original_rt" value="false"/>
16167 <section name="model">
16168 <param name="type" value="none"/>
16169 <section name="linear">
16170 <param name="symmetric_regression" value="false"/>
16171 <param name="x_weight" value=""/>
16172 <param name="y_weight" value=""/>
16173 <param name="x_datum_min" value="1e-15"/>
16174 <param name="x_datum_max" value="1000000000000000.0"/>
16175 <param name="y_datum_min" value="1e-15"/>
16176 <param name="y_datum_max" value="1000000000000000.0"/>
16177 </section>
16178 <section name="b_spline">
16179 <param name="wavelength" value="0.0"/>
16180 <param name="num_nodes" value="5"/>
16181 <param name="extrapolate" value="linear"/>
16182 <param name="boundary_condition" value="2"/>
16183 </section>
16184 <section name="lowess">
16185 <param name="span" value="0.666666666666667"/>
16186 <param name="num_iterations" value="3"/>
16187 <param name="delta" value="-1.0"/>
16188 <param name="interpolation_type" value="cspline"/>
16189 <param name="extrapolation_type" value="four-point-linear"/>
16190 </section>
16191 <section name="interpolated">
16192 <param name="interpolation_type" value="cspline"/>
16193 <param name="extrapolation_type" value="two-point-linear"/>
16194 </section>
16195 </section>
16196 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
16197 <output name="ctd_out" ftype="xml">
16198 <assert_contents>
16199 <is_valid_xml/>
16200 </assert_contents>
16201 </output>
16202 </test>
16203 <test expect_num_outputs="2">
16204 <conditional name="adv_opts_cond">
16205 <param name="adv_opts_selector" value="advanced"/>
16206 <param name="force" value="false"/>
16207 <param name="test" value="true"/>
16208 </conditional>
16209 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
16210 <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16211 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
16212 <param name="invert" value="false"/>
16213 <param name="store_original_rt" value="true"/>
16214 <section name="model">
16215 <param name="type" value="none"/>
16216 <section name="linear">
16217 <param name="symmetric_regression" value="false"/>
16218 <param name="x_weight" value=""/>
16219 <param name="y_weight" value=""/>
16220 <param name="x_datum_min" value="1e-15"/>
16221 <param name="x_datum_max" value="1000000000000000.0"/>
16222 <param name="y_datum_min" value="1e-15"/>
16223 <param name="y_datum_max" value="1000000000000000.0"/>
16224 </section>
16225 <section name="b_spline">
16226 <param name="wavelength" value="0.0"/>
16227 <param name="num_nodes" value="5"/>
16228 <param name="extrapolate" value="linear"/>
16229 <param name="boundary_condition" value="2"/>
16230 </section>
16231 <section name="lowess">
16232 <param name="span" value="0.666666666666667"/>
16233 <param name="num_iterations" value="3"/>
16234 <param name="delta" value="-1.0"/>
16235 <param name="interpolation_type" value="cspline"/>
16236 <param name="extrapolation_type" value="four-point-linear"/>
16237 </section>
16238 <section name="interpolated">
16239 <param name="interpolation_type" value="cspline"/>
16240 <param name="extrapolation_type" value="two-point-linear"/>
16241 </section>
16242 </section>
16243 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
16244 <output name="ctd_out" ftype="xml">
16245 <assert_contents>
16246 <is_valid_xml/>
16247 </assert_contents>
16248 </output>
16249 </test>
16250 </xml>
16251 <xml name="autotest_MapStatistics">
16252 </xml>
16253 <xml name="autotest_MaRaClusterAdapter"/>
16254 <xml name="autotest_MascotAdapterOnline">
16255 <test expect_num_outputs="2">
16256 <conditional name="adv_opts_cond">
16257 <param name="adv_opts_selector" value="advanced"/>
16258 <param name="keep_protein_links" value="true"/>
16259 <param name="force" value="false"/>
16260 <param name="test" value="true"/>
16261 </conditional>
16262 <param name="in" value="spectra_comet.mzML"/>
16263 <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16264 <section name="Mascot_parameters">
16265 <param name="database" value="SwissProt"/>
16266 <param name="search_type" value="MIS"/>
16267 <param name="enzyme" value="Trypsin"/>
16268 <param name="instrument" value="Default"/>
16269 <param name="missed_cleavages" value="1"/>
16270 <param name="precursor_mass_tolerance" value="3.0"/>
16271 <param name="precursor_error_units" value="Da"/>
16272 <param name="fragment_mass_tolerance" value="0.3"/>
16273 <param name="fragment_error_units" value="Da"/>
16274 <param name="charges" value="1,2,3"/>
16275 <param name="taxonomy" value="All entries"/>
16276 <param name="fixed_modifications" value=""/>
16277 <param name="variable_modifications" value=""/>
16278 <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/>
16279 <param name="mass_type" value="monoisotopic"/>
16280 <param name="number_of_hits" value="0"/>
16281 <param name="skip_spectrum_charges" value="false"/>
16282 <param name="search_title" value="OpenMS_search"/>
16283 <param name="username" value="OpenMS"/>
16284 <param name="email" value="openmsjenkins@gmail.com"/>
16285 </section>
16286 <section name="Mascot_server">
16287 <param name="hostname" value="www.matrixscience.com"/>
16288 <param name="host_port" value="80"/>
16289 <param name="server_path" value=""/>
16290 <param name="timeout" value="1500"/>
16291 <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/>
16292 <param name="use_proxy" value="false"/>
16293 <param name="proxy_host" value=""/>
16294 <param name="proxy_port" value="0"/>
16295 <param name="proxy_username" value=""/>
16296 <param name="proxy_password" value=""/>
16297 <param name="login" value="false"/>
16298 <param name="username" value=""/>
16299 <param name="password" value=""/>
16300 <param name="use_ssl" value="false"/>
16301 <param name="export_params" value="_ignoreionsscorebelow=0&amp;_sigthreshold=0.99&amp;_showsubsets=1&amp;show_same_sets=1&amp;report=0&amp;percolate=0&amp;query_master=0"/>
16302 <param name="skip_export" value="false"/>
16303 </section>
16304 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16305 <output name="ctd_out" ftype="xml">
16306 <assert_contents>
16307 <is_valid_xml/>
16308 </assert_contents>
16309 </output>
16310 </test>
16311 </xml>
16312 <xml name="autotest_MascotAdapter">
16313 <test expect_num_outputs="2">
16314 <conditional name="adv_opts_cond">
16315 <param name="adv_opts_selector" value="advanced"/>
16316 <param name="force" value="false"/>
16317 <param name="test" value="true"/>
16318 </conditional>
16319 <param name="in" value="MascotAdapter_1_input.mzData"/>
16320 <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
16321 <param name="out_type" value="mgf"/>
16322 <param name="instrument" value="ESI-TRAP"/>
16323 <param name="precursor_mass_tolerance" value="1.3"/>
16324 <param name="peak_mass_tolerance" value="0.3"/>
16325 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
16326 <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
16327 <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
16328 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
16329 <param name="db" value="MSDB"/>
16330 <param name="hits" value="AUTO"/>
16331 <param name="cleavage" value="Trypsin"/>
16332 <param name="missed_cleavages" value="1"/>
16333 <param name="sig_threshold" value="0.05"/>
16334 <param name="pep_homol" value="1.0"/>
16335 <param name="pep_ident" value="1.0"/>
16336 <param name="pep_rank" value="1"/>
16337 <param name="prot_score" value="1.0"/>
16338 <param name="pep_score" value="1.0"/>
16339 <param name="pep_exp_z" value="1"/>
16340 <param name="show_unassigned" value="1"/>
16341 <param name="first_dim_rt" value="0.0"/>
16342 <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
16343 <param name="mass_type" value="Monoisotopic"/>
16344 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16345 <output name="ctd_out" ftype="xml">
16346 <assert_contents>
16347 <is_valid_xml/>
16348 </assert_contents>
16349 </output>
16350 </test>
16351 <test expect_num_outputs="2">
16352 <conditional name="adv_opts_cond">
16353 <param name="adv_opts_selector" value="advanced"/>
16354 <param name="force" value="false"/>
16355 <param name="test" value="true"/>
16356 </conditional>
16357 <param name="in" value="MascotAdapter_2_input.mascotXML"/>
16358 <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16359 <param name="out_type" value="idXML"/>
16360 <param name="instrument" value="Default"/>
16361 <param name="precursor_mass_tolerance" value="2.0"/>
16362 <param name="peak_mass_tolerance" value="1.0"/>
16363 <param name="taxonomy" value="All entries"/>
16364 <param name="modifications" value=""/>
16365 <param name="variable_modifications" value=""/>
16366 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
16367 <param name="db" value="MSDB"/>
16368 <param name="hits" value="AUTO"/>
16369 <param name="cleavage" value="Trypsin"/>
16370 <param name="missed_cleavages" value="0"/>
16371 <param name="sig_threshold" value="0.05"/>
16372 <param name="pep_homol" value="1.0"/>
16373 <param name="pep_ident" value="1.0"/>
16374 <param name="pep_rank" value="1"/>
16375 <param name="prot_score" value="1.0"/>
16376 <param name="pep_score" value="1.0"/>
16377 <param name="pep_exp_z" value="1"/>
16378 <param name="show_unassigned" value="1"/>
16379 <param name="first_dim_rt" value="0.0"/>
16380 <param name="boundary" value=""/>
16381 <param name="mass_type" value="Monoisotopic"/>
16382 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16383 <output name="ctd_out" ftype="xml">
16384 <assert_contents>
16385 <is_valid_xml/>
16386 </assert_contents>
16387 </output>
16388 </test>
16389 </xml>
16390 <xml name="autotest_MassCalculator">
16391 <test expect_num_outputs="2">
16392 <conditional name="adv_opts_cond">
16393 <param name="adv_opts_selector" value="advanced"/>
16394 <param name="force" value="false"/>
16395 <param name="test" value="true"/>
16396 </conditional>
16397 <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
16398 <param name="in_seq" value=""/>
16399 <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
16400 <param name="charge" value="0 1"/>
16401 <param name="format" value="table"/>
16402 <param name="average_mass" value="false"/>
16403 <param name="fragment_type" value="full"/>
16404 <param name="separator" value=","/>
16405 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
16406 <output name="ctd_out" ftype="xml">
16407 <assert_contents>
16408 <is_valid_xml/>
16409 </assert_contents>
16410 </output>
16411 </test>
16412 <test expect_num_outputs="2">
16413 <conditional name="adv_opts_cond">
16414 <param name="adv_opts_selector" value="advanced"/>
16415 <param name="force" value="false"/>
16416 <param name="test" value="true"/>
16417 </conditional>
16418 <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
16419 <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
16420 <param name="charge" value="1 2 3"/>
16421 <param name="format" value="list"/>
16422 <param name="average_mass" value="false"/>
16423 <param name="fragment_type" value="full"/>
16424 <param name="separator" value=""/>
16425 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
16426 <output name="ctd_out" ftype="xml">
16427 <assert_contents>
16428 <is_valid_xml/>
16429 </assert_contents>
16430 </output>
16431 </test>
16432 </xml>
16433 <xml name="autotest_MassTraceExtractor">
16434 <test expect_num_outputs="2">
16435 <conditional name="adv_opts_cond">
16436 <param name="adv_opts_selector" value="advanced"/>
16437 <param name="force" value="false"/>
16438 <param name="test" value="true"/>
16439 </conditional>
16440 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
16441 <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16442 <param name="out_type" value="featurexml"/>
16443 <section name="algorithm">
16444 <section name="common">
16445 <param name="noise_threshold_int" value="10.0"/>
16446 <param name="chrom_peak_snr" value="3.0"/>
16447 <param name="chrom_fwhm" value="5.0"/>
16448 </section>
16449 <section name="mtd">
16450 <param name="mass_error_ppm" value="20.0"/>
16451 <param name="reestimate_mt_sd" value="true"/>
16452 <param name="quant_method" value="area"/>
16453 <param name="trace_termination_criterion" value="outlier"/>
16454 <param name="trace_termination_outliers" value="5"/>
16455 <param name="min_sample_rate" value="0.5"/>
16456 <param name="min_trace_length" value="5.0"/>
16457 <param name="max_trace_length" value="-1.0"/>
16458 </section>
16459 <section name="epd">
16460 <param name="width_filtering" value="off"/>
16461 <param name="min_fwhm" value="3.0"/>
16462 <param name="max_fwhm" value="60.0"/>
16463 <param name="masstrace_snr_filtering" value="false"/>
16464 <param name="enabled" value="true"/>
16465 </section>
16466 </section>
16467 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16468 <output name="ctd_out" ftype="xml">
16469 <assert_contents>
16470 <is_valid_xml/>
16471 </assert_contents>
16472 </output>
16473 </test>
16474 <test expect_num_outputs="2">
16475 <conditional name="adv_opts_cond">
16476 <param name="adv_opts_selector" value="advanced"/>
16477 <param name="force" value="false"/>
16478 <param name="test" value="true"/>
16479 </conditional>
16480 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
16481 <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16482 <param name="out_type" value="featurexml"/>
16483 <section name="algorithm">
16484 <section name="common">
16485 <param name="noise_threshold_int" value="10.0"/>
16486 <param name="chrom_peak_snr" value="3.0"/>
16487 <param name="chrom_fwhm" value="5.0"/>
16488 </section>
16489 <section name="mtd">
16490 <param name="mass_error_ppm" value="20.0"/>
16491 <param name="reestimate_mt_sd" value="true"/>
16492 <param name="quant_method" value="area"/>
16493 <param name="trace_termination_criterion" value="outlier"/>
16494 <param name="trace_termination_outliers" value="5"/>
16495 <param name="min_sample_rate" value="0.5"/>
16496 <param name="min_trace_length" value="6.0"/>
16497 <param name="max_trace_length" value="12.0"/>
16498 </section>
16499 <section name="epd">
16500 <param name="width_filtering" value="off"/>
16501 <param name="min_fwhm" value="3.0"/>
16502 <param name="max_fwhm" value="60.0"/>
16503 <param name="masstrace_snr_filtering" value="false"/>
16504 <param name="enabled" value="true"/>
16505 </section>
16506 </section>
16507 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16508 <output name="ctd_out" ftype="xml">
16509 <assert_contents>
16510 <is_valid_xml/>
16511 </assert_contents>
16512 </output>
16513 </test>
16514 </xml>
16515 <xml name="autotest_MetaboliteAdductDecharger">
16516 <test expect_num_outputs="2">
16517 <conditional name="adv_opts_cond">
16518 <param name="adv_opts_selector" value="advanced"/>
16519 <param name="force" value="false"/>
16520 <param name="test" value="true"/>
16521 </conditional>
16522 <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
16523 <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16524 <section name="algorithm">
16525 <section name="MetaboliteFeatureDeconvolution">
16526 <param name="charge_min" value="1"/>
16527 <param name="charge_max" value="3"/>
16528 <param name="charge_span_max" value="3"/>
16529 <param name="q_try" value="feature"/>
16530 <param name="retention_max_diff" value="1.0"/>
16531 <param name="retention_max_diff_local" value="1.0"/>
16532 <param name="mass_max_diff" value="0.05"/>
16533 <param name="unit" value="Da"/>
16534 <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
16535 <param name="max_neutrals" value="1"/>
16536 <param name="use_minority_bound" value="true"/>
16537 <param name="max_minority_bound" value="3"/>
16538 <param name="min_rt_overlap" value="0.66"/>
16539 <param name="intensity_filter" value="false"/>
16540 <param name="negative_mode" value="false"/>
16541 <param name="default_map_label" value="decharged features"/>
16542 <param name="verbose_level" value="0"/>
16543 </section>
16544 </section>
16545 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
16546 <output name="ctd_out" ftype="xml">
16547 <assert_contents>
16548 <is_valid_xml/>
16549 </assert_contents>
16550 </output>
16551 </test>
16552 <test expect_num_outputs="3">
16553 <conditional name="adv_opts_cond">
16554 <param name="adv_opts_selector" value="advanced"/>
16555 <param name="force" value="false"/>
16556 <param name="test" value="true"/>
16557 </conditional>
16558 <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
16559 <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16560 <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16561 <section name="algorithm">
16562 <section name="MetaboliteFeatureDeconvolution">
16563 <param name="charge_min" value="1"/>
16564 <param name="charge_max" value="3"/>
16565 <param name="charge_span_max" value="3"/>
16566 <param name="q_try" value="feature"/>
16567 <param name="retention_max_diff" value="1.0"/>
16568 <param name="retention_max_diff_local" value="1.0"/>
16569 <param name="mass_max_diff" value="0.05"/>
16570 <param name="unit" value="Da"/>
16571 <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
16572 <param name="max_neutrals" value="1"/>
16573 <param name="use_minority_bound" value="true"/>
16574 <param name="max_minority_bound" value="3"/>
16575 <param name="min_rt_overlap" value="0.66"/>
16576 <param name="intensity_filter" value="false"/>
16577 <param name="negative_mode" value="false"/>
16578 <param name="default_map_label" value="decharged features"/>
16579 <param name="verbose_level" value="0"/>
16580 </section>
16581 </section>
16582 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
16583 <output name="ctd_out" ftype="xml">
16584 <assert_contents>
16585 <is_valid_xml/>
16586 </assert_contents>
16587 </output>
16588 </test>
16589 </xml>
16590 <xml name="autotest_MetaboliteSpectralMatcher">
16591 </xml>
16592 <xml name="autotest_MetaProSIP">
16593 <test expect_num_outputs="3">
16594 <conditional name="adv_opts_cond">
16595 <param name="adv_opts_selector" value="advanced"/>
16596 <param name="min_correlation_distance_to_averagine" value="-1.0"/>
16597 <param name="pattern_15N_TIC_threshold" value="0.95"/>
16598 <param name="pattern_13C_TIC_threshold" value="0.95"/>
16599 <param name="pattern_2H_TIC_threshold" value="0.95"/>
16600 <param name="pattern_18O_TIC_threshold" value="0.95"/>
16601 <param name="heatmap_bins" value="20"/>
16602 <param name="observed_peak_fraction" value="0.5"/>
16603 <param name="min_consecutive_isotopes" value="2"/>
16604 <param name="score_plot_yaxis_min" value="0.0"/>
16605 <param name="collect_method" value="correlation_maximum"/>
16606 <param name="lowRIA_correlation_threshold" value="-1.0"/>
16607 <param name="force" value="false"/>
16608 <param name="test" value="true"/>
16609 </conditional>
16610 <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
16611 <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
16612 <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/>
16613 <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/>
16614 <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
16615 <param name="mz_tolerance_ppm" value="10.0"/>
16616 <param name="rt_tolerance_s" value="30.0"/>
16617 <param name="intensity_threshold" value="10.0"/>
16618 <param name="correlation_threshold" value="0.7"/>
16619 <param name="xic_threshold" value="0.7"/>
16620 <param name="decomposition_threshold" value="0.7"/>
16621 <param name="weight_merge_window" value="5.0"/>
16622 <param name="plot_extension" value="png"/>
16623 <param name="qc_output_directory" value=""/>
16624 <param name="labeling_element" value="C"/>
16625 <param name="use_unassigned_ids" value="false"/>
16626 <param name="use_averagine_ids" value="false"/>
16627 <param name="report_natural_peptides" value="false"/>
16628 <param name="filter_monoisotopic" value="false"/>
16629 <param name="cluster" value="false"/>
16630 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16631 <output name="ctd_out" ftype="xml">
16632 <assert_contents>
16633 <is_valid_xml/>
16634 </assert_contents>
16635 </output>
16636 </test>
16637 </xml>
16638 <xml name="autotest_MRMMapper">
16639 <test expect_num_outputs="2">
16640 <conditional name="adv_opts_cond">
16641 <param name="adv_opts_selector" value="advanced"/>
16642 <param name="force" value="false"/>
16643 <param name="test" value="true"/>
16644 </conditional>
16645 <param name="in" value="MRMMapping_input.chrom.mzML"/>
16646 <param name="tr" value="MRMMapping_input.TraML"/>
16647 <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16648 <section name="algorithm">
16649 <param name="precursor_tolerance" value="0.3"/>
16650 <param name="product_tolerance" value="0.3"/>
16651 <param name="map_multiple_assays" value="false"/>
16652 <param name="error_on_unmapped" value="false"/>
16653 </section>
16654 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16655 <output name="ctd_out" ftype="xml">
16656 <assert_contents>
16657 <is_valid_xml/>
16658 </assert_contents>
16659 </output>
16660 </test>
16661 <test expect_num_outputs="2">
16662 <conditional name="adv_opts_cond">
16663 <param name="adv_opts_selector" value="advanced"/>
16664 <param name="force" value="false"/>
16665 <param name="test" value="true"/>
16666 </conditional>
16667 <param name="in" value="MRMMapping_input.chrom.mzML"/>
16668 <param name="tr" value="MRMMapping_input_2.TraML"/>
16669 <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16670 <section name="algorithm">
16671 <param name="precursor_tolerance" value="0.01"/>
16672 <param name="product_tolerance" value="0.01"/>
16673 <param name="map_multiple_assays" value="false"/>
16674 <param name="error_on_unmapped" value="false"/>
16675 </section>
16676 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16677 <output name="ctd_out" ftype="xml">
16678 <assert_contents>
16679 <is_valid_xml/>
16680 </assert_contents>
16681 </output>
16682 </test>
16683 </xml>
16684 <xml name="autotest_MRMPairFinder">
16685 </xml>
16686 <xml name="autotest_MRMTransitionGroupPicker">
16687 <test expect_num_outputs="2">
16688 <conditional name="adv_opts_cond">
16689 <param name="adv_opts_selector" value="advanced"/>
16690 <param name="force" value="false"/>
16691 <param name="test" value="true"/>
16692 </conditional>
16693 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
16694 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
16695 <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16696 <section name="algorithm">
16697 <param name="stop_after_feature" value="-1"/>
16698 <param name="stop_after_intensity_ratio" value="0.0001"/>
16699 <param name="min_peak_width" value="-1.0"/>
16700 <param name="peak_integration" value="original"/>
16701 <param name="background_subtraction" value="none"/>
16702 <param name="recalculate_peaks" value="false"/>
16703 <param name="use_precursors" value="false"/>
16704 <param name="use_consensus" value="true"/>
16705 <param name="recalculate_peaks_max_z" value="1.0"/>
16706 <param name="minimal_quality" value="-10000.0"/>
16707 <param name="resample_boundary" value="15.0"/>
16708 <param name="compute_peak_quality" value="false"/>
16709 <param name="compute_peak_shape_metrics" value="false"/>
16710 <param name="compute_total_mi" value="false"/>
16711 <param name="boundary_selection_method" value="largest"/>
16712 <section name="PeakPickerMRM">
16713 <param name="sgolay_frame_length" value="15"/>
16714 <param name="sgolay_polynomial_order" value="3"/>
16715 <param name="gauss_width" value="50.0"/>
16716 <param name="use_gauss" value="true"/>
16717 <param name="peak_width" value="40.0"/>
16718 <param name="signal_to_noise" value="1.0"/>
16719 <param name="sn_win_len" value="1000.0"/>
16720 <param name="sn_bin_count" value="30"/>
16721 <param name="write_sn_log_messages" value="false"/>
16722 <param name="remove_overlapping_peaks" value="true"/>
16723 <param name="method" value="legacy"/>
16724 </section>
16725 <section name="PeakIntegrator">
16726 <param name="integration_type" value="intensity_sum"/>
16727 <param name="baseline_type" value="base_to_base"/>
16728 <param name="fit_EMG" value="false"/>
16729 </section>
16730 </section>
16731 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16732 <output name="ctd_out" ftype="xml">
16733 <assert_contents>
16734 <is_valid_xml/>
16735 </assert_contents>
16736 </output>
16737 </test>
16738 <test expect_num_outputs="2">
16739 <conditional name="adv_opts_cond">
16740 <param name="adv_opts_selector" value="advanced"/>
16741 <param name="force" value="false"/>
16742 <param name="test" value="true"/>
16743 </conditional>
16744 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
16745 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
16746 <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16747 <section name="algorithm">
16748 <param name="stop_after_feature" value="-1"/>
16749 <param name="stop_after_intensity_ratio" value="0.0001"/>
16750 <param name="min_peak_width" value="-1.0"/>
16751 <param name="peak_integration" value="original"/>
16752 <param name="background_subtraction" value="none"/>
16753 <param name="recalculate_peaks" value="false"/>
16754 <param name="use_precursors" value="false"/>
16755 <param name="use_consensus" value="true"/>
16756 <param name="recalculate_peaks_max_z" value="1.0"/>
16757 <param name="minimal_quality" value="-10000.0"/>
16758 <param name="resample_boundary" value="15.0"/>
16759 <param name="compute_peak_quality" value="false"/>
16760 <param name="compute_peak_shape_metrics" value="false"/>
16761 <param name="compute_total_mi" value="true"/>
16762 <param name="boundary_selection_method" value="largest"/>
16763 <section name="PeakPickerMRM">
16764 <param name="sgolay_frame_length" value="15"/>
16765 <param name="sgolay_polynomial_order" value="3"/>
16766 <param name="gauss_width" value="50.0"/>
16767 <param name="use_gauss" value="true"/>
16768 <param name="peak_width" value="40.0"/>
16769 <param name="signal_to_noise" value="1.0"/>
16770 <param name="sn_win_len" value="1000.0"/>
16771 <param name="sn_bin_count" value="30"/>
16772 <param name="write_sn_log_messages" value="false"/>
16773 <param name="remove_overlapping_peaks" value="true"/>
16774 <param name="method" value="legacy"/>
16775 </section>
16776 <section name="PeakIntegrator">
16777 <param name="integration_type" value="intensity_sum"/>
16778 <param name="baseline_type" value="base_to_base"/>
16779 <param name="fit_EMG" value="false"/>
16780 </section>
16781 </section>
16782 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16783 <output name="ctd_out" ftype="xml">
16784 <assert_contents>
16785 <is_valid_xml/>
16786 </assert_contents>
16787 </output>
16788 </test>
16789 </xml>
16790 <xml name="autotest_MSFraggerAdapter"/>
16791 <xml name="autotest_MSGFPlusAdapter">
16792 <test expect_num_outputs="3">
16793 <conditional name="adv_opts_cond">
16794 <param name="adv_opts_selector" value="advanced"/>
16795 <param name="add_decoys" value="false"/>
16796 <param name="legacy_conversion" value="false"/>
16797 <param name="force" value="false"/>
16798 <param name="test" value="true"/>
16799 </conditional>
16800 <param name="in" value="spectra.mzML"/>
16801 <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16802 <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
16803 <param name="database" value="proteins.fasta"/>
16804 <param name="precursor_mass_tolerance" value="10.0"/>
16805 <param name="precursor_error_units" value="ppm"/>
16806 <param name="isotope_error_range" value="0,1"/>
16807 <param name="fragment_method" value="from_spectrum"/>
16808 <param name="instrument" value="high_res"/>
16809 <param name="enzyme" value="Trypsin/P"/>
16810 <param name="protocol" value="none"/>
16811 <param name="tryptic" value="fully"/>
16812 <param name="min_precursor_charge" value="1"/>
16813 <param name="max_precursor_charge" value="3"/>
16814 <param name="min_peptide_length" value="6"/>
16815 <param name="max_peptide_length" value="40"/>
16816 <param name="matches_per_spec" value="1"/>
16817 <param name="add_features" value="false"/>
16818 <param name="max_mods" value="2"/>
16819 <param name="max_missed_cleavages" value="-1"/>
16820 <param name="tasks" value="0"/>
16821 <param name="fixed_modifications" value=""/>
16822 <param name="variable_modifications" value="Oxidation (M)"/>
16823 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
16824 <output name="ctd_out" ftype="xml">
16825 <assert_contents>
16826 <is_valid_xml/>
16827 </assert_contents>
16828 </output>
16829 </test>
16830 </xml>
16831 <xml name="autotest_MSSimulator">
16832 </xml>
16833 <xml name="autotest_MSstatsConverter">
16834 <test expect_num_outputs="2">
16835 <conditional name="adv_opts_cond">
16836 <param name="adv_opts_selector" value="advanced"/>
16837 <param name="retention_time_summarization_method" value="max"/>
16838 <param name="force" value="false"/>
16839 <param name="test" value="true"/>
16840 </conditional>
16841 <param name="in" value="MSstatsConverter_1_in.consensusXML"/>
16842 <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/>
16843 <param name="method" value="LFQ"/>
16844 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
16845 <param name="msstats_condition" value="MSstats_Condition"/>
16846 <param name="msstats_mixture" value="MSstats_Mixture"/>
16847 <param name="labeled_reference_peptides" value="false"/>
16848 <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
16849 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16850 <output name="ctd_out" ftype="xml">
16851 <assert_contents>
16852 <is_valid_xml/>
16853 </assert_contents>
16854 </output>
16855 </test>
16856 <test expect_num_outputs="2">
16857 <conditional name="adv_opts_cond">
16858 <param name="adv_opts_selector" value="advanced"/>
16859 <param name="retention_time_summarization_method" value="manual"/>
16860 <param name="force" value="false"/>
16861 <param name="test" value="true"/>
16862 </conditional>
16863 <param name="in" value="MSstatsConverter_2_in.consensusXML"/>
16864 <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/>
16865 <param name="method" value="ISO"/>
16866 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
16867 <param name="msstats_condition" value="MSstats_Condition"/>
16868 <param name="msstats_mixture" value="MSstats_Mixture"/>
16869 <param name="labeled_reference_peptides" value="false"/>
16870 <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
16871 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16872 <output name="ctd_out" ftype="xml">
16873 <assert_contents>
16874 <is_valid_xml/>
16875 </assert_contents>
16876 </output>
16877 </test>
16878 <test expect_num_outputs="2">
16879 <conditional name="adv_opts_cond">
16880 <param name="adv_opts_selector" value="advanced"/>
16881 <param name="retention_time_summarization_method" value="manual"/>
16882 <param name="force" value="false"/>
16883 <param name="test" value="true"/>
16884 </conditional>
16885 <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
16886 <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/>
16887 <param name="method" value="ISO"/>
16888 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
16889 <param name="msstats_condition" value="MSstats_Condition"/>
16890 <param name="msstats_mixture" value="MSstats_Mixture"/>
16891 <param name="labeled_reference_peptides" value="false"/>
16892 <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
16893 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16894 <output name="ctd_out" ftype="xml">
16895 <assert_contents>
16896 <is_valid_xml/>
16897 </assert_contents>
16898 </output>
16899 </test>
16900 </xml>
16901 <xml name="autotest_MultiplexResolver">
16902 <test expect_num_outputs="3">
16903 <conditional name="adv_opts_cond">
16904 <param name="adv_opts_selector" value="advanced"/>
16905 <param name="force" value="false"/>
16906 <param name="test" value="true"/>
16907 </conditional>
16908 <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
16909 <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16910 <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16911 <section name="algorithm">
16912 <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
16913 <param name="missed_cleavages" value="1"/>
16914 <param name="mass_tolerance" value="0.1"/>
16915 <param name="mz_tolerance" value="10"/>
16916 <param name="rt_tolerance" value="5"/>
16917 </section>
16918 <section name="labels">
16919 <param name="Arg6" value="6.0201290268"/>
16920 <param name="Arg10" value="10.0082686"/>
16921 <param name="Lys4" value="4.0251069836"/>
16922 <param name="Lys6" value="6.0201290268"/>
16923 <param name="Lys8" value="8.0141988132"/>
16924 <param name="Leu3" value="3.01883"/>
16925 <param name="Dimethyl0" value="28.0313"/>
16926 <param name="Dimethyl4" value="32.056407"/>
16927 <param name="Dimethyl6" value="34.063117"/>
16928 <param name="Dimethyl8" value="36.07567"/>
16929 <param name="ICPL0" value="105.021464"/>
16930 <param name="ICPL4" value="109.046571"/>
16931 <param name="ICPL6" value="111.041593"/>
16932 <param name="ICPL10" value="115.0667"/>
16933 </section>
16934 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
16935 <output name="ctd_out" ftype="xml">
16936 <assert_contents>
16937 <is_valid_xml/>
16938 </assert_contents>
16939 </output>
16940 </test>
16941 <test expect_num_outputs="3">
16942 <conditional name="adv_opts_cond">
16943 <param name="adv_opts_selector" value="advanced"/>
16944 <param name="force" value="false"/>
16945 <param name="test" value="true"/>
16946 </conditional>
16947 <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
16948 <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16949 <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16950 <section name="algorithm">
16951 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
16952 <param name="missed_cleavages" value="4"/>
16953 <param name="mass_tolerance" value="0.1"/>
16954 <param name="mz_tolerance" value="10"/>
16955 <param name="rt_tolerance" value="5"/>
16956 </section>
16957 <section name="labels">
16958 <param name="Arg6" value="6.0201290268"/>
16959 <param name="Arg10" value="10.0082686"/>
16960 <param name="Lys4" value="4.0251069836"/>
16961 <param name="Lys6" value="6.0201290268"/>
16962 <param name="Lys8" value="8.0141988132"/>
16963 <param name="Leu3" value="3.01883"/>
16964 <param name="Dimethyl0" value="28.0313"/>
16965 <param name="Dimethyl4" value="32.056407"/>
16966 <param name="Dimethyl6" value="34.063117"/>
16967 <param name="Dimethyl8" value="36.07567"/>
16968 <param name="ICPL0" value="105.021464"/>
16969 <param name="ICPL4" value="109.046571"/>
16970 <param name="ICPL6" value="111.041593"/>
16971 <param name="ICPL10" value="115.0667"/>
16972 </section>
16973 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
16974 <output name="ctd_out" ftype="xml">
16975 <assert_contents>
16976 <is_valid_xml/>
16977 </assert_contents>
16978 </output>
16979 </test>
16980 <test expect_num_outputs="3">
16981 <conditional name="adv_opts_cond">
16982 <param name="adv_opts_selector" value="advanced"/>
16983 <param name="force" value="false"/>
16984 <param name="test" value="true"/>
16985 </conditional>
16986 <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
16987 <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16988 <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16989 <section name="algorithm">
16990 <param name="labels" value="[][Leu3]"/>
16991 <param name="missed_cleavages" value="2"/>
16992 <param name="mass_tolerance" value="0.1"/>
16993 <param name="mz_tolerance" value="10"/>
16994 <param name="rt_tolerance" value="5"/>
16995 </section>
16996 <section name="labels">
16997 <param name="Arg6" value="6.0201290268"/>
16998 <param name="Arg10" value="10.0082686"/>
16999 <param name="Lys4" value="4.0251069836"/>
17000 <param name="Lys6" value="6.0201290268"/>
17001 <param name="Lys8" value="8.0141988132"/>
17002 <param name="Leu3" value="3.01883"/>
17003 <param name="Dimethyl0" value="28.0313"/>
17004 <param name="Dimethyl4" value="32.056407"/>
17005 <param name="Dimethyl6" value="34.063117"/>
17006 <param name="Dimethyl8" value="36.07567"/>
17007 <param name="ICPL0" value="105.021464"/>
17008 <param name="ICPL4" value="109.046571"/>
17009 <param name="ICPL6" value="111.041593"/>
17010 <param name="ICPL10" value="115.0667"/>
17011 </section>
17012 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
17013 <output name="ctd_out" ftype="xml">
17014 <assert_contents>
17015 <is_valid_xml/>
17016 </assert_contents>
17017 </output>
17018 </test>
17019 <test expect_num_outputs="3">
17020 <conditional name="adv_opts_cond">
17021 <param name="adv_opts_selector" value="advanced"/>
17022 <param name="force" value="false"/>
17023 <param name="test" value="true"/>
17024 </conditional>
17025 <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
17026 <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
17027 <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
17028 <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
17029 <section name="algorithm">
17030 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
17031 <param name="missed_cleavages" value="3"/>
17032 <param name="mass_tolerance" value="0.1"/>
17033 <param name="mz_tolerance" value="10"/>
17034 <param name="rt_tolerance" value="10"/>
17035 </section>
17036 <section name="labels">
17037 <param name="Arg6" value="6.0201290268"/>
17038 <param name="Arg10" value="10.0082686"/>
17039 <param name="Lys4" value="4.0251069836"/>
17040 <param name="Lys6" value="6.0201290268"/>
17041 <param name="Lys8" value="8.0141988132"/>
17042 <param name="Leu3" value="3.01883"/>
17043 <param name="Dimethyl0" value="28.0313"/>
17044 <param name="Dimethyl4" value="32.056407"/>
17045 <param name="Dimethyl6" value="34.063117"/>
17046 <param name="Dimethyl8" value="36.07567"/>
17047 <param name="ICPL0" value="105.021464"/>
17048 <param name="ICPL4" value="109.046571"/>
17049 <param name="ICPL6" value="111.041593"/>
17050 <param name="ICPL10" value="115.0667"/>
17051 </section>
17052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
17053 <output name="ctd_out" ftype="xml">
17054 <assert_contents>
17055 <is_valid_xml/>
17056 </assert_contents>
17057 </output>
17058 </test>
17059 </xml>
17060 <xml name="autotest_MyriMatchAdapter">
17061 <test expect_num_outputs="2">
17062 <conditional name="adv_opts_cond">
17063 <param name="adv_opts_selector" value="advanced"/>
17064 <param name="MinPeptideMass" value="0.0"/>
17065 <param name="MaxPeptideMass" value="10000.0"/>
17066 <param name="MinPeptideLength" value="5"/>
17067 <param name="MaxPeptideLength" value="75"/>
17068 <param name="UseSmartPlusThreeModel" value="false"/>
17069 <param name="NumIntensityClasses" value="3"/>
17070 <param name="ClassSizeMultiplier" value="2.0"/>
17071 <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/>
17072 <param name="SpectrumListFilters" value=""/>
17073 <param name="ignoreConfigErrors" value="false"/>
17074 <param name="force" value="false"/>
17075 <param name="test" value="true"/>
17076 </conditional>
17077 <param name="in" value="spectra.mzML"/>
17078 <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
17079 <param name="precursor_mass_tolerance" value="5.0"/>
17080 <param name="precursor_mass_tolerance_unit" value="ppm"/>
17081 <param name="precursor_mass_tolerance_avg" value="false"/>
17082 <param name="fragment_mass_tolerance" value="0.3"/>
17083 <param name="fragment_mass_tolerance_unit" value="Da"/>
17084 <param name="database" value="proteins.fasta"/>
17085 <param name="fixed_modifications" value=""/>
17086 <param name="variable_modifications" value="Oxidation (M)"/>
17087 <param name="NumChargeStates" value="3"/>
17088 <param name="TicCutoffPercentage" value="0.98"/>
17089 <param name="MaxDynamicMods" value="2"/>
17090 <param name="MaxResultRank" value="5"/>
17091 <param name="CleavageRules" value=""/>
17092 <param name="MinTerminiCleavages" value="2"/>
17093 <param name="MaxMissedCleavages" value="-1"/>
17094 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17095 <output name="ctd_out" ftype="xml">
17096 <assert_contents>
17097 <is_valid_xml/>
17098 </assert_contents>
17099 </output>
17100 </test>
17101 </xml>
17102 <xml name="autotest_MzMLSplitter"/>
17103 <xml name="autotest_MzTabExporter">
17104 <test expect_num_outputs="2">
17105 <conditional name="adv_opts_cond">
17106 <param name="adv_opts_selector" value="advanced"/>
17107 <param name="first_run_inference_only" value="false"/>
17108 <param name="force" value="false"/>
17109 <param name="test" value="true"/>
17110 </conditional>
17111 <param name="in" value="MzTabExporter_1_input.consensusXML"/>
17112 <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17113 <param name="opt_columns" value="subfeatures"/>
17114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17115 <output name="ctd_out" ftype="xml">
17116 <assert_contents>
17117 <is_valid_xml/>
17118 </assert_contents>
17119 </output>
17120 </test>
17121 <test expect_num_outputs="2">
17122 <conditional name="adv_opts_cond">
17123 <param name="adv_opts_selector" value="advanced"/>
17124 <param name="first_run_inference_only" value="false"/>
17125 <param name="force" value="false"/>
17126 <param name="test" value="true"/>
17127 </conditional>
17128 <param name="in" value="MzTabExporter_2_input.idXML"/>
17129 <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17130 <param name="opt_columns" value="subfeatures"/>
17131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17132 <output name="ctd_out" ftype="xml">
17133 <assert_contents>
17134 <is_valid_xml/>
17135 </assert_contents>
17136 </output>
17137 </test>
17138 <test expect_num_outputs="2">
17139 <conditional name="adv_opts_cond">
17140 <param name="adv_opts_selector" value="advanced"/>
17141 <param name="first_run_inference_only" value="false"/>
17142 <param name="force" value="false"/>
17143 <param name="test" value="true"/>
17144 </conditional>
17145 <param name="in" value="MzTabExporter_3_input.featureXML"/>
17146 <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17147 <param name="opt_columns" value="subfeatures"/>
17148 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17149 <output name="ctd_out" ftype="xml">
17150 <assert_contents>
17151 <is_valid_xml/>
17152 </assert_contents>
17153 </output>
17154 </test>
17155 <test expect_num_outputs="2">
17156 <conditional name="adv_opts_cond">
17157 <param name="adv_opts_selector" value="advanced"/>
17158 <param name="first_run_inference_only" value="false"/>
17159 <param name="force" value="false"/>
17160 <param name="test" value="true"/>
17161 </conditional>
17162 <param name="in" value="Epifany_2_out.consensusXML"/>
17163 <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17164 <param name="opt_columns" value="subfeatures"/>
17165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17166 <output name="ctd_out" ftype="xml">
17167 <assert_contents>
17168 <is_valid_xml/>
17169 </assert_contents>
17170 </output>
17171 </test>
17172 <test expect_num_outputs="2">
17173 <conditional name="adv_opts_cond">
17174 <param name="adv_opts_selector" value="advanced"/>
17175 <param name="first_run_inference_only" value="true"/>
17176 <param name="force" value="false"/>
17177 <param name="test" value="true"/>
17178 </conditional>
17179 <param name="in" value="MzTabExporter_5_in.consensusXML"/>
17180 <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17181 <param name="opt_columns" value="subfeatures"/>
17182 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17183 <output name="ctd_out" ftype="xml">
17184 <assert_contents>
17185 <is_valid_xml/>
17186 </assert_contents>
17187 </output>
17188 </test>
17189 <test expect_num_outputs="2">
17190 <conditional name="adv_opts_cond">
17191 <param name="adv_opts_selector" value="advanced"/>
17192 <param name="first_run_inference_only" value="false"/>
17193 <param name="force" value="false"/>
17194 <param name="test" value="true"/>
17195 </conditional>
17196 <param name="in" value="MzTabExporter_6_input.idXML"/>
17197 <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17198 <param name="opt_columns" value="subfeatures"/>
17199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17200 <output name="ctd_out" ftype="xml">
17201 <assert_contents>
17202 <is_valid_xml/>
17203 </assert_contents>
17204 </output>
17205 </test>
17206 <test expect_num_outputs="2">
17207 <conditional name="adv_opts_cond">
17208 <param name="adv_opts_selector" value="advanced"/>
17209 <param name="first_run_inference_only" value="false"/>
17210 <param name="force" value="false"/>
17211 <param name="test" value="true"/>
17212 </conditional>
17213 <param name="in" value="MzTabExporter_7_input.consensusXML"/>
17214 <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17215 <param name="opt_columns" value="subfeatures"/>
17216 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17217 <output name="ctd_out" ftype="xml">
17218 <assert_contents>
17219 <is_valid_xml/>
17220 </assert_contents>
17221 </output>
17222 </test>
17223 </xml>
17224 <xml name="autotest_NoiseFilterGaussian">
17225 <test expect_num_outputs="2">
17226 <conditional name="adv_opts_cond">
17227 <param name="adv_opts_selector" value="advanced"/>
17228 <param name="processOption" value="inmemory"/>
17229 <param name="force" value="false"/>
17230 <param name="test" value="true"/>
17231 </conditional>
17232 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
17233 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17234 <section name="algorithm">
17235 <param name="gaussian_width" value="1.0"/>
17236 <param name="ppm_tolerance" value="10.0"/>
17237 <param name="use_ppm_tolerance" value="false"/>
17238 </section>
17239 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17240 <output name="ctd_out" ftype="xml">
17241 <assert_contents>
17242 <is_valid_xml/>
17243 </assert_contents>
17244 </output>
17245 </test>
17246 <test expect_num_outputs="2">
17247 <conditional name="adv_opts_cond">
17248 <param name="adv_opts_selector" value="advanced"/>
17249 <param name="processOption" value="inmemory"/>
17250 <param name="force" value="false"/>
17251 <param name="test" value="true"/>
17252 </conditional>
17253 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
17254 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17255 <section name="algorithm">
17256 <param name="gaussian_width" value="50.0"/>
17257 <param name="ppm_tolerance" value="10.0"/>
17258 <param name="use_ppm_tolerance" value="false"/>
17259 </section>
17260 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17261 <output name="ctd_out" ftype="xml">
17262 <assert_contents>
17263 <is_valid_xml/>
17264 </assert_contents>
17265 </output>
17266 </test>
17267 <test expect_num_outputs="2">
17268 <conditional name="adv_opts_cond">
17269 <param name="adv_opts_selector" value="advanced"/>
17270 <param name="processOption" value="lowmemory"/>
17271 <param name="force" value="false"/>
17272 <param name="test" value="true"/>
17273 </conditional>
17274 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
17275 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17276 <section name="algorithm">
17277 <param name="gaussian_width" value="1.0"/>
17278 <param name="ppm_tolerance" value="10.0"/>
17279 <param name="use_ppm_tolerance" value="false"/>
17280 </section>
17281 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17282 <output name="ctd_out" ftype="xml">
17283 <assert_contents>
17284 <is_valid_xml/>
17285 </assert_contents>
17286 </output>
17287 </test>
17288 <test expect_num_outputs="2">
17289 <conditional name="adv_opts_cond">
17290 <param name="adv_opts_selector" value="advanced"/>
17291 <param name="processOption" value="lowmemory"/>
17292 <param name="force" value="false"/>
17293 <param name="test" value="true"/>
17294 </conditional>
17295 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
17296 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17297 <section name="algorithm">
17298 <param name="gaussian_width" value="50.0"/>
17299 <param name="ppm_tolerance" value="10.0"/>
17300 <param name="use_ppm_tolerance" value="false"/>
17301 </section>
17302 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17303 <output name="ctd_out" ftype="xml">
17304 <assert_contents>
17305 <is_valid_xml/>
17306 </assert_contents>
17307 </output>
17308 </test>
17309 </xml>
17310 <xml name="autotest_NoiseFilterSGolay">
17311 <test expect_num_outputs="2">
17312 <conditional name="adv_opts_cond">
17313 <param name="adv_opts_selector" value="advanced"/>
17314 <param name="processOption" value="inmemory"/>
17315 <param name="force" value="false"/>
17316 <param name="test" value="true"/>
17317 </conditional>
17318 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
17319 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17320 <section name="algorithm">
17321 <param name="frame_length" value="9"/>
17322 <param name="polynomial_order" value="4"/>
17323 </section>
17324 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17325 <output name="ctd_out" ftype="xml">
17326 <assert_contents>
17327 <is_valid_xml/>
17328 </assert_contents>
17329 </output>
17330 </test>
17331 <test expect_num_outputs="2">
17332 <conditional name="adv_opts_cond">
17333 <param name="adv_opts_selector" value="advanced"/>
17334 <param name="processOption" value="inmemory"/>
17335 <param name="force" value="false"/>
17336 <param name="test" value="true"/>
17337 </conditional>
17338 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
17339 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17340 <section name="algorithm">
17341 <param name="frame_length" value="11"/>
17342 <param name="polynomial_order" value="4"/>
17343 </section>
17344 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17345 <output name="ctd_out" ftype="xml">
17346 <assert_contents>
17347 <is_valid_xml/>
17348 </assert_contents>
17349 </output>
17350 </test>
17351 <test expect_num_outputs="2">
17352 <conditional name="adv_opts_cond">
17353 <param name="adv_opts_selector" value="advanced"/>
17354 <param name="processOption" value="lowmemory"/>
17355 <param name="force" value="false"/>
17356 <param name="test" value="true"/>
17357 </conditional>
17358 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
17359 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17360 <section name="algorithm">
17361 <param name="frame_length" value="9"/>
17362 <param name="polynomial_order" value="4"/>
17363 </section>
17364 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17365 <output name="ctd_out" ftype="xml">
17366 <assert_contents>
17367 <is_valid_xml/>
17368 </assert_contents>
17369 </output>
17370 </test>
17371 <test expect_num_outputs="2">
17372 <conditional name="adv_opts_cond">
17373 <param name="adv_opts_selector" value="advanced"/>
17374 <param name="processOption" value="lowmemory"/>
17375 <param name="force" value="false"/>
17376 <param name="test" value="true"/>
17377 </conditional>
17378 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
17379 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
17380 <section name="algorithm">
17381 <param name="frame_length" value="11"/>
17382 <param name="polynomial_order" value="4"/>
17383 </section>
17384 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17385 <output name="ctd_out" ftype="xml">
17386 <assert_contents>
17387 <is_valid_xml/>
17388 </assert_contents>
17389 </output>
17390 </test>
17391 </xml>
17392 <xml name="autotest_NovorAdapter"/>
17393 <xml name="autotest_NucleicAcidSearchEngine">
17394 <test expect_num_outputs="3">
17395 <conditional name="adv_opts_cond">
17396 <param name="adv_opts_selector" value="advanced"/>
17397 <param name="decharge_ms2" value="false"/>
17398 <param name="force" value="false"/>
17399 <param name="test" value="true"/>
17400 </conditional>
17401 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
17402 <param name="database" value="NucleicAcidSearchEngine_1.fasta"/>
17403 <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17404 <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
17405 <section name="precursor">
17406 <param name="mass_tolerance" value="5.0"/>
17407 <param name="mass_tolerance_unit" value="ppm"/>
17408 <param name="min_charge" value="-2"/>
17409 <param name="max_charge" value="-14"/>
17410 <param name="include_unknown_charge" value="true"/>
17411 <param name="use_avg_mass" value="false"/>
17412 <param name="use_adducts" value="false"/>
17413 <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
17414 <param name="isotopes" value="0 1 2"/>
17415 </section>
17416 <section name="fragment">
17417 <param name="mass_tolerance" value="5.0"/>
17418 <param name="mass_tolerance_unit" value="ppm"/>
17419 <param name="ions" value="a-B,c,w,y"/>
17420 </section>
17421 <section name="modifications">
17422 <param name="variable" value=""/>
17423 <param name="variable_max_per_oligo" value="2"/>
17424 <param name="resolve_ambiguities" value="false"/>
17425 </section>
17426 <section name="oligo">
17427 <param name="min_size" value="5"/>
17428 <param name="max_size" value="0"/>
17429 <param name="missed_cleavages" value="22"/>
17430 <param name="enzyme" value="no cleavage"/>
17431 </section>
17432 <section name="report">
17433 <param name="top_hits" value="1"/>
17434 </section>
17435 <section name="fdr">
17436 <param name="decoy_pattern" value="DECOY_"/>
17437 <param name="cutoff" value="0.05"/>
17438 <param name="remove_decoys" value="true"/>
17439 </section>
17440 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/>
17441 <output name="ctd_out" ftype="xml">
17442 <assert_contents>
17443 <is_valid_xml/>
17444 </assert_contents>
17445 </output>
17446 </test>
17447 </xml>
17448 <xml name="autotest_OMSSAAdapter">
17449 <test expect_num_outputs="2">
17450 <conditional name="adv_opts_cond">
17451 <param name="adv_opts_selector" value="advanced"/>
17452 <param name="pc" value="1"/>
17453 <param name="hs" value="4"/>
17454 <param name="tez" value="1"/>
17455 <param name="tom" value="0"/>
17456 <param name="tem" value="0"/>
17457 <param name="tex" value="1446.94"/>
17458 <param name="zt" value="3"/>
17459 <param name="z1" value="0.95"/>
17460 <param name="zc" value="1"/>
17461 <param name="zcc" value="2"/>
17462 <param name="zoh" value="2"/>
17463 <param name="no" value="4"/>
17464 <param name="nox" value="40"/>
17465 <param name="i" value="1,4"/>
17466 <param name="sp" value="100"/>
17467 <param name="sb1" value="1"/>
17468 <param name="sct" value="0"/>
17469 <param name="x" value="0"/>
17470 <param name="hm" value="2"/>
17471 <param name="ht" value="6"/>
17472 <param name="mm" value="128"/>
17473 <param name="mnm" value="false"/>
17474 <param name="is" value="0.0"/>
17475 <param name="ir" value="0.0"/>
17476 <param name="ii" value="0.0"/>
17477 <param name="chunk_size" value="0"/>
17478 <param name="force" value="false"/>
17479 <param name="test" value="true"/>
17480 </conditional>
17481 <param name="in" value="spectra.mzML"/>
17482 <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
17483 <param name="precursor_mass_tolerance" value="5.0"/>
17484 <param name="precursor_error_units" value="ppm"/>
17485 <param name="fragment_mass_tolerance" value="0.3"/>
17486 <param name="database" value="proteins.fasta"/>
17487 <param name="min_precursor_charge" value="1"/>
17488 <param name="max_precursor_charge" value="3"/>
17489 <param name="fixed_modifications" value=""/>
17490 <param name="variable_modifications" value="Oxidation (M)"/>
17491 <param name="v" value="1"/>
17492 <param name="enzyme" value="Trypsin"/>
17493 <param name="hl" value="30"/>
17494 <param name="he" value="1.0"/>
17495 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17496 <output name="ctd_out" ftype="xml">
17497 <assert_contents>
17498 <is_valid_xml/>
17499 </assert_contents>
17500 </output>
17501 </test>
17502 </xml>
17503 <xml name="autotest_OpenPepXLLF">
17504 <test expect_num_outputs="5">
17505 <conditional name="adv_opts_cond">
17506 <param name="adv_opts_selector" value="advanced"/>
17507 <param name="force" value="false"/>
17508 <param name="test" value="true"/>
17509 </conditional>
17510 <param name="in" value="OpenPepXLLF_input.mzML"/>
17511 <param name="database" value="OpenPepXLLF_input.fasta"/>
17512 <param name="decoy_string" value="decoy"/>
17513 <param name="decoy_prefix" value="true"/>
17514 <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
17515 <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
17516 <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
17517 <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
17518 <section name="precursor">
17519 <param name="mass_tolerance" value="10.0"/>
17520 <param name="mass_tolerance_unit" value="ppm"/>
17521 <param name="min_charge" value="3"/>
17522 <param name="max_charge" value="7"/>
17523 <param name="corrections" value="2 1 0"/>
17524 </section>
17525 <section name="fragment">
17526 <param name="mass_tolerance" value="20.0"/>
17527 <param name="mass_tolerance_xlinks" value="20.0"/>
17528 <param name="mass_tolerance_unit" value="ppm"/>
17529 </section>
17530 <section name="modifications">
17531 <param name="fixed" value=""/>
17532 <param name="variable" value=""/>
17533 <param name="variable_max_per_peptide" value="2"/>
17534 </section>
17535 <section name="peptide">
17536 <param name="min_size" value="5"/>
17537 <param name="missed_cleavages" value="2"/>
17538 <param name="enzyme" value="Trypsin"/>
17539 </section>
17540 <section name="cross_linker">
17541 <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
17542 <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
17543 <param name="mass" value="138.0680796"/>
17544 <param name="mass_mono_link" value="156.07864431 155.094628715"/>
17545 <param name="name" value="DSS"/>
17546 </section>
17547 <section name="algorithm">
17548 <param name="number_top_hits" value="5"/>
17549 <param name="deisotope" value="auto"/>
17550 <param name="use_sequence_tags" value="false"/>
17551 <param name="sequence_tag_min_length" value="2"/>
17552 </section>
17553 <section name="ions">
17554 <param name="b_ions" value="true"/>
17555 <param name="y_ions" value="true"/>
17556 <param name="a_ions" value="false"/>
17557 <param name="x_ions" value="false"/>
17558 <param name="c_ions" value="false"/>
17559 <param name="z_ions" value="false"/>
17560 <param name="neutral_losses" value="true"/>
17561 </section>
17562 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
17563 <output name="ctd_out" ftype="xml">
17564 <assert_contents>
17565 <is_valid_xml/>
17566 </assert_contents>
17567 </output>
17568 </test>
17569 <test expect_num_outputs="2">
17570 <conditional name="adv_opts_cond">
17571 <param name="adv_opts_selector" value="advanced"/>
17572 <param name="force" value="false"/>
17573 <param name="test" value="true"/>
17574 </conditional>
17575 <param name="in" value="OpenPepXLLF_input2.mzML"/>
17576 <param name="database" value="OpenPepXLLF_input2.fasta"/>
17577 <param name="decoy_string" value="decoy_"/>
17578 <param name="decoy_prefix" value="true"/>
17579 <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
17580 <section name="precursor">
17581 <param name="mass_tolerance" value="10.0"/>
17582 <param name="mass_tolerance_unit" value="ppm"/>
17583 <param name="min_charge" value="3"/>
17584 <param name="max_charge" value="7"/>
17585 <param name="corrections" value="1 0"/>
17586 </section>
17587 <section name="fragment">
17588 <param name="mass_tolerance" value="0.2"/>
17589 <param name="mass_tolerance_xlinks" value="0.3"/>
17590 <param name="mass_tolerance_unit" value="Da"/>
17591 </section>
17592 <section name="modifications">
17593 <param name="fixed" value="Carbamidomethyl (C)"/>
17594 <param name="variable" value="Oxidation (M)"/>
17595 <param name="variable_max_per_peptide" value="1"/>
17596 </section>
17597 <section name="peptide">
17598 <param name="min_size" value="5"/>
17599 <param name="missed_cleavages" value="1"/>
17600 <param name="enzyme" value="Trypsin"/>
17601 </section>
17602 <section name="cross_linker">
17603 <param name="residue1" value="&quot;D&quot; &quot;E&quot; &quot;C-term&quot;"/>
17604 <param name="residue2" value="&quot;K&quot; &quot;S&quot; &quot;T&quot; &quot;Y&quot; &quot;N-term&quot;"/>
17605 <param name="mass" value="-18.010595"/>
17606 <param name="mass_mono_link" value=""/>
17607 <param name="name" value="DMTMM"/>
17608 </section>
17609 <section name="algorithm">
17610 <param name="number_top_hits" value="1"/>
17611 <param name="deisotope" value="auto"/>
17612 <param name="use_sequence_tags" value="false"/>
17613 <param name="sequence_tag_min_length" value="2"/>
17614 </section>
17615 <section name="ions">
17616 <param name="b_ions" value="true"/>
17617 <param name="y_ions" value="true"/>
17618 <param name="a_ions" value="false"/>
17619 <param name="x_ions" value="false"/>
17620 <param name="c_ions" value="false"/>
17621 <param name="z_ions" value="false"/>
17622 <param name="neutral_losses" value="true"/>
17623 </section>
17624 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
17625 <output name="ctd_out" ftype="xml">
17626 <assert_contents>
17627 <is_valid_xml/>
17628 </assert_contents>
17629 </output>
17630 </test>
17631 </xml>
17632 <xml name="autotest_OpenPepXL">
17633 <test expect_num_outputs="5">
17634 <conditional name="adv_opts_cond">
17635 <param name="adv_opts_selector" value="advanced"/>
17636 <param name="force" value="false"/>
17637 <param name="test" value="true"/>
17638 </conditional>
17639 <param name="in" value="OpenPepXL_input.mzML"/>
17640 <param name="consensus" value="OpenPepXL_input.consensusXML"/>
17641 <param name="database" value="OpenPepXL_input.fasta"/>
17642 <param name="decoy_string" value="decoy"/>
17643 <param name="decoy_prefix" value="true"/>
17644 <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
17645 <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
17646 <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
17647 <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
17648 <section name="precursor">
17649 <param name="mass_tolerance" value="10.0"/>
17650 <param name="mass_tolerance_unit" value="ppm"/>
17651 <param name="min_charge" value="3"/>
17652 <param name="max_charge" value="7"/>
17653 <param name="corrections" value="2 1 0"/>
17654 </section>
17655 <section name="fragment">
17656 <param name="mass_tolerance" value="0.2"/>
17657 <param name="mass_tolerance_xlinks" value="0.3"/>
17658 <param name="mass_tolerance_unit" value="Da"/>
17659 </section>
17660 <section name="modifications">
17661 <param name="fixed" value=""/>
17662 <param name="variable" value=""/>
17663 <param name="variable_max_per_peptide" value="2"/>
17664 </section>
17665 <section name="peptide">
17666 <param name="min_size" value="5"/>
17667 <param name="missed_cleavages" value="2"/>
17668 <param name="enzyme" value="Trypsin"/>
17669 </section>
17670 <section name="cross_linker">
17671 <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
17672 <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
17673 <param name="mass_light" value="138.0680796"/>
17674 <param name="mass_iso_shift" value="12.075321"/>
17675 <param name="mass_mono_link" value="156.07864431 155.094628715"/>
17676 <param name="name" value="DSS"/>
17677 </section>
17678 <section name="algorithm">
17679 <param name="number_top_hits" value="5"/>
17680 <param name="deisotope" value="auto"/>
17681 </section>
17682 <section name="ions">
17683 <param name="b_ions" value="true"/>
17684 <param name="y_ions" value="true"/>
17685 <param name="a_ions" value="false"/>
17686 <param name="x_ions" value="false"/>
17687 <param name="c_ions" value="false"/>
17688 <param name="z_ions" value="false"/>
17689 <param name="neutral_losses" value="true"/>
17690 </section>
17691 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
17692 <output name="ctd_out" ftype="xml">
17693 <assert_contents>
17694 <is_valid_xml/>
17695 </assert_contents>
17696 </output>
17697 </test>
17698 </xml>
17699 <xml name="autotest_OpenSwathAnalyzer">
17700 <test expect_num_outputs="2">
17701 <conditional name="adv_opts_cond">
17702 <param name="adv_opts_selector" value="advanced"/>
17703 <param name="force" value="false"/>
17704 <param name="test" value="true"/>
17705 </conditional>
17706 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17707 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17708 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
17709 <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17710 <param name="no_strict" value="false"/>
17711 <param name="min_upper_edge_dist" value="0.0"/>
17712 <section name="model">
17713 <param name="type" value="linear"/>
17714 <param name="symmetric_regression" value="false"/>
17715 </section>
17716 <section name="algorithm">
17717 <param name="stop_report_after_feature" value="-1"/>
17718 <param name="rt_extraction_window" value="-1.0"/>
17719 <param name="rt_normalization_factor" value="1.0"/>
17720 <param name="quantification_cutoff" value="0.0"/>
17721 <param name="write_convex_hull" value="false"/>
17722 <param name="spectrum_addition_method" value="simple"/>
17723 <param name="add_up_spectra" value="1"/>
17724 <param name="spacing_for_spectra_resampling" value="0.005"/>
17725 <param name="uis_threshold_sn" value="-1"/>
17726 <param name="uis_threshold_peak_area" value="0"/>
17727 <param name="scoring_model" value="default"/>
17728 <param name="im_extra_drift" value="0.0"/>
17729 <param name="strict" value="true"/>
17730 <section name="TransitionGroupPicker">
17731 <param name="stop_after_feature" value="-1"/>
17732 <param name="stop_after_intensity_ratio" value="0.0001"/>
17733 <param name="min_peak_width" value="-1.0"/>
17734 <param name="peak_integration" value="original"/>
17735 <param name="background_subtraction" value="none"/>
17736 <param name="recalculate_peaks" value="false"/>
17737 <param name="use_precursors" value="false"/>
17738 <param name="use_consensus" value="true"/>
17739 <param name="recalculate_peaks_max_z" value="1.0"/>
17740 <param name="minimal_quality" value="-10000.0"/>
17741 <param name="resample_boundary" value="15.0"/>
17742 <param name="compute_peak_quality" value="false"/>
17743 <param name="compute_peak_shape_metrics" value="false"/>
17744 <param name="compute_total_mi" value="false"/>
17745 <param name="boundary_selection_method" value="largest"/>
17746 <section name="PeakPickerMRM">
17747 <param name="sgolay_frame_length" value="15"/>
17748 <param name="sgolay_polynomial_order" value="3"/>
17749 <param name="gauss_width" value="50.0"/>
17750 <param name="use_gauss" value="true"/>
17751 <param name="peak_width" value="40.0"/>
17752 <param name="signal_to_noise" value="1.0"/>
17753 <param name="sn_win_len" value="1000.0"/>
17754 <param name="sn_bin_count" value="30"/>
17755 <param name="write_sn_log_messages" value="false"/>
17756 <param name="remove_overlapping_peaks" value="false"/>
17757 <param name="method" value="legacy"/>
17758 </section>
17759 <section name="PeakIntegrator">
17760 <param name="integration_type" value="intensity_sum"/>
17761 <param name="baseline_type" value="base_to_base"/>
17762 <param name="fit_EMG" value="false"/>
17763 </section>
17764 </section>
17765 <section name="DIAScoring">
17766 <param name="dia_extraction_window" value="0.05"/>
17767 <param name="dia_extraction_unit" value="Th"/>
17768 <param name="dia_centroided" value="false"/>
17769 <param name="dia_byseries_intensity_min" value="300.0"/>
17770 <param name="dia_byseries_ppm_diff" value="10.0"/>
17771 <param name="dia_nr_isotopes" value="4"/>
17772 <param name="dia_nr_charges" value="4"/>
17773 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17774 </section>
17775 <section name="EMGScoring">
17776 <param name="interpolation_step" value="0.2"/>
17777 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17778 <param name="max_iteration" value="500"/>
17779 <section name="statistics">
17780 <param name="mean" value="1.0"/>
17781 <param name="variance" value="1.0"/>
17782 </section>
17783 </section>
17784 <section name="Scores">
17785 <param name="use_shape_score" value="true"/>
17786 <param name="use_coelution_score" value="true"/>
17787 <param name="use_rt_score" value="true"/>
17788 <param name="use_library_score" value="true"/>
17789 <param name="use_elution_model_score" value="true"/>
17790 <param name="use_intensity_score" value="true"/>
17791 <param name="use_nr_peaks_score" value="true"/>
17792 <param name="use_total_xic_score" value="true"/>
17793 <param name="use_total_mi_score" value="false"/>
17794 <param name="use_sn_score" value="true"/>
17795 <param name="use_mi_score" value="false"/>
17796 <param name="use_dia_scores" value="true"/>
17797 <param name="use_ms1_correlation" value="false"/>
17798 <param name="use_sonar_scores" value="false"/>
17799 <param name="use_ion_mobility_scores" value="false"/>
17800 <param name="use_ms1_fullscan" value="false"/>
17801 <param name="use_ms1_mi" value="false"/>
17802 <param name="use_uis_scores" value="false"/>
17803 </section>
17804 </section>
17805 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17806 <output name="ctd_out" ftype="xml">
17807 <assert_contents>
17808 <is_valid_xml/>
17809 </assert_contents>
17810 </output>
17811 </test>
17812 <test expect_num_outputs="2">
17813 <conditional name="adv_opts_cond">
17814 <param name="adv_opts_selector" value="advanced"/>
17815 <param name="force" value="false"/>
17816 <param name="test" value="true"/>
17817 </conditional>
17818 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17819 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17820 <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17821 <param name="no_strict" value="false"/>
17822 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
17823 <param name="min_upper_edge_dist" value="0.0"/>
17824 <section name="model">
17825 <param name="type" value="linear"/>
17826 <param name="symmetric_regression" value="false"/>
17827 </section>
17828 <section name="algorithm">
17829 <param name="stop_report_after_feature" value="-1"/>
17830 <param name="rt_extraction_window" value="-1.0"/>
17831 <param name="rt_normalization_factor" value="1.0"/>
17832 <param name="quantification_cutoff" value="0.0"/>
17833 <param name="write_convex_hull" value="false"/>
17834 <param name="spectrum_addition_method" value="simple"/>
17835 <param name="add_up_spectra" value="1"/>
17836 <param name="spacing_for_spectra_resampling" value="0.005"/>
17837 <param name="uis_threshold_sn" value="-1"/>
17838 <param name="uis_threshold_peak_area" value="0"/>
17839 <param name="scoring_model" value="default"/>
17840 <param name="im_extra_drift" value="0.0"/>
17841 <param name="strict" value="true"/>
17842 <section name="TransitionGroupPicker">
17843 <param name="stop_after_feature" value="-1"/>
17844 <param name="stop_after_intensity_ratio" value="0.0001"/>
17845 <param name="min_peak_width" value="-1.0"/>
17846 <param name="peak_integration" value="original"/>
17847 <param name="background_subtraction" value="none"/>
17848 <param name="recalculate_peaks" value="false"/>
17849 <param name="use_precursors" value="false"/>
17850 <param name="use_consensus" value="true"/>
17851 <param name="recalculate_peaks_max_z" value="1.0"/>
17852 <param name="minimal_quality" value="-10000.0"/>
17853 <param name="resample_boundary" value="15.0"/>
17854 <param name="compute_peak_quality" value="false"/>
17855 <param name="compute_peak_shape_metrics" value="false"/>
17856 <param name="compute_total_mi" value="false"/>
17857 <param name="boundary_selection_method" value="largest"/>
17858 <section name="PeakPickerMRM">
17859 <param name="sgolay_frame_length" value="15"/>
17860 <param name="sgolay_polynomial_order" value="3"/>
17861 <param name="gauss_width" value="50.0"/>
17862 <param name="use_gauss" value="true"/>
17863 <param name="peak_width" value="40.0"/>
17864 <param name="signal_to_noise" value="1.0"/>
17865 <param name="sn_win_len" value="1000.0"/>
17866 <param name="sn_bin_count" value="30"/>
17867 <param name="write_sn_log_messages" value="false"/>
17868 <param name="remove_overlapping_peaks" value="false"/>
17869 <param name="method" value="legacy"/>
17870 </section>
17871 <section name="PeakIntegrator">
17872 <param name="integration_type" value="intensity_sum"/>
17873 <param name="baseline_type" value="base_to_base"/>
17874 <param name="fit_EMG" value="false"/>
17875 </section>
17876 </section>
17877 <section name="DIAScoring">
17878 <param name="dia_extraction_window" value="0.05"/>
17879 <param name="dia_extraction_unit" value="Th"/>
17880 <param name="dia_centroided" value="false"/>
17881 <param name="dia_byseries_intensity_min" value="300.0"/>
17882 <param name="dia_byseries_ppm_diff" value="10.0"/>
17883 <param name="dia_nr_isotopes" value="4"/>
17884 <param name="dia_nr_charges" value="4"/>
17885 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17886 </section>
17887 <section name="EMGScoring">
17888 <param name="interpolation_step" value="0.2"/>
17889 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17890 <param name="max_iteration" value="500"/>
17891 <section name="statistics">
17892 <param name="mean" value="1.0"/>
17893 <param name="variance" value="1.0"/>
17894 </section>
17895 </section>
17896 <section name="Scores">
17897 <param name="use_shape_score" value="true"/>
17898 <param name="use_coelution_score" value="true"/>
17899 <param name="use_rt_score" value="true"/>
17900 <param name="use_library_score" value="true"/>
17901 <param name="use_elution_model_score" value="true"/>
17902 <param name="use_intensity_score" value="true"/>
17903 <param name="use_nr_peaks_score" value="true"/>
17904 <param name="use_total_xic_score" value="true"/>
17905 <param name="use_total_mi_score" value="false"/>
17906 <param name="use_sn_score" value="true"/>
17907 <param name="use_mi_score" value="false"/>
17908 <param name="use_dia_scores" value="true"/>
17909 <param name="use_ms1_correlation" value="false"/>
17910 <param name="use_sonar_scores" value="false"/>
17911 <param name="use_ion_mobility_scores" value="false"/>
17912 <param name="use_ms1_fullscan" value="false"/>
17913 <param name="use_ms1_mi" value="false"/>
17914 <param name="use_uis_scores" value="false"/>
17915 </section>
17916 </section>
17917 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17918 <output name="ctd_out" ftype="xml">
17919 <assert_contents>
17920 <is_valid_xml/>
17921 </assert_contents>
17922 </output>
17923 </test>
17924 <test expect_num_outputs="2">
17925 <conditional name="adv_opts_cond">
17926 <param name="adv_opts_selector" value="advanced"/>
17927 <param name="force" value="false"/>
17928 <param name="test" value="true"/>
17929 </conditional>
17930 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17931 <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
17932 <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17933 <param name="no_strict" value="false"/>
17934 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
17935 <param name="min_upper_edge_dist" value="0.0"/>
17936 <section name="model">
17937 <param name="type" value="linear"/>
17938 <param name="symmetric_regression" value="false"/>
17939 </section>
17940 <section name="algorithm">
17941 <param name="stop_report_after_feature" value="-1"/>
17942 <param name="rt_extraction_window" value="-1.0"/>
17943 <param name="rt_normalization_factor" value="1.0"/>
17944 <param name="quantification_cutoff" value="0.0"/>
17945 <param name="write_convex_hull" value="false"/>
17946 <param name="spectrum_addition_method" value="simple"/>
17947 <param name="add_up_spectra" value="1"/>
17948 <param name="spacing_for_spectra_resampling" value="0.005"/>
17949 <param name="uis_threshold_sn" value="-1"/>
17950 <param name="uis_threshold_peak_area" value="0"/>
17951 <param name="scoring_model" value="default"/>
17952 <param name="im_extra_drift" value="0.0"/>
17953 <param name="strict" value="true"/>
17954 <section name="TransitionGroupPicker">
17955 <param name="stop_after_feature" value="-1"/>
17956 <param name="stop_after_intensity_ratio" value="0.0001"/>
17957 <param name="min_peak_width" value="-1.0"/>
17958 <param name="peak_integration" value="original"/>
17959 <param name="background_subtraction" value="none"/>
17960 <param name="recalculate_peaks" value="false"/>
17961 <param name="use_precursors" value="false"/>
17962 <param name="use_consensus" value="true"/>
17963 <param name="recalculate_peaks_max_z" value="1.0"/>
17964 <param name="minimal_quality" value="-10000.0"/>
17965 <param name="resample_boundary" value="15.0"/>
17966 <param name="compute_peak_quality" value="false"/>
17967 <param name="compute_peak_shape_metrics" value="false"/>
17968 <param name="compute_total_mi" value="false"/>
17969 <param name="boundary_selection_method" value="largest"/>
17970 <section name="PeakPickerMRM">
17971 <param name="sgolay_frame_length" value="15"/>
17972 <param name="sgolay_polynomial_order" value="3"/>
17973 <param name="gauss_width" value="50.0"/>
17974 <param name="use_gauss" value="true"/>
17975 <param name="peak_width" value="40.0"/>
17976 <param name="signal_to_noise" value="1.0"/>
17977 <param name="sn_win_len" value="1000.0"/>
17978 <param name="sn_bin_count" value="30"/>
17979 <param name="write_sn_log_messages" value="true"/>
17980 <param name="remove_overlapping_peaks" value="false"/>
17981 <param name="method" value="legacy"/>
17982 </section>
17983 <section name="PeakIntegrator">
17984 <param name="integration_type" value="intensity_sum"/>
17985 <param name="baseline_type" value="base_to_base"/>
17986 <param name="fit_EMG" value="false"/>
17987 </section>
17988 </section>
17989 <section name="DIAScoring">
17990 <param name="dia_extraction_window" value="0.05"/>
17991 <param name="dia_extraction_unit" value="Th"/>
17992 <param name="dia_centroided" value="false"/>
17993 <param name="dia_byseries_intensity_min" value="8.0"/>
17994 <param name="dia_byseries_ppm_diff" value="15.0"/>
17995 <param name="dia_nr_isotopes" value="4"/>
17996 <param name="dia_nr_charges" value="4"/>
17997 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17998 </section>
17999 <section name="EMGScoring">
18000 <param name="interpolation_step" value="0.2"/>
18001 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18002 <param name="max_iteration" value="500"/>
18003 <section name="statistics">
18004 <param name="mean" value="1.0"/>
18005 <param name="variance" value="1.0"/>
18006 </section>
18007 </section>
18008 <section name="Scores">
18009 <param name="use_shape_score" value="true"/>
18010 <param name="use_coelution_score" value="true"/>
18011 <param name="use_rt_score" value="true"/>
18012 <param name="use_library_score" value="true"/>
18013 <param name="use_elution_model_score" value="true"/>
18014 <param name="use_intensity_score" value="true"/>
18015 <param name="use_nr_peaks_score" value="true"/>
18016 <param name="use_total_xic_score" value="true"/>
18017 <param name="use_total_mi_score" value="false"/>
18018 <param name="use_sn_score" value="true"/>
18019 <param name="use_mi_score" value="false"/>
18020 <param name="use_dia_scores" value="true"/>
18021 <param name="use_ms1_correlation" value="false"/>
18022 <param name="use_sonar_scores" value="false"/>
18023 <param name="use_ion_mobility_scores" value="false"/>
18024 <param name="use_ms1_fullscan" value="false"/>
18025 <param name="use_ms1_mi" value="false"/>
18026 <param name="use_uis_scores" value="false"/>
18027 </section>
18028 </section>
18029 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18030 <output name="ctd_out" ftype="xml">
18031 <assert_contents>
18032 <is_valid_xml/>
18033 </assert_contents>
18034 </output>
18035 </test>
18036 <test expect_num_outputs="2">
18037 <conditional name="adv_opts_cond">
18038 <param name="adv_opts_selector" value="advanced"/>
18039 <param name="force" value="false"/>
18040 <param name="test" value="true"/>
18041 </conditional>
18042 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
18043 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
18044 <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18045 <param name="no_strict" value="false"/>
18046 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
18047 <param name="min_upper_edge_dist" value="0.0"/>
18048 <section name="model">
18049 <param name="type" value="linear"/>
18050 <param name="symmetric_regression" value="false"/>
18051 </section>
18052 <section name="algorithm">
18053 <param name="stop_report_after_feature" value="-1"/>
18054 <param name="rt_extraction_window" value="-1.0"/>
18055 <param name="rt_normalization_factor" value="1.0"/>
18056 <param name="quantification_cutoff" value="0.0"/>
18057 <param name="write_convex_hull" value="false"/>
18058 <param name="spectrum_addition_method" value="simple"/>
18059 <param name="add_up_spectra" value="1"/>
18060 <param name="spacing_for_spectra_resampling" value="0.005"/>
18061 <param name="uis_threshold_sn" value="-1"/>
18062 <param name="uis_threshold_peak_area" value="0"/>
18063 <param name="scoring_model" value="default"/>
18064 <param name="im_extra_drift" value="0.0"/>
18065 <param name="strict" value="true"/>
18066 <section name="TransitionGroupPicker">
18067 <param name="stop_after_feature" value="-1"/>
18068 <param name="stop_after_intensity_ratio" value="0.0001"/>
18069 <param name="min_peak_width" value="-1.0"/>
18070 <param name="peak_integration" value="original"/>
18071 <param name="background_subtraction" value="none"/>
18072 <param name="recalculate_peaks" value="false"/>
18073 <param name="use_precursors" value="false"/>
18074 <param name="use_consensus" value="true"/>
18075 <param name="recalculate_peaks_max_z" value="1.0"/>
18076 <param name="minimal_quality" value="-10000.0"/>
18077 <param name="resample_boundary" value="15.0"/>
18078 <param name="compute_peak_quality" value="false"/>
18079 <param name="compute_peak_shape_metrics" value="false"/>
18080 <param name="compute_total_mi" value="false"/>
18081 <param name="boundary_selection_method" value="largest"/>
18082 <section name="PeakPickerMRM">
18083 <param name="sgolay_frame_length" value="15"/>
18084 <param name="sgolay_polynomial_order" value="3"/>
18085 <param name="gauss_width" value="50.0"/>
18086 <param name="use_gauss" value="true"/>
18087 <param name="peak_width" value="40.0"/>
18088 <param name="signal_to_noise" value="1.0"/>
18089 <param name="sn_win_len" value="1000.0"/>
18090 <param name="sn_bin_count" value="30"/>
18091 <param name="write_sn_log_messages" value="true"/>
18092 <param name="remove_overlapping_peaks" value="false"/>
18093 <param name="method" value="legacy"/>
18094 </section>
18095 <section name="PeakIntegrator">
18096 <param name="integration_type" value="intensity_sum"/>
18097 <param name="baseline_type" value="base_to_base"/>
18098 <param name="fit_EMG" value="false"/>
18099 </section>
18100 </section>
18101 <section name="DIAScoring">
18102 <param name="dia_extraction_window" value="0.05"/>
18103 <param name="dia_extraction_unit" value="Th"/>
18104 <param name="dia_centroided" value="false"/>
18105 <param name="dia_byseries_intensity_min" value="8.0"/>
18106 <param name="dia_byseries_ppm_diff" value="15.0"/>
18107 <param name="dia_nr_isotopes" value="4"/>
18108 <param name="dia_nr_charges" value="4"/>
18109 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18110 </section>
18111 <section name="EMGScoring">
18112 <param name="interpolation_step" value="0.2"/>
18113 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18114 <param name="max_iteration" value="500"/>
18115 <section name="statistics">
18116 <param name="mean" value="1.0"/>
18117 <param name="variance" value="1.0"/>
18118 </section>
18119 </section>
18120 <section name="Scores">
18121 <param name="use_shape_score" value="true"/>
18122 <param name="use_coelution_score" value="true"/>
18123 <param name="use_rt_score" value="true"/>
18124 <param name="use_library_score" value="true"/>
18125 <param name="use_elution_model_score" value="true"/>
18126 <param name="use_intensity_score" value="true"/>
18127 <param name="use_nr_peaks_score" value="true"/>
18128 <param name="use_total_xic_score" value="true"/>
18129 <param name="use_total_mi_score" value="false"/>
18130 <param name="use_sn_score" value="true"/>
18131 <param name="use_mi_score" value="false"/>
18132 <param name="use_dia_scores" value="true"/>
18133 <param name="use_ms1_correlation" value="false"/>
18134 <param name="use_sonar_scores" value="false"/>
18135 <param name="use_ion_mobility_scores" value="false"/>
18136 <param name="use_ms1_fullscan" value="false"/>
18137 <param name="use_ms1_mi" value="false"/>
18138 <param name="use_uis_scores" value="false"/>
18139 </section>
18140 </section>
18141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18142 <output name="ctd_out" ftype="xml">
18143 <assert_contents>
18144 <is_valid_xml/>
18145 </assert_contents>
18146 </output>
18147 </test>
18148 <test expect_num_outputs="2">
18149 <conditional name="adv_opts_cond">
18150 <param name="adv_opts_selector" value="advanced"/>
18151 <param name="force" value="false"/>
18152 <param name="test" value="true"/>
18153 </conditional>
18154 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
18155 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
18156 <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18157 <param name="no_strict" value="false"/>
18158 <param name="min_upper_edge_dist" value="0.0"/>
18159 <section name="model">
18160 <param name="type" value="linear"/>
18161 <param name="symmetric_regression" value="false"/>
18162 </section>
18163 <section name="algorithm">
18164 <param name="stop_report_after_feature" value="-1"/>
18165 <param name="rt_extraction_window" value="-1.0"/>
18166 <param name="rt_normalization_factor" value="1.0"/>
18167 <param name="quantification_cutoff" value="0.0"/>
18168 <param name="write_convex_hull" value="false"/>
18169 <param name="spectrum_addition_method" value="simple"/>
18170 <param name="add_up_spectra" value="1"/>
18171 <param name="spacing_for_spectra_resampling" value="0.005"/>
18172 <param name="uis_threshold_sn" value="-1"/>
18173 <param name="uis_threshold_peak_area" value="0"/>
18174 <param name="scoring_model" value="default"/>
18175 <param name="im_extra_drift" value="0.0"/>
18176 <param name="strict" value="true"/>
18177 <section name="TransitionGroupPicker">
18178 <param name="stop_after_feature" value="-1"/>
18179 <param name="stop_after_intensity_ratio" value="0.0001"/>
18180 <param name="min_peak_width" value="-1.0"/>
18181 <param name="peak_integration" value="original"/>
18182 <param name="background_subtraction" value="original"/>
18183 <param name="recalculate_peaks" value="false"/>
18184 <param name="use_precursors" value="false"/>
18185 <param name="use_consensus" value="true"/>
18186 <param name="recalculate_peaks_max_z" value="1.0"/>
18187 <param name="minimal_quality" value="-10000.0"/>
18188 <param name="resample_boundary" value="15.0"/>
18189 <param name="compute_peak_quality" value="false"/>
18190 <param name="compute_peak_shape_metrics" value="false"/>
18191 <param name="compute_total_mi" value="false"/>
18192 <param name="boundary_selection_method" value="largest"/>
18193 <section name="PeakPickerMRM">
18194 <param name="sgolay_frame_length" value="15"/>
18195 <param name="sgolay_polynomial_order" value="3"/>
18196 <param name="gauss_width" value="50.0"/>
18197 <param name="use_gauss" value="true"/>
18198 <param name="peak_width" value="40.0"/>
18199 <param name="signal_to_noise" value="1.0"/>
18200 <param name="sn_win_len" value="1000.0"/>
18201 <param name="sn_bin_count" value="30"/>
18202 <param name="write_sn_log_messages" value="true"/>
18203 <param name="remove_overlapping_peaks" value="false"/>
18204 <param name="method" value="legacy"/>
18205 </section>
18206 <section name="PeakIntegrator">
18207 <param name="integration_type" value="intensity_sum"/>
18208 <param name="baseline_type" value="base_to_base"/>
18209 <param name="fit_EMG" value="false"/>
18210 </section>
18211 </section>
18212 <section name="DIAScoring">
18213 <param name="dia_extraction_window" value="0.05"/>
18214 <param name="dia_extraction_unit" value="Th"/>
18215 <param name="dia_centroided" value="false"/>
18216 <param name="dia_byseries_intensity_min" value="300.0"/>
18217 <param name="dia_byseries_ppm_diff" value="10.0"/>
18218 <param name="dia_nr_isotopes" value="4"/>
18219 <param name="dia_nr_charges" value="4"/>
18220 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18221 </section>
18222 <section name="EMGScoring">
18223 <param name="interpolation_step" value="0.2"/>
18224 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18225 <param name="max_iteration" value="500"/>
18226 <section name="statistics">
18227 <param name="mean" value="1.0"/>
18228 <param name="variance" value="1.0"/>
18229 </section>
18230 </section>
18231 <section name="Scores">
18232 <param name="use_shape_score" value="true"/>
18233 <param name="use_coelution_score" value="true"/>
18234 <param name="use_rt_score" value="true"/>
18235 <param name="use_library_score" value="true"/>
18236 <param name="use_elution_model_score" value="true"/>
18237 <param name="use_intensity_score" value="true"/>
18238 <param name="use_nr_peaks_score" value="true"/>
18239 <param name="use_total_xic_score" value="true"/>
18240 <param name="use_total_mi_score" value="false"/>
18241 <param name="use_sn_score" value="true"/>
18242 <param name="use_mi_score" value="false"/>
18243 <param name="use_dia_scores" value="true"/>
18244 <param name="use_ms1_correlation" value="false"/>
18245 <param name="use_sonar_scores" value="false"/>
18246 <param name="use_ion_mobility_scores" value="false"/>
18247 <param name="use_ms1_fullscan" value="false"/>
18248 <param name="use_ms1_mi" value="false"/>
18249 <param name="use_uis_scores" value="false"/>
18250 </section>
18251 </section>
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="force" value="false"/>
18263 <param name="test" value="true"/>
18264 </conditional>
18265 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
18266 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
18267 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
18268 <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18269 <param name="no_strict" value="false"/>
18270 <param name="min_upper_edge_dist" value="0.0"/>
18271 <section name="model">
18272 <param name="type" value="linear"/>
18273 <param name="symmetric_regression" value="false"/>
18274 </section>
18275 <section name="algorithm">
18276 <param name="stop_report_after_feature" value="-1"/>
18277 <param name="rt_extraction_window" value="-1.0"/>
18278 <param name="rt_normalization_factor" value="1.0"/>
18279 <param name="quantification_cutoff" value="0.0"/>
18280 <param name="write_convex_hull" value="false"/>
18281 <param name="spectrum_addition_method" value="simple"/>
18282 <param name="add_up_spectra" value="1"/>
18283 <param name="spacing_for_spectra_resampling" value="0.005"/>
18284 <param name="uis_threshold_sn" value="-1"/>
18285 <param name="uis_threshold_peak_area" value="0"/>
18286 <param name="scoring_model" value="default"/>
18287 <param name="im_extra_drift" value="0.0"/>
18288 <param name="strict" value="true"/>
18289 <section name="TransitionGroupPicker">
18290 <param name="stop_after_feature" value="-1"/>
18291 <param name="stop_after_intensity_ratio" value="0.0001"/>
18292 <param name="min_peak_width" value="-1.0"/>
18293 <param name="peak_integration" value="original"/>
18294 <param name="background_subtraction" value="none"/>
18295 <param name="recalculate_peaks" value="false"/>
18296 <param name="use_precursors" value="false"/>
18297 <param name="use_consensus" value="true"/>
18298 <param name="recalculate_peaks_max_z" value="1.0"/>
18299 <param name="minimal_quality" value="-10000.0"/>
18300 <param name="resample_boundary" value="15.0"/>
18301 <param name="compute_peak_quality" value="false"/>
18302 <param name="compute_peak_shape_metrics" value="false"/>
18303 <param name="compute_total_mi" value="false"/>
18304 <param name="boundary_selection_method" value="largest"/>
18305 <section name="PeakPickerMRM">
18306 <param name="sgolay_frame_length" value="15"/>
18307 <param name="sgolay_polynomial_order" value="3"/>
18308 <param name="gauss_width" value="50.0"/>
18309 <param name="use_gauss" value="true"/>
18310 <param name="peak_width" value="40.0"/>
18311 <param name="signal_to_noise" value="1.0"/>
18312 <param name="sn_win_len" value="1000.0"/>
18313 <param name="sn_bin_count" value="30"/>
18314 <param name="write_sn_log_messages" value="false"/>
18315 <param name="remove_overlapping_peaks" value="false"/>
18316 <param name="method" value="legacy"/>
18317 </section>
18318 <section name="PeakIntegrator">
18319 <param name="integration_type" value="intensity_sum"/>
18320 <param name="baseline_type" value="base_to_base"/>
18321 <param name="fit_EMG" value="false"/>
18322 </section>
18323 </section>
18324 <section name="DIAScoring">
18325 <param name="dia_extraction_window" value="0.05"/>
18326 <param name="dia_extraction_unit" value="Th"/>
18327 <param name="dia_centroided" value="false"/>
18328 <param name="dia_byseries_intensity_min" value="300.0"/>
18329 <param name="dia_byseries_ppm_diff" value="10.0"/>
18330 <param name="dia_nr_isotopes" value="4"/>
18331 <param name="dia_nr_charges" value="4"/>
18332 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18333 </section>
18334 <section name="EMGScoring">
18335 <param name="interpolation_step" value="0.2"/>
18336 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18337 <param name="max_iteration" value="500"/>
18338 <section name="statistics">
18339 <param name="mean" value="1.0"/>
18340 <param name="variance" value="1.0"/>
18341 </section>
18342 </section>
18343 <section name="Scores">
18344 <param name="use_shape_score" value="true"/>
18345 <param name="use_coelution_score" value="true"/>
18346 <param name="use_rt_score" value="true"/>
18347 <param name="use_library_score" value="true"/>
18348 <param name="use_elution_model_score" value="true"/>
18349 <param name="use_intensity_score" value="true"/>
18350 <param name="use_nr_peaks_score" value="true"/>
18351 <param name="use_total_xic_score" value="true"/>
18352 <param name="use_total_mi_score" value="true"/>
18353 <param name="use_sn_score" value="true"/>
18354 <param name="use_mi_score" value="true"/>
18355 <param name="use_dia_scores" value="true"/>
18356 <param name="use_ms1_correlation" value="false"/>
18357 <param name="use_sonar_scores" value="false"/>
18358 <param name="use_ion_mobility_scores" value="false"/>
18359 <param name="use_ms1_fullscan" value="false"/>
18360 <param name="use_ms1_mi" value="true"/>
18361 <param name="use_uis_scores" value="false"/>
18362 </section>
18363 </section>
18364 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18365 <output name="ctd_out" ftype="xml">
18366 <assert_contents>
18367 <is_valid_xml/>
18368 </assert_contents>
18369 </output>
18370 </test>
18371 <test expect_num_outputs="2">
18372 <conditional name="adv_opts_cond">
18373 <param name="adv_opts_selector" value="advanced"/>
18374 <param name="force" value="false"/>
18375 <param name="test" value="true"/>
18376 </conditional>
18377 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
18378 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
18379 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
18380 <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18381 <param name="no_strict" value="false"/>
18382 <param name="min_upper_edge_dist" value="0.0"/>
18383 <section name="model">
18384 <param name="type" value="linear"/>
18385 <param name="symmetric_regression" value="false"/>
18386 </section>
18387 <section name="algorithm">
18388 <param name="stop_report_after_feature" value="-1"/>
18389 <param name="rt_extraction_window" value="-1.0"/>
18390 <param name="rt_normalization_factor" value="1.0"/>
18391 <param name="quantification_cutoff" value="0.0"/>
18392 <param name="write_convex_hull" value="false"/>
18393 <param name="spectrum_addition_method" value="simple"/>
18394 <param name="add_up_spectra" value="1"/>
18395 <param name="spacing_for_spectra_resampling" value="0.005"/>
18396 <param name="uis_threshold_sn" value="-1"/>
18397 <param name="uis_threshold_peak_area" value="0"/>
18398 <param name="scoring_model" value="default"/>
18399 <param name="im_extra_drift" value="0.0"/>
18400 <param name="strict" value="true"/>
18401 <section name="TransitionGroupPicker">
18402 <param name="stop_after_feature" value="-1"/>
18403 <param name="stop_after_intensity_ratio" value="0.0001"/>
18404 <param name="min_peak_width" value="-1.0"/>
18405 <param name="peak_integration" value="original"/>
18406 <param name="background_subtraction" value="none"/>
18407 <param name="recalculate_peaks" value="false"/>
18408 <param name="use_precursors" value="false"/>
18409 <param name="use_consensus" value="true"/>
18410 <param name="recalculate_peaks_max_z" value="1.0"/>
18411 <param name="minimal_quality" value="-10000.0"/>
18412 <param name="resample_boundary" value="15.0"/>
18413 <param name="compute_peak_quality" value="false"/>
18414 <param name="compute_peak_shape_metrics" value="false"/>
18415 <param name="compute_total_mi" value="false"/>
18416 <param name="boundary_selection_method" value="largest"/>
18417 <section name="PeakPickerMRM">
18418 <param name="sgolay_frame_length" value="15"/>
18419 <param name="sgolay_polynomial_order" value="3"/>
18420 <param name="gauss_width" value="50.0"/>
18421 <param name="use_gauss" value="true"/>
18422 <param name="peak_width" value="40.0"/>
18423 <param name="signal_to_noise" value="1.0"/>
18424 <param name="sn_win_len" value="1000.0"/>
18425 <param name="sn_bin_count" value="30"/>
18426 <param name="write_sn_log_messages" value="false"/>
18427 <param name="remove_overlapping_peaks" value="false"/>
18428 <param name="method" value="legacy"/>
18429 </section>
18430 <section name="PeakIntegrator">
18431 <param name="integration_type" value="intensity_sum"/>
18432 <param name="baseline_type" value="base_to_base"/>
18433 <param name="fit_EMG" value="false"/>
18434 </section>
18435 </section>
18436 <section name="DIAScoring">
18437 <param name="dia_extraction_window" value="0.05"/>
18438 <param name="dia_extraction_unit" value="Th"/>
18439 <param name="dia_centroided" value="false"/>
18440 <param name="dia_byseries_intensity_min" value="300.0"/>
18441 <param name="dia_byseries_ppm_diff" value="10.0"/>
18442 <param name="dia_nr_isotopes" value="4"/>
18443 <param name="dia_nr_charges" value="4"/>
18444 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18445 </section>
18446 <section name="EMGScoring">
18447 <param name="interpolation_step" value="0.2"/>
18448 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18449 <param name="max_iteration" value="500"/>
18450 <section name="statistics">
18451 <param name="mean" value="1.0"/>
18452 <param name="variance" value="1.0"/>
18453 </section>
18454 </section>
18455 <section name="Scores">
18456 <param name="use_shape_score" value="true"/>
18457 <param name="use_coelution_score" value="true"/>
18458 <param name="use_rt_score" value="true"/>
18459 <param name="use_library_score" value="true"/>
18460 <param name="use_elution_model_score" value="true"/>
18461 <param name="use_intensity_score" value="true"/>
18462 <param name="use_nr_peaks_score" value="true"/>
18463 <param name="use_total_xic_score" value="true"/>
18464 <param name="use_total_mi_score" value="false"/>
18465 <param name="use_sn_score" value="true"/>
18466 <param name="use_mi_score" value="true"/>
18467 <param name="use_dia_scores" value="true"/>
18468 <param name="use_ms1_correlation" value="false"/>
18469 <param name="use_sonar_scores" value="false"/>
18470 <param name="use_ion_mobility_scores" value="false"/>
18471 <param name="use_ms1_fullscan" value="false"/>
18472 <param name="use_ms1_mi" value="false"/>
18473 <param name="use_uis_scores" value="false"/>
18474 </section>
18475 </section>
18476 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18477 <output name="ctd_out" ftype="xml">
18478 <assert_contents>
18479 <is_valid_xml/>
18480 </assert_contents>
18481 </output>
18482 </test>
18483 <test expect_num_outputs="2">
18484 <conditional name="adv_opts_cond">
18485 <param name="adv_opts_selector" value="advanced"/>
18486 <param name="force" value="false"/>
18487 <param name="test" value="true"/>
18488 </conditional>
18489 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
18490 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
18491 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
18492 <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18493 <param name="no_strict" value="false"/>
18494 <param name="min_upper_edge_dist" value="0.0"/>
18495 <section name="model">
18496 <param name="type" value="linear"/>
18497 <param name="symmetric_regression" value="false"/>
18498 </section>
18499 <section name="algorithm">
18500 <param name="stop_report_after_feature" value="-1"/>
18501 <param name="rt_extraction_window" value="-1.0"/>
18502 <param name="rt_normalization_factor" value="1.0"/>
18503 <param name="quantification_cutoff" value="0.0"/>
18504 <param name="write_convex_hull" value="false"/>
18505 <param name="spectrum_addition_method" value="simple"/>
18506 <param name="add_up_spectra" value="1"/>
18507 <param name="spacing_for_spectra_resampling" value="0.005"/>
18508 <param name="uis_threshold_sn" value="-1"/>
18509 <param name="uis_threshold_peak_area" value="0"/>
18510 <param name="scoring_model" value="default"/>
18511 <param name="im_extra_drift" value="0.0"/>
18512 <param name="strict" value="true"/>
18513 <section name="TransitionGroupPicker">
18514 <param name="stop_after_feature" value="-1"/>
18515 <param name="stop_after_intensity_ratio" value="0.0001"/>
18516 <param name="min_peak_width" value="-1.0"/>
18517 <param name="peak_integration" value="original"/>
18518 <param name="background_subtraction" value="none"/>
18519 <param name="recalculate_peaks" value="false"/>
18520 <param name="use_precursors" value="false"/>
18521 <param name="use_consensus" value="true"/>
18522 <param name="recalculate_peaks_max_z" value="1.0"/>
18523 <param name="minimal_quality" value="-10000.0"/>
18524 <param name="resample_boundary" value="15.0"/>
18525 <param name="compute_peak_quality" value="false"/>
18526 <param name="compute_peak_shape_metrics" value="false"/>
18527 <param name="compute_total_mi" value="false"/>
18528 <param name="boundary_selection_method" value="largest"/>
18529 <section name="PeakPickerMRM">
18530 <param name="sgolay_frame_length" value="15"/>
18531 <param name="sgolay_polynomial_order" value="3"/>
18532 <param name="gauss_width" value="50.0"/>
18533 <param name="use_gauss" value="true"/>
18534 <param name="peak_width" value="40.0"/>
18535 <param name="signal_to_noise" value="1.0"/>
18536 <param name="sn_win_len" value="1000.0"/>
18537 <param name="sn_bin_count" value="30"/>
18538 <param name="write_sn_log_messages" value="false"/>
18539 <param name="remove_overlapping_peaks" value="false"/>
18540 <param name="method" value="legacy"/>
18541 </section>
18542 <section name="PeakIntegrator">
18543 <param name="integration_type" value="intensity_sum"/>
18544 <param name="baseline_type" value="base_to_base"/>
18545 <param name="fit_EMG" value="false"/>
18546 </section>
18547 </section>
18548 <section name="DIAScoring">
18549 <param name="dia_extraction_window" value="0.05"/>
18550 <param name="dia_extraction_unit" value="Th"/>
18551 <param name="dia_centroided" value="false"/>
18552 <param name="dia_byseries_intensity_min" value="300.0"/>
18553 <param name="dia_byseries_ppm_diff" value="10.0"/>
18554 <param name="dia_nr_isotopes" value="4"/>
18555 <param name="dia_nr_charges" value="4"/>
18556 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18557 </section>
18558 <section name="EMGScoring">
18559 <param name="interpolation_step" value="0.2"/>
18560 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18561 <param name="max_iteration" value="500"/>
18562 <section name="statistics">
18563 <param name="mean" value="1.0"/>
18564 <param name="variance" value="1.0"/>
18565 </section>
18566 </section>
18567 <section name="Scores">
18568 <param name="use_shape_score" value="true"/>
18569 <param name="use_coelution_score" value="true"/>
18570 <param name="use_rt_score" value="true"/>
18571 <param name="use_library_score" value="true"/>
18572 <param name="use_elution_model_score" value="true"/>
18573 <param name="use_intensity_score" value="true"/>
18574 <param name="use_nr_peaks_score" value="true"/>
18575 <param name="use_total_xic_score" value="true"/>
18576 <param name="use_total_mi_score" value="true"/>
18577 <param name="use_sn_score" value="true"/>
18578 <param name="use_mi_score" value="true"/>
18579 <param name="use_dia_scores" value="true"/>
18580 <param name="use_ms1_correlation" value="false"/>
18581 <param name="use_sonar_scores" value="false"/>
18582 <param name="use_ion_mobility_scores" value="false"/>
18583 <param name="use_ms1_fullscan" value="false"/>
18584 <param name="use_ms1_mi" value="false"/>
18585 <param name="use_uis_scores" value="false"/>
18586 </section>
18587 </section>
18588 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18589 <output name="ctd_out" ftype="xml">
18590 <assert_contents>
18591 <is_valid_xml/>
18592 </assert_contents>
18593 </output>
18594 </test>
18595 <test expect_num_outputs="2">
18596 <conditional name="adv_opts_cond">
18597 <param name="adv_opts_selector" value="advanced"/>
18598 <param name="force" value="false"/>
18599 <param name="test" value="true"/>
18600 </conditional>
18601 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
18602 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
18603 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
18604 <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18605 <param name="no_strict" value="false"/>
18606 <param name="min_upper_edge_dist" value="0.0"/>
18607 <section name="model">
18608 <param name="type" value="linear"/>
18609 <param name="symmetric_regression" value="false"/>
18610 </section>
18611 <section name="algorithm">
18612 <param name="stop_report_after_feature" value="-1"/>
18613 <param name="rt_extraction_window" value="-1.0"/>
18614 <param name="rt_normalization_factor" value="1.0"/>
18615 <param name="quantification_cutoff" value="0.0"/>
18616 <param name="write_convex_hull" value="false"/>
18617 <param name="spectrum_addition_method" value="simple"/>
18618 <param name="add_up_spectra" value="1"/>
18619 <param name="spacing_for_spectra_resampling" value="0.005"/>
18620 <param name="uis_threshold_sn" value="-1"/>
18621 <param name="uis_threshold_peak_area" value="0"/>
18622 <param name="scoring_model" value="default"/>
18623 <param name="im_extra_drift" value="0.0"/>
18624 <param name="strict" value="true"/>
18625 <section name="TransitionGroupPicker">
18626 <param name="stop_after_feature" value="-1"/>
18627 <param name="stop_after_intensity_ratio" value="0.0001"/>
18628 <param name="min_peak_width" value="-1.0"/>
18629 <param name="peak_integration" value="original"/>
18630 <param name="background_subtraction" value="none"/>
18631 <param name="recalculate_peaks" value="false"/>
18632 <param name="use_precursors" value="false"/>
18633 <param name="use_consensus" value="true"/>
18634 <param name="recalculate_peaks_max_z" value="1.0"/>
18635 <param name="minimal_quality" value="-10000.0"/>
18636 <param name="resample_boundary" value="15.0"/>
18637 <param name="compute_peak_quality" value="false"/>
18638 <param name="compute_peak_shape_metrics" value="false"/>
18639 <param name="compute_total_mi" value="false"/>
18640 <param name="boundary_selection_method" value="largest"/>
18641 <section name="PeakPickerMRM">
18642 <param name="sgolay_frame_length" value="15"/>
18643 <param name="sgolay_polynomial_order" value="3"/>
18644 <param name="gauss_width" value="50.0"/>
18645 <param name="use_gauss" value="true"/>
18646 <param name="peak_width" value="40.0"/>
18647 <param name="signal_to_noise" value="1.0"/>
18648 <param name="sn_win_len" value="1000.0"/>
18649 <param name="sn_bin_count" value="30"/>
18650 <param name="write_sn_log_messages" value="false"/>
18651 <param name="remove_overlapping_peaks" value="false"/>
18652 <param name="method" value="legacy"/>
18653 </section>
18654 <section name="PeakIntegrator">
18655 <param name="integration_type" value="intensity_sum"/>
18656 <param name="baseline_type" value="base_to_base"/>
18657 <param name="fit_EMG" value="false"/>
18658 </section>
18659 </section>
18660 <section name="DIAScoring">
18661 <param name="dia_extraction_window" value="0.05"/>
18662 <param name="dia_extraction_unit" value="Th"/>
18663 <param name="dia_centroided" value="false"/>
18664 <param name="dia_byseries_intensity_min" value="300.0"/>
18665 <param name="dia_byseries_ppm_diff" value="10.0"/>
18666 <param name="dia_nr_isotopes" value="4"/>
18667 <param name="dia_nr_charges" value="4"/>
18668 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18669 </section>
18670 <section name="EMGScoring">
18671 <param name="interpolation_step" value="0.2"/>
18672 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18673 <param name="max_iteration" value="500"/>
18674 <section name="statistics">
18675 <param name="mean" value="1.0"/>
18676 <param name="variance" value="1.0"/>
18677 </section>
18678 </section>
18679 <section name="Scores">
18680 <param name="use_shape_score" value="true"/>
18681 <param name="use_coelution_score" value="true"/>
18682 <param name="use_rt_score" value="true"/>
18683 <param name="use_library_score" value="true"/>
18684 <param name="use_elution_model_score" value="true"/>
18685 <param name="use_intensity_score" value="true"/>
18686 <param name="use_nr_peaks_score" value="true"/>
18687 <param name="use_total_xic_score" value="true"/>
18688 <param name="use_total_mi_score" value="true"/>
18689 <param name="use_sn_score" value="true"/>
18690 <param name="use_mi_score" value="false"/>
18691 <param name="use_dia_scores" value="true"/>
18692 <param name="use_ms1_correlation" value="false"/>
18693 <param name="use_sonar_scores" value="false"/>
18694 <param name="use_ion_mobility_scores" value="false"/>
18695 <param name="use_ms1_fullscan" value="false"/>
18696 <param name="use_ms1_mi" value="false"/>
18697 <param name="use_uis_scores" value="false"/>
18698 </section>
18699 </section>
18700 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18701 <output name="ctd_out" ftype="xml">
18702 <assert_contents>
18703 <is_valid_xml/>
18704 </assert_contents>
18705 </output>
18706 </test>
18707 </xml>
18708 <xml name="autotest_OpenSwathAssayGenerator">
18709 <test expect_num_outputs="2">
18710 <conditional name="adv_opts_cond">
18711 <param name="adv_opts_selector" value="advanced"/>
18712 <param name="max_num_alternative_localizations" value="10000"/>
18713 <param name="disable_identification_ms2_precursors" value="false"/>
18714 <param name="disable_identification_specific_losses" value="false"/>
18715 <param name="enable_identification_unspecific_losses" value="false"/>
18716 <param name="enable_swath_specifity" value="false"/>
18717 <param name="force" value="false"/>
18718 <param name="test" value="true"/>
18719 </conditional>
18720 <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
18721 <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
18722 <param name="out_type" value="TraML"/>
18723 <param name="min_transitions" value="6"/>
18724 <param name="max_transitions" value="6"/>
18725 <param name="allowed_fragment_types" value="b,y"/>
18726 <param name="allowed_fragment_charges" value="2,3"/>
18727 <param name="enable_detection_specific_losses" value="true"/>
18728 <param name="enable_detection_unspecific_losses" value="false"/>
18729 <param name="precursor_mz_threshold" value="0.025"/>
18730 <param name="precursor_lower_mz_limit" value="400.0"/>
18731 <param name="precursor_upper_mz_limit" value="1200.0"/>
18732 <param name="product_mz_threshold" value="0.025"/>
18733 <param name="product_lower_mz_limit" value="350.0"/>
18734 <param name="product_upper_mz_limit" value="2000.0"/>
18735 <param name="enable_ipf" value="false"/>
18736 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18737 <output name="ctd_out" ftype="xml">
18738 <assert_contents>
18739 <is_valid_xml/>
18740 </assert_contents>
18741 </output>
18742 </test>
18743 <test expect_num_outputs="2">
18744 <conditional name="adv_opts_cond">
18745 <param name="adv_opts_selector" value="advanced"/>
18746 <param name="max_num_alternative_localizations" value="10000"/>
18747 <param name="disable_identification_ms2_precursors" value="false"/>
18748 <param name="disable_identification_specific_losses" value="false"/>
18749 <param name="enable_identification_unspecific_losses" value="false"/>
18750 <param name="enable_swath_specifity" value="false"/>
18751 <param name="force" value="false"/>
18752 <param name="test" value="true"/>
18753 </conditional>
18754 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
18755 <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
18756 <param name="out_type" value="TraML"/>
18757 <param name="min_transitions" value="6"/>
18758 <param name="max_transitions" value="6"/>
18759 <param name="allowed_fragment_types" value="b,y"/>
18760 <param name="allowed_fragment_charges" value="1,2,3,4"/>
18761 <param name="enable_detection_specific_losses" value="false"/>
18762 <param name="enable_detection_unspecific_losses" value="false"/>
18763 <param name="precursor_mz_threshold" value="0.025"/>
18764 <param name="precursor_lower_mz_limit" value="400.0"/>
18765 <param name="precursor_upper_mz_limit" value="1200.0"/>
18766 <param name="product_mz_threshold" value="0.025"/>
18767 <param name="product_lower_mz_limit" value="350.0"/>
18768 <param name="product_upper_mz_limit" value="2000.0"/>
18769 <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/>
18770 <param name="enable_ipf" value="true"/>
18771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18772 <output name="ctd_out" ftype="xml">
18773 <assert_contents>
18774 <is_valid_xml/>
18775 </assert_contents>
18776 </output>
18777 </test>
18778 <test expect_num_outputs="2">
18779 <conditional name="adv_opts_cond">
18780 <param name="adv_opts_selector" value="advanced"/>
18781 <param name="max_num_alternative_localizations" value="10000"/>
18782 <param name="disable_identification_ms2_precursors" value="false"/>
18783 <param name="disable_identification_specific_losses" value="false"/>
18784 <param name="enable_identification_unspecific_losses" value="false"/>
18785 <param name="enable_swath_specifity" value="false"/>
18786 <param name="force" value="false"/>
18787 <param name="test" value="true"/>
18788 </conditional>
18789 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
18790 <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
18791 <param name="out_type" value="TraML"/>
18792 <param name="min_transitions" value="6"/>
18793 <param name="max_transitions" value="6"/>
18794 <param name="allowed_fragment_types" value="b,y"/>
18795 <param name="allowed_fragment_charges" value="1,2,3,4"/>
18796 <param name="enable_detection_specific_losses" value="false"/>
18797 <param name="enable_detection_unspecific_losses" value="false"/>
18798 <param name="precursor_mz_threshold" value="0.025"/>
18799 <param name="precursor_lower_mz_limit" value="400.0"/>
18800 <param name="precursor_upper_mz_limit" value="1200.0"/>
18801 <param name="product_mz_threshold" value="0.025"/>
18802 <param name="product_lower_mz_limit" value="350.0"/>
18803 <param name="product_upper_mz_limit" value="2000.0"/>
18804 <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/>
18805 <param name="enable_ipf" value="true"/>
18806 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18807 <output name="ctd_out" ftype="xml">
18808 <assert_contents>
18809 <is_valid_xml/>
18810 </assert_contents>
18811 </output>
18812 </test>
18813 </xml>
18814 <xml name="autotest_OpenSwathChromatogramExtractor">
18815 <test expect_num_outputs="2">
18816 <conditional name="adv_opts_cond">
18817 <param name="adv_opts_selector" value="advanced"/>
18818 <param name="extraction_function" value="tophat"/>
18819 <param name="force" value="false"/>
18820 <param name="test" value="true"/>
18821 </conditional>
18822 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18823 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
18824 <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18825 <param name="min_upper_edge_dist" value="0.0"/>
18826 <param name="rt_window" value="-1.0"/>
18827 <param name="ion_mobility_window" value="-1.0"/>
18828 <param name="mz_window" value="0.05"/>
18829 <param name="ppm" value="false"/>
18830 <param name="is_swath" value="false"/>
18831 <param name="extract_MS1" value="false"/>
18832 <section name="model">
18833 <param name="type" value="linear"/>
18834 <param name="symmetric_regression" value="false"/>
18835 </section>
18836 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18837 <output name="ctd_out" ftype="xml">
18838 <assert_contents>
18839 <is_valid_xml/>
18840 </assert_contents>
18841 </output>
18842 </test>
18843 <test expect_num_outputs="2">
18844 <conditional name="adv_opts_cond">
18845 <param name="adv_opts_selector" value="advanced"/>
18846 <param name="extraction_function" value="tophat"/>
18847 <param name="force" value="false"/>
18848 <param name="test" value="true"/>
18849 </conditional>
18850 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18851 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
18852 <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
18853 <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18854 <param name="min_upper_edge_dist" value="0.0"/>
18855 <param name="rt_window" value="50.0"/>
18856 <param name="ion_mobility_window" value="-1.0"/>
18857 <param name="mz_window" value="0.05"/>
18858 <param name="ppm" value="false"/>
18859 <param name="is_swath" value="false"/>
18860 <param name="extract_MS1" value="false"/>
18861 <section name="model">
18862 <param name="type" value="linear"/>
18863 <param name="symmetric_regression" value="false"/>
18864 </section>
18865 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18866 <output name="ctd_out" ftype="xml">
18867 <assert_contents>
18868 <is_valid_xml/>
18869 </assert_contents>
18870 </output>
18871 </test>
18872 <test expect_num_outputs="2">
18873 <conditional name="adv_opts_cond">
18874 <param name="adv_opts_selector" value="advanced"/>
18875 <param name="extraction_function" value="tophat"/>
18876 <param name="force" value="false"/>
18877 <param name="test" value="true"/>
18878 </conditional>
18879 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18880 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
18881 <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18882 <param name="min_upper_edge_dist" value="0.0"/>
18883 <param name="rt_window" value="-1.0"/>
18884 <param name="ion_mobility_window" value="-1.0"/>
18885 <param name="mz_window" value="0.05"/>
18886 <param name="ppm" value="false"/>
18887 <param name="is_swath" value="false"/>
18888 <param name="extract_MS1" value="true"/>
18889 <section name="model">
18890 <param name="type" value="linear"/>
18891 <param name="symmetric_regression" value="false"/>
18892 </section>
18893 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18894 <output name="ctd_out" ftype="xml">
18895 <assert_contents>
18896 <is_valid_xml/>
18897 </assert_contents>
18898 </output>
18899 </test>
18900 <test expect_num_outputs="2">
18901 <conditional name="adv_opts_cond">
18902 <param name="adv_opts_selector" value="advanced"/>
18903 <param name="extraction_function" value="tophat"/>
18904 <param name="force" value="false"/>
18905 <param name="test" value="true"/>
18906 </conditional>
18907 <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
18908 <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
18909 <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18910 <param name="min_upper_edge_dist" value="0.0"/>
18911 <param name="rt_window" value="-1.0"/>
18912 <param name="ion_mobility_window" value="0.05"/>
18913 <param name="mz_window" value="0.05"/>
18914 <param name="ppm" value="false"/>
18915 <param name="is_swath" value="true"/>
18916 <param name="extract_MS1" value="false"/>
18917 <section name="model">
18918 <param name="type" value="linear"/>
18919 <param name="symmetric_regression" value="false"/>
18920 </section>
18921 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18922 <output name="ctd_out" ftype="xml">
18923 <assert_contents>
18924 <is_valid_xml/>
18925 </assert_contents>
18926 </output>
18927 </test>
18928 <test expect_num_outputs="2">
18929 <conditional name="adv_opts_cond">
18930 <param name="adv_opts_selector" value="advanced"/>
18931 <param name="extraction_function" value="tophat"/>
18932 <param name="force" value="false"/>
18933 <param name="test" value="true"/>
18934 </conditional>
18935 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18936 <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
18937 <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18938 <param name="min_upper_edge_dist" value="0.0"/>
18939 <param name="rt_window" value="-1.0"/>
18940 <param name="ion_mobility_window" value="-1.0"/>
18941 <param name="mz_window" value="0.05"/>
18942 <param name="ppm" value="false"/>
18943 <param name="is_swath" value="false"/>
18944 <param name="extract_MS1" value="true"/>
18945 <section name="model">
18946 <param name="type" value="linear"/>
18947 <param name="symmetric_regression" value="false"/>
18948 </section>
18949 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18950 <output name="ctd_out" ftype="xml">
18951 <assert_contents>
18952 <is_valid_xml/>
18953 </assert_contents>
18954 </output>
18955 </test>
18956 </xml>
18957 <xml name="autotest_OpenSwathConfidenceScoring">
18958 <test expect_num_outputs="2">
18959 <conditional name="adv_opts_cond">
18960 <param name="adv_opts_selector" value="advanced"/>
18961 <param name="force" value="false"/>
18962 <param name="test" value="true"/>
18963 </conditional>
18964 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
18965 <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
18966 <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18967 <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
18968 <param name="decoys" value="1"/>
18969 <param name="transitions" value="2"/>
18970 <section name="GLM">
18971 <param name="intercept" value="3.87333466"/>
18972 <param name="delta_rt" value="-0.02898629"/>
18973 <param name="dist_int" value="-7.75880768"/>
18974 </section>
18975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18976 <output name="ctd_out" ftype="xml">
18977 <assert_contents>
18978 <is_valid_xml/>
18979 </assert_contents>
18980 </output>
18981 </test>
18982 </xml>
18983 <xml name="autotest_OpenSwathDecoyGenerator">
18984 <test expect_num_outputs="2">
18985 <conditional name="adv_opts_cond">
18986 <param name="adv_opts_selector" value="advanced"/>
18987 <param name="min_decoy_fraction" value="0.8"/>
18988 <param name="aim_decoy_fraction" value="1.0"/>
18989 <param name="shuffle_max_attempts" value="30"/>
18990 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
18991 <param name="shift_precursor_mz_shift" value="0.0"/>
18992 <param name="shift_product_mz_shift" value="20.0"/>
18993 <param name="product_mz_threshold" value="0.025"/>
18994 <param name="allowed_fragment_types" value="b,y"/>
18995 <param name="allowed_fragment_charges" value="1,2,3,4"/>
18996 <param name="enable_detection_specific_losses" value="false"/>
18997 <param name="enable_detection_unspecific_losses" value="false"/>
18998 <param name="separate" value="true"/>
18999 <param name="force" value="false"/>
19000 <param name="test" value="true"/>
19001 </conditional>
19002 <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/>
19003 <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
19004 <param name="out_type" value="TraML"/>
19005 <param name="method" value="pseudo-reverse"/>
19006 <param name="decoy_tag" value="DECOY_"/>
19007 <param name="switchKR" value="false"/>
19008 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19009 <output name="ctd_out" ftype="xml">
19010 <assert_contents>
19011 <is_valid_xml/>
19012 </assert_contents>
19013 </output>
19014 </test>
19015 <test expect_num_outputs="2">
19016 <conditional name="adv_opts_cond">
19017 <param name="adv_opts_selector" value="advanced"/>
19018 <param name="min_decoy_fraction" value="0.8"/>
19019 <param name="aim_decoy_fraction" value="1.0"/>
19020 <param name="shuffle_max_attempts" value="30"/>
19021 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
19022 <param name="shift_precursor_mz_shift" value="0.0"/>
19023 <param name="shift_product_mz_shift" value="20.0"/>
19024 <param name="product_mz_threshold" value="0.8"/>
19025 <param name="allowed_fragment_types" value="b,y"/>
19026 <param name="allowed_fragment_charges" value="1,2,3,4"/>
19027 <param name="enable_detection_specific_losses" value="false"/>
19028 <param name="enable_detection_unspecific_losses" value="false"/>
19029 <param name="separate" value="false"/>
19030 <param name="force" value="false"/>
19031 <param name="test" value="true"/>
19032 </conditional>
19033 <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/>
19034 <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
19035 <param name="out_type" value="TraML"/>
19036 <param name="method" value="pseudo-reverse"/>
19037 <param name="decoy_tag" value="DECOY_"/>
19038 <param name="switchKR" value="false"/>
19039 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19040 <output name="ctd_out" ftype="xml">
19041 <assert_contents>
19042 <is_valid_xml/>
19043 </assert_contents>
19044 </output>
19045 </test>
19046 <test expect_num_outputs="2">
19047 <conditional name="adv_opts_cond">
19048 <param name="adv_opts_selector" value="advanced"/>
19049 <param name="min_decoy_fraction" value="0.8"/>
19050 <param name="aim_decoy_fraction" value="1.0"/>
19051 <param name="shuffle_max_attempts" value="30"/>
19052 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
19053 <param name="shift_precursor_mz_shift" value="0.0"/>
19054 <param name="shift_product_mz_shift" value="20.0"/>
19055 <param name="product_mz_threshold" value="0.025"/>
19056 <param name="allowed_fragment_types" value="b,y"/>
19057 <param name="allowed_fragment_charges" value="1,2,3,4"/>
19058 <param name="enable_detection_specific_losses" value="false"/>
19059 <param name="enable_detection_unspecific_losses" value="false"/>
19060 <param name="separate" value="true"/>
19061 <param name="force" value="false"/>
19062 <param name="test" value="true"/>
19063 </conditional>
19064 <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/>
19065 <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
19066 <param name="out_type" value="TraML"/>
19067 <param name="method" value="pseudo-reverse"/>
19068 <param name="decoy_tag" value="DECOY_"/>
19069 <param name="switchKR" value="false"/>
19070 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19071 <output name="ctd_out" ftype="xml">
19072 <assert_contents>
19073 <is_valid_xml/>
19074 </assert_contents>
19075 </output>
19076 </test>
19077 <test expect_num_outputs="2">
19078 <conditional name="adv_opts_cond">
19079 <param name="adv_opts_selector" value="advanced"/>
19080 <param name="min_decoy_fraction" value="0.4"/>
19081 <param name="aim_decoy_fraction" value="1.0"/>
19082 <param name="shuffle_max_attempts" value="30"/>
19083 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
19084 <param name="shift_precursor_mz_shift" value="0.0"/>
19085 <param name="shift_product_mz_shift" value="20.0"/>
19086 <param name="product_mz_threshold" value="0.025"/>
19087 <param name="allowed_fragment_types" value="b,y"/>
19088 <param name="allowed_fragment_charges" value="1,2,3,4"/>
19089 <param name="enable_detection_specific_losses" value="true"/>
19090 <param name="enable_detection_unspecific_losses" value="true"/>
19091 <param name="separate" value="true"/>
19092 <param name="force" value="false"/>
19093 <param name="test" value="true"/>
19094 </conditional>
19095 <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/>
19096 <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/>
19097 <param name="out_type" value="TraML"/>
19098 <param name="method" value="pseudo-reverse"/>
19099 <param name="decoy_tag" value="DECOY_"/>
19100 <param name="switchKR" value="true"/>
19101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19102 <output name="ctd_out" ftype="xml">
19103 <assert_contents>
19104 <is_valid_xml/>
19105 </assert_contents>
19106 </output>
19107 </test>
19108 </xml>
19109 <xml name="autotest_OpenSwathDIAPreScoring">
19110 </xml>
19111 <xml name="autotest_OpenSwathFeatureXMLToTSV">
19112 <test expect_num_outputs="2">
19113 <conditional name="adv_opts_cond">
19114 <param name="adv_opts_selector" value="advanced"/>
19115 <param name="force" value="false"/>
19116 <param name="test" value="true"/>
19117 </conditional>
19118 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
19119 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
19120 <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
19121 <param name="short_format" value="true"/>
19122 <param name="best_scoring_peptide" value=""/>
19123 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19124 <output name="ctd_out" ftype="xml">
19125 <assert_contents>
19126 <is_valid_xml/>
19127 </assert_contents>
19128 </output>
19129 </test>
19130 <test expect_num_outputs="2">
19131 <conditional name="adv_opts_cond">
19132 <param name="adv_opts_selector" value="advanced"/>
19133 <param name="force" value="false"/>
19134 <param name="test" value="true"/>
19135 </conditional>
19136 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
19137 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
19138 <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/>
19139 <param name="short_format" value="false"/>
19140 <param name="best_scoring_peptide" value=""/>
19141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19142 <output name="ctd_out" ftype="xml">
19143 <assert_contents>
19144 <is_valid_xml/>
19145 </assert_contents>
19146 </output>
19147 </test>
19148 <test expect_num_outputs="2">
19149 <conditional name="adv_opts_cond">
19150 <param name="adv_opts_selector" value="advanced"/>
19151 <param name="force" value="false"/>
19152 <param name="test" value="true"/>
19153 </conditional>
19154 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
19155 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
19156 <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
19157 <param name="short_format" value="true"/>
19158 <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
19159 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19160 <output name="ctd_out" ftype="xml">
19161 <assert_contents>
19162 <is_valid_xml/>
19163 </assert_contents>
19164 </output>
19165 </test>
19166 </xml>
19167 <xml name="autotest_OpenSwathFileSplitter"/>
19168 <xml name="autotest_OpenSwathMzMLFileCacher">
19169 <test expect_num_outputs="2">
19170 <conditional name="adv_opts_cond">
19171 <param name="adv_opts_selector" value="advanced"/>
19172 <param name="lossy_mass_accuracy" value="-1.0"/>
19173 <param name="process_lowmemory" value="false"/>
19174 <param name="lowmem_batchsize" value="500"/>
19175 <param name="force" value="false"/>
19176 <param name="test" value="true"/>
19177 </conditional>
19178 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
19179 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19180 <param name="out_type" value="mzml"/>
19181 <param name="lossy_compression" value="true"/>
19182 <param name="full_meta" value="true"/>
19183 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19184 <output name="ctd_out" ftype="xml">
19185 <assert_contents>
19186 <is_valid_xml/>
19187 </assert_contents>
19188 </output>
19189 </test>
19190 <test expect_num_outputs="2">
19191 <conditional name="adv_opts_cond">
19192 <param name="adv_opts_selector" value="advanced"/>
19193 <param name="lossy_mass_accuracy" value="-1.0"/>
19194 <param name="process_lowmemory" value="false"/>
19195 <param name="lowmem_batchsize" value="500"/>
19196 <param name="force" value="false"/>
19197 <param name="test" value="true"/>
19198 </conditional>
19199 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
19200 <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19201 <param name="out_type" value="mzml"/>
19202 <param name="lossy_compression" value="true"/>
19203 <param name="full_meta" value="true"/>
19204 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19205 <output name="ctd_out" ftype="xml">
19206 <assert_contents>
19207 <is_valid_xml/>
19208 </assert_contents>
19209 </output>
19210 </test>
19211 <test expect_num_outputs="2">
19212 <conditional name="adv_opts_cond">
19213 <param name="adv_opts_selector" value="advanced"/>
19214 <param name="lossy_mass_accuracy" value="0.0001"/>
19215 <param name="process_lowmemory" value="false"/>
19216 <param name="lowmem_batchsize" value="500"/>
19217 <param name="force" value="false"/>
19218 <param name="test" value="true"/>
19219 </conditional>
19220 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
19221 <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
19222 <param name="out_type" value="sqmass"/>
19223 <param name="lossy_compression" value="true"/>
19224 <param name="full_meta" value="true"/>
19225 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19226 <output name="ctd_out" ftype="xml">
19227 <assert_contents>
19228 <is_valid_xml/>
19229 </assert_contents>
19230 </output>
19231 </test>
19232 <test expect_num_outputs="2">
19233 <conditional name="adv_opts_cond">
19234 <param name="adv_opts_selector" value="advanced"/>
19235 <param name="lossy_mass_accuracy" value="-1.0"/>
19236 <param name="process_lowmemory" value="false"/>
19237 <param name="lowmem_batchsize" value="500"/>
19238 <param name="force" value="false"/>
19239 <param name="test" value="true"/>
19240 </conditional>
19241 <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
19242 <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19243 <param name="out_type" value="mzml"/>
19244 <param name="lossy_compression" value="true"/>
19245 <param name="full_meta" value="true"/>
19246 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19247 <output name="ctd_out" ftype="xml">
19248 <assert_contents>
19249 <is_valid_xml/>
19250 </assert_contents>
19251 </output>
19252 </test>
19253 <test expect_num_outputs="2">
19254 <conditional name="adv_opts_cond">
19255 <param name="adv_opts_selector" value="advanced"/>
19256 <param name="lossy_mass_accuracy" value="-1.0"/>
19257 <param name="process_lowmemory" value="false"/>
19258 <param name="lowmem_batchsize" value="500"/>
19259 <param name="force" value="false"/>
19260 <param name="test" value="true"/>
19261 </conditional>
19262 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
19263 <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
19264 <param name="out_type" value="sqmass"/>
19265 <param name="lossy_compression" value="true"/>
19266 <param name="full_meta" value="true"/>
19267 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19268 <output name="ctd_out" ftype="xml">
19269 <assert_contents>
19270 <is_valid_xml/>
19271 </assert_contents>
19272 </output>
19273 </test>
19274 <test expect_num_outputs="2">
19275 <conditional name="adv_opts_cond">
19276 <param name="adv_opts_selector" value="advanced"/>
19277 <param name="lossy_mass_accuracy" value="-1.0"/>
19278 <param name="process_lowmemory" value="false"/>
19279 <param name="lowmem_batchsize" value="500"/>
19280 <param name="force" value="false"/>
19281 <param name="test" value="true"/>
19282 </conditional>
19283 <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
19284 <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19285 <param name="out_type" value="mzml"/>
19286 <param name="lossy_compression" value="true"/>
19287 <param name="full_meta" value="true"/>
19288 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19289 <output name="ctd_out" ftype="xml">
19290 <assert_contents>
19291 <is_valid_xml/>
19292 </assert_contents>
19293 </output>
19294 </test>
19295 <test expect_num_outputs="2">
19296 <conditional name="adv_opts_cond">
19297 <param name="adv_opts_selector" value="advanced"/>
19298 <param name="lossy_mass_accuracy" value="-1.0"/>
19299 <param name="process_lowmemory" value="true"/>
19300 <param name="lowmem_batchsize" value="500"/>
19301 <param name="force" value="false"/>
19302 <param name="test" value="true"/>
19303 </conditional>
19304 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
19305 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19306 <param name="out_type" value="mzml"/>
19307 <param name="lossy_compression" value="true"/>
19308 <param name="full_meta" value="true"/>
19309 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19310 <output name="ctd_out" ftype="xml">
19311 <assert_contents>
19312 <is_valid_xml/>
19313 </assert_contents>
19314 </output>
19315 </test>
19316 <test expect_num_outputs="2">
19317 <conditional name="adv_opts_cond">
19318 <param name="adv_opts_selector" value="advanced"/>
19319 <param name="lossy_mass_accuracy" value="-1.0"/>
19320 <param name="process_lowmemory" value="false"/>
19321 <param name="lowmem_batchsize" value="500"/>
19322 <param name="force" value="false"/>
19323 <param name="test" value="true"/>
19324 </conditional>
19325 <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
19326 <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/>
19327 <param name="out_type" value="mzML"/>
19328 <param name="lossy_compression" value="true"/>
19329 <param name="full_meta" value="true"/>
19330 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19331 <output name="ctd_out" ftype="xml">
19332 <assert_contents>
19333 <is_valid_xml/>
19334 </assert_contents>
19335 </output>
19336 </test>
19337 <test expect_num_outputs="2">
19338 <conditional name="adv_opts_cond">
19339 <param name="adv_opts_selector" value="advanced"/>
19340 <param name="lossy_mass_accuracy" value="-1.0"/>
19341 <param name="process_lowmemory" value="false"/>
19342 <param name="lowmem_batchsize" value="500"/>
19343 <param name="force" value="false"/>
19344 <param name="test" value="true"/>
19345 </conditional>
19346 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
19347 <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/>
19348 <param name="out_type" value="mzML"/>
19349 <param name="lossy_compression" value="true"/>
19350 <param name="full_meta" value="true"/>
19351 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19352 <output name="ctd_out" ftype="xml">
19353 <assert_contents>
19354 <is_valid_xml/>
19355 </assert_contents>
19356 </output>
19357 </test>
19358 <test expect_num_outputs="2">
19359 <conditional name="adv_opts_cond">
19360 <param name="adv_opts_selector" value="advanced"/>
19361 <param name="lossy_mass_accuracy" value="0.0001"/>
19362 <param name="process_lowmemory" value="false"/>
19363 <param name="lowmem_batchsize" value="500"/>
19364 <param name="force" value="false"/>
19365 <param name="test" value="true"/>
19366 </conditional>
19367 <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/>
19368 <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19369 <param name="out_type" value="mzml"/>
19370 <param name="lossy_compression" value="false"/>
19371 <param name="full_meta" value="false"/>
19372 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19373 <output name="ctd_out" ftype="xml">
19374 <assert_contents>
19375 <is_valid_xml/>
19376 </assert_contents>
19377 </output>
19378 </test>
19379 </xml>
19380 <xml name="autotest_OpenSwathRewriteToFeatureXML">
19381 </xml>
19382 <xml name="autotest_OpenSwathRTNormalizer">
19383 <test expect_num_outputs="2">
19384 <conditional name="adv_opts_cond">
19385 <param name="adv_opts_selector" value="advanced"/>
19386 <param name="force" value="false"/>
19387 <param name="test" value="true"/>
19388 </conditional>
19389 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
19390 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
19391 <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
19392 <param name="min_rsq" value="0.95"/>
19393 <param name="min_coverage" value="0.6"/>
19394 <param name="estimateBestPeptides" value="false"/>
19395 <section name="RTNormalization">
19396 <param name="outlierMethod" value="iter_residual"/>
19397 <param name="useIterativeChauvenet" value="false"/>
19398 <param name="RANSACMaxIterations" value="1000"/>
19399 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19400 <param name="RANSACSamplingSize" value="10"/>
19401 </section>
19402 <section name="algorithm">
19403 <param name="stop_report_after_feature" value="-1"/>
19404 <param name="rt_extraction_window" value="-1.0"/>
19405 <param name="rt_normalization_factor" value="1.0"/>
19406 <param name="quantification_cutoff" value="0.0"/>
19407 <param name="write_convex_hull" value="false"/>
19408 <param name="spectrum_addition_method" value="simple"/>
19409 <param name="add_up_spectra" value="1"/>
19410 <param name="spacing_for_spectra_resampling" value="0.005"/>
19411 <param name="uis_threshold_sn" value="-1"/>
19412 <param name="uis_threshold_peak_area" value="0"/>
19413 <param name="scoring_model" value="default"/>
19414 <param name="im_extra_drift" value="0.0"/>
19415 <param name="strict" value="true"/>
19416 <section name="TransitionGroupPicker">
19417 <param name="stop_after_feature" value="-1"/>
19418 <param name="stop_after_intensity_ratio" value="0.0001"/>
19419 <param name="min_peak_width" value="-1.0"/>
19420 <param name="peak_integration" value="original"/>
19421 <param name="background_subtraction" value="none"/>
19422 <param name="recalculate_peaks" value="false"/>
19423 <param name="use_precursors" value="false"/>
19424 <param name="use_consensus" value="true"/>
19425 <param name="recalculate_peaks_max_z" value="1.0"/>
19426 <param name="minimal_quality" value="-10000.0"/>
19427 <param name="resample_boundary" value="15.0"/>
19428 <param name="compute_peak_quality" value="false"/>
19429 <param name="compute_peak_shape_metrics" value="false"/>
19430 <param name="compute_total_mi" value="false"/>
19431 <param name="boundary_selection_method" value="largest"/>
19432 <section name="PeakPickerMRM">
19433 <param name="sgolay_frame_length" value="15"/>
19434 <param name="sgolay_polynomial_order" value="3"/>
19435 <param name="gauss_width" value="50.0"/>
19436 <param name="use_gauss" value="true"/>
19437 <param name="peak_width" value="-1.0"/>
19438 <param name="signal_to_noise" value="1.0"/>
19439 <param name="sn_win_len" value="1000.0"/>
19440 <param name="sn_bin_count" value="30"/>
19441 <param name="write_sn_log_messages" value="false"/>
19442 <param name="remove_overlapping_peaks" value="false"/>
19443 <param name="method" value="corrected"/>
19444 </section>
19445 <section name="PeakIntegrator">
19446 <param name="integration_type" value="intensity_sum"/>
19447 <param name="baseline_type" value="base_to_base"/>
19448 <param name="fit_EMG" value="false"/>
19449 </section>
19450 </section>
19451 <section name="DIAScoring">
19452 <param name="dia_extraction_window" value="0.05"/>
19453 <param name="dia_extraction_unit" value="Th"/>
19454 <param name="dia_centroided" value="false"/>
19455 <param name="dia_byseries_intensity_min" value="300.0"/>
19456 <param name="dia_byseries_ppm_diff" value="10.0"/>
19457 <param name="dia_nr_isotopes" value="4"/>
19458 <param name="dia_nr_charges" value="4"/>
19459 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19460 </section>
19461 <section name="EMGScoring">
19462 <param name="interpolation_step" value="0.2"/>
19463 <param name="tolerance_stdev_bounding_box" value="3.0"/>
19464 <param name="max_iteration" value="500"/>
19465 <section name="statistics">
19466 <param name="mean" value="1.0"/>
19467 <param name="variance" value="1.0"/>
19468 </section>
19469 </section>
19470 <section name="Scores">
19471 <param name="use_shape_score" value="true"/>
19472 <param name="use_coelution_score" value="true"/>
19473 <param name="use_rt_score" value="true"/>
19474 <param name="use_library_score" value="true"/>
19475 <param name="use_elution_model_score" value="true"/>
19476 <param name="use_intensity_score" value="true"/>
19477 <param name="use_nr_peaks_score" value="true"/>
19478 <param name="use_total_xic_score" value="true"/>
19479 <param name="use_total_mi_score" value="false"/>
19480 <param name="use_sn_score" value="true"/>
19481 <param name="use_mi_score" value="false"/>
19482 <param name="use_dia_scores" value="true"/>
19483 <param name="use_ms1_correlation" value="false"/>
19484 <param name="use_sonar_scores" value="false"/>
19485 <param name="use_ion_mobility_scores" value="false"/>
19486 <param name="use_ms1_fullscan" value="false"/>
19487 <param name="use_ms1_mi" value="false"/>
19488 <param name="use_uis_scores" value="false"/>
19489 </section>
19490 </section>
19491 <section name="peptideEstimation">
19492 <param name="InitialQualityCutoff" value="0.5"/>
19493 <param name="OverallQualityCutoff" value="5.5"/>
19494 <param name="NrRTBins" value="10"/>
19495 <param name="MinPeptidesPerBin" value="1"/>
19496 <param name="MinBinsFilled" value="8"/>
19497 </section>
19498 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19499 <output name="ctd_out" ftype="xml">
19500 <assert_contents>
19501 <is_valid_xml/>
19502 </assert_contents>
19503 </output>
19504 </test>
19505 <test expect_num_outputs="2">
19506 <conditional name="adv_opts_cond">
19507 <param name="adv_opts_selector" value="advanced"/>
19508 <param name="force" value="false"/>
19509 <param name="test" value="true"/>
19510 </conditional>
19511 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
19512 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
19513 <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
19514 <param name="min_rsq" value="0.95"/>
19515 <param name="min_coverage" value="0.6"/>
19516 <param name="estimateBestPeptides" value="true"/>
19517 <section name="RTNormalization">
19518 <param name="outlierMethod" value="iter_residual"/>
19519 <param name="useIterativeChauvenet" value="false"/>
19520 <param name="RANSACMaxIterations" value="1000"/>
19521 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19522 <param name="RANSACSamplingSize" value="10"/>
19523 </section>
19524 <section name="algorithm">
19525 <param name="stop_report_after_feature" value="-1"/>
19526 <param name="rt_extraction_window" value="-1.0"/>
19527 <param name="rt_normalization_factor" value="1.0"/>
19528 <param name="quantification_cutoff" value="0.0"/>
19529 <param name="write_convex_hull" value="false"/>
19530 <param name="spectrum_addition_method" value="simple"/>
19531 <param name="add_up_spectra" value="1"/>
19532 <param name="spacing_for_spectra_resampling" value="0.005"/>
19533 <param name="uis_threshold_sn" value="-1"/>
19534 <param name="uis_threshold_peak_area" value="0"/>
19535 <param name="scoring_model" value="default"/>
19536 <param name="im_extra_drift" value="0.0"/>
19537 <param name="strict" value="true"/>
19538 <section name="TransitionGroupPicker">
19539 <param name="stop_after_feature" value="-1"/>
19540 <param name="stop_after_intensity_ratio" value="0.0001"/>
19541 <param name="min_peak_width" value="-1.0"/>
19542 <param name="peak_integration" value="original"/>
19543 <param name="background_subtraction" value="none"/>
19544 <param name="recalculate_peaks" value="false"/>
19545 <param name="use_precursors" value="false"/>
19546 <param name="use_consensus" value="true"/>
19547 <param name="recalculate_peaks_max_z" value="1.0"/>
19548 <param name="minimal_quality" value="-10000.0"/>
19549 <param name="resample_boundary" value="15.0"/>
19550 <param name="compute_peak_quality" value="false"/>
19551 <param name="compute_peak_shape_metrics" value="false"/>
19552 <param name="compute_total_mi" value="false"/>
19553 <param name="boundary_selection_method" value="largest"/>
19554 <section name="PeakPickerMRM">
19555 <param name="sgolay_frame_length" value="15"/>
19556 <param name="sgolay_polynomial_order" value="3"/>
19557 <param name="gauss_width" value="50.0"/>
19558 <param name="use_gauss" value="true"/>
19559 <param name="peak_width" value="-1.0"/>
19560 <param name="signal_to_noise" value="1.0"/>
19561 <param name="sn_win_len" value="1000.0"/>
19562 <param name="sn_bin_count" value="30"/>
19563 <param name="write_sn_log_messages" value="false"/>
19564 <param name="remove_overlapping_peaks" value="false"/>
19565 <param name="method" value="corrected"/>
19566 </section>
19567 <section name="PeakIntegrator">
19568 <param name="integration_type" value="intensity_sum"/>
19569 <param name="baseline_type" value="base_to_base"/>
19570 <param name="fit_EMG" value="false"/>
19571 </section>
19572 </section>
19573 <section name="DIAScoring">
19574 <param name="dia_extraction_window" value="0.05"/>
19575 <param name="dia_extraction_unit" value="Th"/>
19576 <param name="dia_centroided" value="false"/>
19577 <param name="dia_byseries_intensity_min" value="300.0"/>
19578 <param name="dia_byseries_ppm_diff" value="10.0"/>
19579 <param name="dia_nr_isotopes" value="4"/>
19580 <param name="dia_nr_charges" value="4"/>
19581 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19582 </section>
19583 <section name="EMGScoring">
19584 <param name="interpolation_step" value="0.2"/>
19585 <param name="tolerance_stdev_bounding_box" value="3.0"/>
19586 <param name="max_iteration" value="500"/>
19587 <section name="statistics">
19588 <param name="mean" value="1.0"/>
19589 <param name="variance" value="1.0"/>
19590 </section>
19591 </section>
19592 <section name="Scores">
19593 <param name="use_shape_score" value="true"/>
19594 <param name="use_coelution_score" value="true"/>
19595 <param name="use_rt_score" value="true"/>
19596 <param name="use_library_score" value="true"/>
19597 <param name="use_elution_model_score" value="true"/>
19598 <param name="use_intensity_score" value="true"/>
19599 <param name="use_nr_peaks_score" value="true"/>
19600 <param name="use_total_xic_score" value="true"/>
19601 <param name="use_total_mi_score" value="false"/>
19602 <param name="use_sn_score" value="true"/>
19603 <param name="use_mi_score" value="false"/>
19604 <param name="use_dia_scores" value="true"/>
19605 <param name="use_ms1_correlation" value="false"/>
19606 <param name="use_sonar_scores" value="false"/>
19607 <param name="use_ion_mobility_scores" value="false"/>
19608 <param name="use_ms1_fullscan" value="false"/>
19609 <param name="use_ms1_mi" value="false"/>
19610 <param name="use_uis_scores" value="false"/>
19611 </section>
19612 </section>
19613 <section name="peptideEstimation">
19614 <param name="InitialQualityCutoff" value="0.5"/>
19615 <param name="OverallQualityCutoff" value="5.5"/>
19616 <param name="NrRTBins" value="3"/>
19617 <param name="MinPeptidesPerBin" value="1"/>
19618 <param name="MinBinsFilled" value="3"/>
19619 </section>
19620 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19621 <output name="ctd_out" ftype="xml">
19622 <assert_contents>
19623 <is_valid_xml/>
19624 </assert_contents>
19625 </output>
19626 </test>
19627 <test expect_num_outputs="2">
19628 <conditional name="adv_opts_cond">
19629 <param name="adv_opts_selector" value="advanced"/>
19630 <param name="force" value="false"/>
19631 <param name="test" value="true"/>
19632 </conditional>
19633 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
19634 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
19635 <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
19636 <param name="min_rsq" value="0.95"/>
19637 <param name="min_coverage" value="0.6"/>
19638 <param name="estimateBestPeptides" value="false"/>
19639 <section name="RTNormalization">
19640 <param name="outlierMethod" value="iter_residual"/>
19641 <param name="useIterativeChauvenet" value="false"/>
19642 <param name="RANSACMaxIterations" value="1000"/>
19643 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19644 <param name="RANSACSamplingSize" value="10"/>
19645 </section>
19646 <section name="algorithm">
19647 <param name="stop_report_after_feature" value="-1"/>
19648 <param name="rt_extraction_window" value="-1.0"/>
19649 <param name="rt_normalization_factor" value="1.0"/>
19650 <param name="quantification_cutoff" value="0.0"/>
19651 <param name="write_convex_hull" value="false"/>
19652 <param name="spectrum_addition_method" value="simple"/>
19653 <param name="add_up_spectra" value="1"/>
19654 <param name="spacing_for_spectra_resampling" value="0.005"/>
19655 <param name="uis_threshold_sn" value="-1"/>
19656 <param name="uis_threshold_peak_area" value="0"/>
19657 <param name="scoring_model" value="default"/>
19658 <param name="im_extra_drift" value="0.0"/>
19659 <param name="strict" value="true"/>
19660 <section name="TransitionGroupPicker">
19661 <param name="stop_after_feature" value="-1"/>
19662 <param name="stop_after_intensity_ratio" value="0.0001"/>
19663 <param name="min_peak_width" value="-1.0"/>
19664 <param name="peak_integration" value="original"/>
19665 <param name="background_subtraction" value="none"/>
19666 <param name="recalculate_peaks" value="false"/>
19667 <param name="use_precursors" value="false"/>
19668 <param name="use_consensus" value="true"/>
19669 <param name="recalculate_peaks_max_z" value="1.0"/>
19670 <param name="minimal_quality" value="-10000.0"/>
19671 <param name="resample_boundary" value="15.0"/>
19672 <param name="compute_peak_quality" value="false"/>
19673 <param name="compute_peak_shape_metrics" value="false"/>
19674 <param name="compute_total_mi" value="false"/>
19675 <param name="boundary_selection_method" value="largest"/>
19676 <section name="PeakPickerMRM">
19677 <param name="sgolay_frame_length" value="15"/>
19678 <param name="sgolay_polynomial_order" value="3"/>
19679 <param name="gauss_width" value="50.0"/>
19680 <param name="use_gauss" value="true"/>
19681 <param name="peak_width" value="-1.0"/>
19682 <param name="signal_to_noise" value="1.0"/>
19683 <param name="sn_win_len" value="1000.0"/>
19684 <param name="sn_bin_count" value="30"/>
19685 <param name="write_sn_log_messages" value="false"/>
19686 <param name="remove_overlapping_peaks" value="false"/>
19687 <param name="method" value="corrected"/>
19688 </section>
19689 <section name="PeakIntegrator">
19690 <param name="integration_type" value="intensity_sum"/>
19691 <param name="baseline_type" value="base_to_base"/>
19692 <param name="fit_EMG" value="false"/>
19693 </section>
19694 </section>
19695 <section name="DIAScoring">
19696 <param name="dia_extraction_window" value="0.05"/>
19697 <param name="dia_extraction_unit" value="Th"/>
19698 <param name="dia_centroided" value="false"/>
19699 <param name="dia_byseries_intensity_min" value="300.0"/>
19700 <param name="dia_byseries_ppm_diff" value="10.0"/>
19701 <param name="dia_nr_isotopes" value="4"/>
19702 <param name="dia_nr_charges" value="4"/>
19703 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19704 </section>
19705 <section name="EMGScoring">
19706 <param name="interpolation_step" value="0.2"/>
19707 <param name="tolerance_stdev_bounding_box" value="3.0"/>
19708 <param name="max_iteration" value="500"/>
19709 <section name="statistics">
19710 <param name="mean" value="1.0"/>
19711 <param name="variance" value="1.0"/>
19712 </section>
19713 </section>
19714 <section name="Scores">
19715 <param name="use_shape_score" value="true"/>
19716 <param name="use_coelution_score" value="true"/>
19717 <param name="use_rt_score" value="true"/>
19718 <param name="use_library_score" value="true"/>
19719 <param name="use_elution_model_score" value="true"/>
19720 <param name="use_intensity_score" value="true"/>
19721 <param name="use_nr_peaks_score" value="true"/>
19722 <param name="use_total_xic_score" value="true"/>
19723 <param name="use_total_mi_score" value="false"/>
19724 <param name="use_sn_score" value="true"/>
19725 <param name="use_mi_score" value="false"/>
19726 <param name="use_dia_scores" value="true"/>
19727 <param name="use_ms1_correlation" value="false"/>
19728 <param name="use_sonar_scores" value="false"/>
19729 <param name="use_ion_mobility_scores" value="false"/>
19730 <param name="use_ms1_fullscan" value="false"/>
19731 <param name="use_ms1_mi" value="false"/>
19732 <param name="use_uis_scores" value="false"/>
19733 </section>
19734 </section>
19735 <section name="peptideEstimation">
19736 <param name="InitialQualityCutoff" value="0.5"/>
19737 <param name="OverallQualityCutoff" value="5.5"/>
19738 <param name="NrRTBins" value="10"/>
19739 <param name="MinPeptidesPerBin" value="1"/>
19740 <param name="MinBinsFilled" value="8"/>
19741 </section>
19742 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
19743 <output name="ctd_out" ftype="xml">
19744 <assert_contents>
19745 <is_valid_xml/>
19746 </assert_contents>
19747 </output>
19748 </test>
19749 </xml>
19750 <xml name="autotest_OpenSwathWorkflow">
19751 <test expect_num_outputs="4">
19752 <conditional name="adv_opts_cond">
19753 <param name="adv_opts_selector" value="advanced"/>
19754 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19755 <param name="sort_swath_maps" value="false"/>
19756 <param name="enable_ms1" value="false"/>
19757 <param name="enable_ipf" value="true"/>
19758 <param name="out_chrom_type" value="mzML"/>
19759 <param name="min_upper_edge_dist" value="0.0"/>
19760 <param name="extra_rt_extraction_window" value="0.0"/>
19761 <param name="mz_extraction_window_unit" value="ppm"/>
19762 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
19763 <param name="use_ms1_ion_mobility" value="true"/>
19764 <param name="matching_window_only" value="false"/>
19765 <param name="irt_mz_extraction_window" value="50.0"/>
19766 <param name="irt_mz_extraction_window_unit" value="ppm"/>
19767 <param name="irt_im_extraction_window" value="-1.0"/>
19768 <param name="min_rsq" value="0.95"/>
19769 <param name="min_coverage" value="0.6"/>
19770 <param name="split_file_input" value="false"/>
19771 <param name="use_elution_model_score" value="false"/>
19772 <param name="readOptions" value="normal"/>
19773 <param name="mz_correction_function" value="none"/>
19774 <param name="extraction_function" value="tophat"/>
19775 <param name="batchSize" value="1000"/>
19776 <param name="ms1_isotopes" value="3"/>
19777 <param name="force" value="false"/>
19778 <param name="test" value="false"/>
19779 </conditional>
19780 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19781 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19782 <param name="tr_type" value=""/>
19783 <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19784 <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19785 <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/>
19786 <param name="sonar" value="false"/>
19787 <param name="rt_extraction_window" value="600.0"/>
19788 <param name="ion_mobility_window" value="-1.0"/>
19789 <param name="mz_extraction_window" value="50.0"/>
19790 <param name="mz_extraction_window_ms1" value="50.0"/>
19791 <param name="im_extraction_window_ms1" value="-1.0"/>
19792 <section name="Debugging"/>
19793 <section name="Calibration">
19794 <param name="ms1_im_calibration" value="false"/>
19795 <param name="im_correction_function" value="linear"/>
19796 <param name="debug_im_file" value=""/>
19797 <param name="debug_mz_file" value=""/>
19798 </section>
19799 <section name="Library">
19800 <param name="retentionTimeInterpretation" value="iRT"/>
19801 <param name="override_group_label_check" value="false"/>
19802 <param name="force_invalid_mods" value="false"/>
19803 </section>
19804 <section name="RTNormalization">
19805 <param name="alignmentMethod" value="linear"/>
19806 <param name="outlierMethod" value="iter_residual"/>
19807 <param name="useIterativeChauvenet" value="false"/>
19808 <param name="RANSACMaxIterations" value="1000"/>
19809 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19810 <param name="RANSACSamplingSize" value="10"/>
19811 <param name="estimateBestPeptides" value="false"/>
19812 <param name="InitialQualityCutoff" value="0.5"/>
19813 <param name="OverallQualityCutoff" value="5.5"/>
19814 <param name="NrRTBins" value="10"/>
19815 <param name="MinPeptidesPerBin" value="1"/>
19816 <param name="MinBinsFilled" value="8"/>
19817 <section name="lowess">
19818 <param name="span" value="0.05"/>
19819 </section>
19820 <section name="b_spline">
19821 <param name="num_nodes" value="5"/>
19822 </section>
19823 </section>
19824 <section name="Scoring">
19825 <param name="stop_report_after_feature" value="5"/>
19826 <param name="rt_normalization_factor" value="100.0"/>
19827 <param name="quantification_cutoff" value="0.0"/>
19828 <param name="write_convex_hull" value="false"/>
19829 <param name="spectrum_addition_method" value="simple"/>
19830 <param name="add_up_spectra" value="1"/>
19831 <param name="spacing_for_spectra_resampling" value="0.005"/>
19832 <param name="uis_threshold_sn" value="-1"/>
19833 <param name="uis_threshold_peak_area" value="0"/>
19834 <param name="scoring_model" value="default"/>
19835 <param name="im_extra_drift" value="0.0"/>
19836 <param name="strict" value="true"/>
19837 <section name="TransitionGroupPicker">
19838 <param name="stop_after_feature" value="-1"/>
19839 <param name="min_peak_width" value="-1.0"/>
19840 <param name="peak_integration" value="original"/>
19841 <param name="background_subtraction" value="none"/>
19842 <param name="recalculate_peaks" value="true"/>
19843 <param name="use_precursors" value="false"/>
19844 <param name="use_consensus" value="true"/>
19845 <param name="recalculate_peaks_max_z" value="0.75"/>
19846 <param name="minimal_quality" value="-1.5"/>
19847 <param name="resample_boundary" value="15.0"/>
19848 <param name="compute_peak_quality" value="false"/>
19849 <param name="compute_peak_shape_metrics" value="false"/>
19850 <param name="compute_total_mi" value="false"/>
19851 <param name="boundary_selection_method" value="largest"/>
19852 <section name="PeakPickerMRM">
19853 <param name="sgolay_frame_length" value="11"/>
19854 <param name="sgolay_polynomial_order" value="3"/>
19855 <param name="gauss_width" value="30.0"/>
19856 <param name="use_gauss" value="false"/>
19857 <param name="peak_width" value="-1.0"/>
19858 <param name="signal_to_noise" value="0.1"/>
19859 <param name="write_sn_log_messages" value="false"/>
19860 <param name="remove_overlapping_peaks" value="true"/>
19861 <param name="method" value="corrected"/>
19862 </section>
19863 <section name="PeakIntegrator">
19864 <param name="integration_type" value="intensity_sum"/>
19865 <param name="baseline_type" value="base_to_base"/>
19866 <param name="fit_EMG" value="false"/>
19867 </section>
19868 </section>
19869 <section name="DIAScoring">
19870 <param name="dia_extraction_window" value="0.05"/>
19871 <param name="dia_extraction_unit" value="Th"/>
19872 <param name="dia_centroided" value="false"/>
19873 <param name="dia_byseries_intensity_min" value="300.0"/>
19874 <param name="dia_byseries_ppm_diff" value="10.0"/>
19875 <param name="dia_nr_isotopes" value="4"/>
19876 <param name="dia_nr_charges" value="4"/>
19877 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19878 </section>
19879 <section name="EMGScoring">
19880 <param name="max_iteration" value="10"/>
19881 </section>
19882 <section name="Scores">
19883 <param name="use_shape_score" value="true"/>
19884 <param name="use_coelution_score" value="true"/>
19885 <param name="use_rt_score" value="true"/>
19886 <param name="use_library_score" value="true"/>
19887 <param name="use_intensity_score" value="true"/>
19888 <param name="use_nr_peaks_score" value="true"/>
19889 <param name="use_total_xic_score" value="true"/>
19890 <param name="use_total_mi_score" value="false"/>
19891 <param name="use_sn_score" value="true"/>
19892 <param name="use_mi_score" value="true"/>
19893 <param name="use_dia_scores" value="true"/>
19894 <param name="use_ms1_correlation" value="false"/>
19895 <param name="use_sonar_scores" value="false"/>
19896 <param name="use_ion_mobility_scores" value="false"/>
19897 <param name="use_ms1_fullscan" value="false"/>
19898 <param name="use_ms1_mi" value="true"/>
19899 <param name="use_uis_scores" value="false"/>
19900 </section>
19901 </section>
19902 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
19903 <output name="ctd_out" ftype="xml">
19904 <assert_contents>
19905 <is_valid_xml/>
19906 </assert_contents>
19907 </output>
19908 </test>
19909 <test expect_num_outputs="3">
19910 <conditional name="adv_opts_cond">
19911 <param name="adv_opts_selector" value="advanced"/>
19912 <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
19913 <param name="sort_swath_maps" value="false"/>
19914 <param name="enable_ms1" value="false"/>
19915 <param name="enable_ipf" value="true"/>
19916 <param name="out_chrom_type" value="mzML"/>
19917 <param name="min_upper_edge_dist" value="0.0"/>
19918 <param name="extra_rt_extraction_window" value="0.0"/>
19919 <param name="mz_extraction_window_unit" value="ppm"/>
19920 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
19921 <param name="use_ms1_ion_mobility" value="true"/>
19922 <param name="matching_window_only" value="false"/>
19923 <param name="irt_mz_extraction_window" value="50.0"/>
19924 <param name="irt_mz_extraction_window_unit" value="ppm"/>
19925 <param name="irt_im_extraction_window" value="-1.0"/>
19926 <param name="min_rsq" value="0.95"/>
19927 <param name="min_coverage" value="0.6"/>
19928 <param name="split_file_input" value="false"/>
19929 <param name="use_elution_model_score" value="false"/>
19930 <param name="readOptions" value="normal"/>
19931 <param name="mz_correction_function" value="none"/>
19932 <param name="extraction_function" value="tophat"/>
19933 <param name="batchSize" value="1000"/>
19934 <param name="ms1_isotopes" value="3"/>
19935 <param name="force" value="false"/>
19936 <param name="test" value="false"/>
19937 </conditional>
19938 <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
19939 <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
19940 <param name="tr_type" value=""/>
19941 <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19942 <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19943 <param name="sonar" value="false"/>
19944 <param name="rt_extraction_window" value="600.0"/>
19945 <param name="ion_mobility_window" value="-1.0"/>
19946 <param name="mz_extraction_window" value="50.0"/>
19947 <param name="mz_extraction_window_ms1" value="50.0"/>
19948 <param name="im_extraction_window_ms1" value="-1.0"/>
19949 <section name="Debugging"/>
19950 <section name="Calibration">
19951 <param name="ms1_im_calibration" value="false"/>
19952 <param name="im_correction_function" value="linear"/>
19953 <param name="debug_im_file" value=""/>
19954 <param name="debug_mz_file" value=""/>
19955 </section>
19956 <section name="Library">
19957 <param name="retentionTimeInterpretation" value="iRT"/>
19958 <param name="override_group_label_check" value="false"/>
19959 <param name="force_invalid_mods" value="false"/>
19960 </section>
19961 <section name="RTNormalization">
19962 <param name="alignmentMethod" value="linear"/>
19963 <param name="outlierMethod" value="iter_residual"/>
19964 <param name="useIterativeChauvenet" value="false"/>
19965 <param name="RANSACMaxIterations" value="1000"/>
19966 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19967 <param name="RANSACSamplingSize" value="10"/>
19968 <param name="estimateBestPeptides" value="false"/>
19969 <param name="InitialQualityCutoff" value="0.5"/>
19970 <param name="OverallQualityCutoff" value="5.5"/>
19971 <param name="NrRTBins" value="10"/>
19972 <param name="MinPeptidesPerBin" value="1"/>
19973 <param name="MinBinsFilled" value="8"/>
19974 <section name="lowess">
19975 <param name="span" value="0.05"/>
19976 </section>
19977 <section name="b_spline">
19978 <param name="num_nodes" value="5"/>
19979 </section>
19980 </section>
19981 <section name="Scoring">
19982 <param name="stop_report_after_feature" value="5"/>
19983 <param name="rt_normalization_factor" value="100.0"/>
19984 <param name="quantification_cutoff" value="0.0"/>
19985 <param name="write_convex_hull" value="false"/>
19986 <param name="spectrum_addition_method" value="simple"/>
19987 <param name="add_up_spectra" value="1"/>
19988 <param name="spacing_for_spectra_resampling" value="0.005"/>
19989 <param name="uis_threshold_sn" value="-1"/>
19990 <param name="uis_threshold_peak_area" value="0"/>
19991 <param name="scoring_model" value="default"/>
19992 <param name="im_extra_drift" value="0.0"/>
19993 <param name="strict" value="true"/>
19994 <section name="TransitionGroupPicker">
19995 <param name="stop_after_feature" value="-1"/>
19996 <param name="min_peak_width" value="-1.0"/>
19997 <param name="peak_integration" value="original"/>
19998 <param name="background_subtraction" value="none"/>
19999 <param name="recalculate_peaks" value="true"/>
20000 <param name="use_precursors" value="false"/>
20001 <param name="use_consensus" value="true"/>
20002 <param name="recalculate_peaks_max_z" value="0.75"/>
20003 <param name="minimal_quality" value="-1.5"/>
20004 <param name="resample_boundary" value="15.0"/>
20005 <param name="compute_peak_quality" value="false"/>
20006 <param name="compute_peak_shape_metrics" value="false"/>
20007 <param name="compute_total_mi" value="false"/>
20008 <param name="boundary_selection_method" value="largest"/>
20009 <section name="PeakPickerMRM">
20010 <param name="sgolay_frame_length" value="11"/>
20011 <param name="sgolay_polynomial_order" value="3"/>
20012 <param name="gauss_width" value="30.0"/>
20013 <param name="use_gauss" value="false"/>
20014 <param name="peak_width" value="-1.0"/>
20015 <param name="signal_to_noise" value="0.1"/>
20016 <param name="write_sn_log_messages" value="false"/>
20017 <param name="remove_overlapping_peaks" value="true"/>
20018 <param name="method" value="corrected"/>
20019 </section>
20020 <section name="PeakIntegrator">
20021 <param name="integration_type" value="intensity_sum"/>
20022 <param name="baseline_type" value="base_to_base"/>
20023 <param name="fit_EMG" value="false"/>
20024 </section>
20025 </section>
20026 <section name="DIAScoring">
20027 <param name="dia_extraction_window" value="0.05"/>
20028 <param name="dia_extraction_unit" value="Th"/>
20029 <param name="dia_centroided" value="false"/>
20030 <param name="dia_byseries_intensity_min" value="300.0"/>
20031 <param name="dia_byseries_ppm_diff" value="10.0"/>
20032 <param name="dia_nr_isotopes" value="4"/>
20033 <param name="dia_nr_charges" value="4"/>
20034 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20035 </section>
20036 <section name="EMGScoring">
20037 <param name="max_iteration" value="10"/>
20038 </section>
20039 <section name="Scores">
20040 <param name="use_shape_score" value="true"/>
20041 <param name="use_coelution_score" value="true"/>
20042 <param name="use_rt_score" value="true"/>
20043 <param name="use_library_score" value="true"/>
20044 <param name="use_intensity_score" value="true"/>
20045 <param name="use_nr_peaks_score" value="true"/>
20046 <param name="use_total_xic_score" value="true"/>
20047 <param name="use_total_mi_score" value="false"/>
20048 <param name="use_sn_score" value="true"/>
20049 <param name="use_mi_score" value="true"/>
20050 <param name="use_dia_scores" value="true"/>
20051 <param name="use_ms1_correlation" value="false"/>
20052 <param name="use_sonar_scores" value="false"/>
20053 <param name="use_ion_mobility_scores" value="false"/>
20054 <param name="use_ms1_fullscan" value="false"/>
20055 <param name="use_ms1_mi" value="true"/>
20056 <param name="use_uis_scores" value="false"/>
20057 </section>
20058 </section>
20059 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20060 <output name="ctd_out" ftype="xml">
20061 <assert_contents>
20062 <is_valid_xml/>
20063 </assert_contents>
20064 </output>
20065 </test>
20066 <test expect_num_outputs="3">
20067 <conditional name="adv_opts_cond">
20068 <param name="adv_opts_selector" value="advanced"/>
20069 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20070 <param name="sort_swath_maps" value="false"/>
20071 <param name="enable_ms1" value="true"/>
20072 <param name="enable_ipf" value="true"/>
20073 <param name="out_chrom_type" value="mzML"/>
20074 <param name="min_upper_edge_dist" value="0.0"/>
20075 <param name="extra_rt_extraction_window" value="0.0"/>
20076 <param name="mz_extraction_window_unit" value="ppm"/>
20077 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20078 <param name="use_ms1_ion_mobility" value="true"/>
20079 <param name="matching_window_only" value="false"/>
20080 <param name="irt_mz_extraction_window" value="50.0"/>
20081 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20082 <param name="irt_im_extraction_window" value="-1.0"/>
20083 <param name="min_rsq" value="0.95"/>
20084 <param name="min_coverage" value="0.6"/>
20085 <param name="split_file_input" value="false"/>
20086 <param name="use_elution_model_score" value="false"/>
20087 <param name="readOptions" value="normal"/>
20088 <param name="mz_correction_function" value="none"/>
20089 <param name="extraction_function" value="tophat"/>
20090 <param name="batchSize" value="1000"/>
20091 <param name="ms1_isotopes" value="3"/>
20092 <param name="force" value="false"/>
20093 <param name="test" value="false"/>
20094 </conditional>
20095 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20096 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20097 <param name="tr_type" value=""/>
20098 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20099 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20100 <param name="sonar" value="false"/>
20101 <param name="rt_extraction_window" value="600.0"/>
20102 <param name="ion_mobility_window" value="-1.0"/>
20103 <param name="mz_extraction_window" value="50.0"/>
20104 <param name="mz_extraction_window_ms1" value="50.0"/>
20105 <param name="im_extraction_window_ms1" value="-1.0"/>
20106 <section name="Debugging"/>
20107 <section name="Calibration">
20108 <param name="ms1_im_calibration" value="false"/>
20109 <param name="im_correction_function" value="linear"/>
20110 <param name="debug_im_file" value=""/>
20111 <param name="debug_mz_file" value=""/>
20112 </section>
20113 <section name="Library">
20114 <param name="retentionTimeInterpretation" value="iRT"/>
20115 <param name="override_group_label_check" value="false"/>
20116 <param name="force_invalid_mods" value="false"/>
20117 </section>
20118 <section name="RTNormalization">
20119 <param name="alignmentMethod" value="linear"/>
20120 <param name="outlierMethod" value="iter_residual"/>
20121 <param name="useIterativeChauvenet" value="false"/>
20122 <param name="RANSACMaxIterations" value="1000"/>
20123 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20124 <param name="RANSACSamplingSize" value="10"/>
20125 <param name="estimateBestPeptides" value="false"/>
20126 <param name="InitialQualityCutoff" value="0.5"/>
20127 <param name="OverallQualityCutoff" value="5.5"/>
20128 <param name="NrRTBins" value="10"/>
20129 <param name="MinPeptidesPerBin" value="1"/>
20130 <param name="MinBinsFilled" value="8"/>
20131 <section name="lowess">
20132 <param name="span" value="0.05"/>
20133 </section>
20134 <section name="b_spline">
20135 <param name="num_nodes" value="5"/>
20136 </section>
20137 </section>
20138 <section name="Scoring">
20139 <param name="stop_report_after_feature" value="5"/>
20140 <param name="rt_normalization_factor" value="100.0"/>
20141 <param name="quantification_cutoff" value="0.0"/>
20142 <param name="write_convex_hull" value="false"/>
20143 <param name="spectrum_addition_method" value="simple"/>
20144 <param name="add_up_spectra" value="1"/>
20145 <param name="spacing_for_spectra_resampling" value="0.005"/>
20146 <param name="uis_threshold_sn" value="-1"/>
20147 <param name="uis_threshold_peak_area" value="0"/>
20148 <param name="scoring_model" value="default"/>
20149 <param name="im_extra_drift" value="0.0"/>
20150 <param name="strict" value="true"/>
20151 <section name="TransitionGroupPicker">
20152 <param name="stop_after_feature" value="-1"/>
20153 <param name="min_peak_width" value="-1.0"/>
20154 <param name="peak_integration" value="original"/>
20155 <param name="background_subtraction" value="none"/>
20156 <param name="recalculate_peaks" value="true"/>
20157 <param name="use_precursors" value="false"/>
20158 <param name="use_consensus" value="true"/>
20159 <param name="recalculate_peaks_max_z" value="0.75"/>
20160 <param name="minimal_quality" value="-1.5"/>
20161 <param name="resample_boundary" value="15.0"/>
20162 <param name="compute_peak_quality" value="false"/>
20163 <param name="compute_peak_shape_metrics" value="false"/>
20164 <param name="compute_total_mi" value="false"/>
20165 <param name="boundary_selection_method" value="largest"/>
20166 <section name="PeakPickerMRM">
20167 <param name="sgolay_frame_length" value="11"/>
20168 <param name="sgolay_polynomial_order" value="3"/>
20169 <param name="gauss_width" value="30.0"/>
20170 <param name="use_gauss" value="false"/>
20171 <param name="peak_width" value="-1.0"/>
20172 <param name="signal_to_noise" value="0.1"/>
20173 <param name="write_sn_log_messages" value="false"/>
20174 <param name="remove_overlapping_peaks" value="true"/>
20175 <param name="method" value="corrected"/>
20176 </section>
20177 <section name="PeakIntegrator">
20178 <param name="integration_type" value="intensity_sum"/>
20179 <param name="baseline_type" value="base_to_base"/>
20180 <param name="fit_EMG" value="false"/>
20181 </section>
20182 </section>
20183 <section name="DIAScoring">
20184 <param name="dia_extraction_window" value="0.05"/>
20185 <param name="dia_extraction_unit" value="Th"/>
20186 <param name="dia_centroided" value="false"/>
20187 <param name="dia_byseries_intensity_min" value="300.0"/>
20188 <param name="dia_byseries_ppm_diff" value="10.0"/>
20189 <param name="dia_nr_isotopes" value="4"/>
20190 <param name="dia_nr_charges" value="4"/>
20191 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20192 </section>
20193 <section name="EMGScoring">
20194 <param name="max_iteration" value="10"/>
20195 </section>
20196 <section name="Scores">
20197 <param name="use_shape_score" value="true"/>
20198 <param name="use_coelution_score" value="true"/>
20199 <param name="use_rt_score" value="true"/>
20200 <param name="use_library_score" value="true"/>
20201 <param name="use_intensity_score" value="true"/>
20202 <param name="use_nr_peaks_score" value="true"/>
20203 <param name="use_total_xic_score" value="true"/>
20204 <param name="use_total_mi_score" value="false"/>
20205 <param name="use_sn_score" value="true"/>
20206 <param name="use_mi_score" value="true"/>
20207 <param name="use_dia_scores" value="true"/>
20208 <param name="use_ms1_correlation" value="false"/>
20209 <param name="use_sonar_scores" value="false"/>
20210 <param name="use_ion_mobility_scores" value="false"/>
20211 <param name="use_ms1_fullscan" value="false"/>
20212 <param name="use_ms1_mi" value="true"/>
20213 <param name="use_uis_scores" value="false"/>
20214 </section>
20215 </section>
20216 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20217 <output name="ctd_out" ftype="xml">
20218 <assert_contents>
20219 <is_valid_xml/>
20220 </assert_contents>
20221 </output>
20222 </test>
20223 <test expect_num_outputs="3">
20224 <conditional name="adv_opts_cond">
20225 <param name="adv_opts_selector" value="advanced"/>
20226 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20227 <param name="sort_swath_maps" value="false"/>
20228 <param name="enable_ms1" value="true"/>
20229 <param name="enable_ipf" value="true"/>
20230 <param name="out_chrom_type" value="mzML"/>
20231 <param name="min_upper_edge_dist" value="0.0"/>
20232 <param name="extra_rt_extraction_window" value="0.0"/>
20233 <param name="mz_extraction_window_unit" value="ppm"/>
20234 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20235 <param name="use_ms1_ion_mobility" value="true"/>
20236 <param name="matching_window_only" value="false"/>
20237 <param name="irt_mz_extraction_window" value="50.0"/>
20238 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20239 <param name="irt_im_extraction_window" value="-1.0"/>
20240 <param name="min_rsq" value="0.95"/>
20241 <param name="min_coverage" value="0.6"/>
20242 <param name="split_file_input" value="false"/>
20243 <param name="use_elution_model_score" value="false"/>
20244 <param name="readOptions" value="normal"/>
20245 <param name="mz_correction_function" value="none"/>
20246 <param name="extraction_function" value="tophat"/>
20247 <param name="batchSize" value="1000"/>
20248 <param name="ms1_isotopes" value="3"/>
20249 <param name="force" value="false"/>
20250 <param name="test" value="false"/>
20251 </conditional>
20252 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20253 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20254 <param name="tr_type" value=""/>
20255 <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
20256 <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20257 <param name="sonar" value="false"/>
20258 <param name="rt_extraction_window" value="600.0"/>
20259 <param name="ion_mobility_window" value="-1.0"/>
20260 <param name="mz_extraction_window" value="50.0"/>
20261 <param name="mz_extraction_window_ms1" value="50.0"/>
20262 <param name="im_extraction_window_ms1" value="-1.0"/>
20263 <section name="Debugging"/>
20264 <section name="Calibration">
20265 <param name="ms1_im_calibration" value="false"/>
20266 <param name="im_correction_function" value="linear"/>
20267 <param name="debug_im_file" value=""/>
20268 <param name="debug_mz_file" value=""/>
20269 </section>
20270 <section name="Library">
20271 <param name="retentionTimeInterpretation" value="iRT"/>
20272 <param name="override_group_label_check" value="false"/>
20273 <param name="force_invalid_mods" value="false"/>
20274 </section>
20275 <section name="RTNormalization">
20276 <param name="alignmentMethod" value="linear"/>
20277 <param name="outlierMethod" value="iter_residual"/>
20278 <param name="useIterativeChauvenet" value="false"/>
20279 <param name="RANSACMaxIterations" value="1000"/>
20280 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20281 <param name="RANSACSamplingSize" value="10"/>
20282 <param name="estimateBestPeptides" value="false"/>
20283 <param name="InitialQualityCutoff" value="0.5"/>
20284 <param name="OverallQualityCutoff" value="5.5"/>
20285 <param name="NrRTBins" value="10"/>
20286 <param name="MinPeptidesPerBin" value="1"/>
20287 <param name="MinBinsFilled" value="8"/>
20288 <section name="lowess">
20289 <param name="span" value="0.05"/>
20290 </section>
20291 <section name="b_spline">
20292 <param name="num_nodes" value="5"/>
20293 </section>
20294 </section>
20295 <section name="Scoring">
20296 <param name="stop_report_after_feature" value="5"/>
20297 <param name="rt_normalization_factor" value="100.0"/>
20298 <param name="quantification_cutoff" value="0.0"/>
20299 <param name="write_convex_hull" value="false"/>
20300 <param name="spectrum_addition_method" value="simple"/>
20301 <param name="add_up_spectra" value="1"/>
20302 <param name="spacing_for_spectra_resampling" value="0.005"/>
20303 <param name="uis_threshold_sn" value="-1"/>
20304 <param name="uis_threshold_peak_area" value="0"/>
20305 <param name="scoring_model" value="default"/>
20306 <param name="im_extra_drift" value="0.0"/>
20307 <param name="strict" value="true"/>
20308 <section name="TransitionGroupPicker">
20309 <param name="stop_after_feature" value="-1"/>
20310 <param name="min_peak_width" value="-1.0"/>
20311 <param name="peak_integration" value="original"/>
20312 <param name="background_subtraction" value="none"/>
20313 <param name="recalculate_peaks" value="true"/>
20314 <param name="use_precursors" value="false"/>
20315 <param name="use_consensus" value="true"/>
20316 <param name="recalculate_peaks_max_z" value="0.75"/>
20317 <param name="minimal_quality" value="-1.5"/>
20318 <param name="resample_boundary" value="15.0"/>
20319 <param name="compute_peak_quality" value="false"/>
20320 <param name="compute_peak_shape_metrics" value="false"/>
20321 <param name="compute_total_mi" value="false"/>
20322 <param name="boundary_selection_method" value="largest"/>
20323 <section name="PeakPickerMRM">
20324 <param name="sgolay_frame_length" value="11"/>
20325 <param name="sgolay_polynomial_order" value="3"/>
20326 <param name="gauss_width" value="30.0"/>
20327 <param name="use_gauss" value="false"/>
20328 <param name="peak_width" value="-1.0"/>
20329 <param name="signal_to_noise" value="0.1"/>
20330 <param name="write_sn_log_messages" value="false"/>
20331 <param name="remove_overlapping_peaks" value="true"/>
20332 <param name="method" value="corrected"/>
20333 </section>
20334 <section name="PeakIntegrator">
20335 <param name="integration_type" value="intensity_sum"/>
20336 <param name="baseline_type" value="base_to_base"/>
20337 <param name="fit_EMG" value="false"/>
20338 </section>
20339 </section>
20340 <section name="DIAScoring">
20341 <param name="dia_extraction_window" value="0.05"/>
20342 <param name="dia_extraction_unit" value="Th"/>
20343 <param name="dia_centroided" value="false"/>
20344 <param name="dia_byseries_intensity_min" value="300.0"/>
20345 <param name="dia_byseries_ppm_diff" value="10.0"/>
20346 <param name="dia_nr_isotopes" value="4"/>
20347 <param name="dia_nr_charges" value="4"/>
20348 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20349 </section>
20350 <section name="EMGScoring">
20351 <param name="max_iteration" value="10"/>
20352 </section>
20353 <section name="Scores">
20354 <param name="use_shape_score" value="true"/>
20355 <param name="use_coelution_score" value="true"/>
20356 <param name="use_rt_score" value="true"/>
20357 <param name="use_library_score" value="true"/>
20358 <param name="use_intensity_score" value="true"/>
20359 <param name="use_nr_peaks_score" value="true"/>
20360 <param name="use_total_xic_score" value="true"/>
20361 <param name="use_total_mi_score" value="false"/>
20362 <param name="use_sn_score" value="true"/>
20363 <param name="use_mi_score" value="true"/>
20364 <param name="use_dia_scores" value="true"/>
20365 <param name="use_ms1_correlation" value="false"/>
20366 <param name="use_sonar_scores" value="false"/>
20367 <param name="use_ion_mobility_scores" value="false"/>
20368 <param name="use_ms1_fullscan" value="false"/>
20369 <param name="use_ms1_mi" value="true"/>
20370 <param name="use_uis_scores" value="false"/>
20371 </section>
20372 </section>
20373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
20374 <output name="ctd_out" ftype="xml">
20375 <assert_contents>
20376 <is_valid_xml/>
20377 </assert_contents>
20378 </output>
20379 </test>
20380 <test expect_num_outputs="3">
20381 <conditional name="adv_opts_cond">
20382 <param name="adv_opts_selector" value="advanced"/>
20383 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20384 <param name="sort_swath_maps" value="false"/>
20385 <param name="enable_ms1" value="true"/>
20386 <param name="enable_ipf" value="true"/>
20387 <param name="out_chrom_type" value="mzML"/>
20388 <param name="min_upper_edge_dist" value="0.0"/>
20389 <param name="extra_rt_extraction_window" value="0.0"/>
20390 <param name="mz_extraction_window_unit" value="ppm"/>
20391 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20392 <param name="use_ms1_ion_mobility" value="true"/>
20393 <param name="matching_window_only" value="false"/>
20394 <param name="irt_mz_extraction_window" value="50.0"/>
20395 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20396 <param name="irt_im_extraction_window" value="-1.0"/>
20397 <param name="min_rsq" value="0.95"/>
20398 <param name="min_coverage" value="0.6"/>
20399 <param name="split_file_input" value="false"/>
20400 <param name="use_elution_model_score" value="false"/>
20401 <param name="readOptions" value="cache"/>
20402 <param name="mz_correction_function" value="none"/>
20403 <param name="extraction_function" value="tophat"/>
20404 <param name="batchSize" value="1000"/>
20405 <param name="ms1_isotopes" value="3"/>
20406 <param name="force" value="false"/>
20407 <param name="test" value="false"/>
20408 </conditional>
20409 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20410 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20411 <param name="tr_type" value=""/>
20412 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20413 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20414 <param name="sonar" value="false"/>
20415 <param name="rt_extraction_window" value="600.0"/>
20416 <param name="ion_mobility_window" value="-1.0"/>
20417 <param name="mz_extraction_window" value="50.0"/>
20418 <param name="mz_extraction_window_ms1" value="50.0"/>
20419 <param name="im_extraction_window_ms1" value="-1.0"/>
20420 <section name="Debugging"/>
20421 <section name="Calibration">
20422 <param name="ms1_im_calibration" value="false"/>
20423 <param name="im_correction_function" value="linear"/>
20424 <param name="debug_im_file" value=""/>
20425 <param name="debug_mz_file" value=""/>
20426 </section>
20427 <section name="Library">
20428 <param name="retentionTimeInterpretation" value="iRT"/>
20429 <param name="override_group_label_check" value="false"/>
20430 <param name="force_invalid_mods" value="false"/>
20431 </section>
20432 <section name="RTNormalization">
20433 <param name="alignmentMethod" value="linear"/>
20434 <param name="outlierMethod" value="iter_residual"/>
20435 <param name="useIterativeChauvenet" value="false"/>
20436 <param name="RANSACMaxIterations" value="1000"/>
20437 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20438 <param name="RANSACSamplingSize" value="10"/>
20439 <param name="estimateBestPeptides" value="false"/>
20440 <param name="InitialQualityCutoff" value="0.5"/>
20441 <param name="OverallQualityCutoff" value="5.5"/>
20442 <param name="NrRTBins" value="10"/>
20443 <param name="MinPeptidesPerBin" value="1"/>
20444 <param name="MinBinsFilled" value="8"/>
20445 <section name="lowess">
20446 <param name="span" value="0.05"/>
20447 </section>
20448 <section name="b_spline">
20449 <param name="num_nodes" value="5"/>
20450 </section>
20451 </section>
20452 <section name="Scoring">
20453 <param name="stop_report_after_feature" value="5"/>
20454 <param name="rt_normalization_factor" value="100.0"/>
20455 <param name="quantification_cutoff" value="0.0"/>
20456 <param name="write_convex_hull" value="false"/>
20457 <param name="spectrum_addition_method" value="simple"/>
20458 <param name="add_up_spectra" value="1"/>
20459 <param name="spacing_for_spectra_resampling" value="0.005"/>
20460 <param name="uis_threshold_sn" value="-1"/>
20461 <param name="uis_threshold_peak_area" value="0"/>
20462 <param name="scoring_model" value="default"/>
20463 <param name="im_extra_drift" value="0.0"/>
20464 <param name="strict" value="true"/>
20465 <section name="TransitionGroupPicker">
20466 <param name="stop_after_feature" value="-1"/>
20467 <param name="min_peak_width" value="-1.0"/>
20468 <param name="peak_integration" value="original"/>
20469 <param name="background_subtraction" value="none"/>
20470 <param name="recalculate_peaks" value="true"/>
20471 <param name="use_precursors" value="false"/>
20472 <param name="use_consensus" value="true"/>
20473 <param name="recalculate_peaks_max_z" value="0.75"/>
20474 <param name="minimal_quality" value="-1.5"/>
20475 <param name="resample_boundary" value="15.0"/>
20476 <param name="compute_peak_quality" value="false"/>
20477 <param name="compute_peak_shape_metrics" value="false"/>
20478 <param name="compute_total_mi" value="false"/>
20479 <param name="boundary_selection_method" value="largest"/>
20480 <section name="PeakPickerMRM">
20481 <param name="sgolay_frame_length" value="11"/>
20482 <param name="sgolay_polynomial_order" value="3"/>
20483 <param name="gauss_width" value="30.0"/>
20484 <param name="use_gauss" value="false"/>
20485 <param name="peak_width" value="-1.0"/>
20486 <param name="signal_to_noise" value="0.1"/>
20487 <param name="write_sn_log_messages" value="false"/>
20488 <param name="remove_overlapping_peaks" value="true"/>
20489 <param name="method" value="corrected"/>
20490 </section>
20491 <section name="PeakIntegrator">
20492 <param name="integration_type" value="intensity_sum"/>
20493 <param name="baseline_type" value="base_to_base"/>
20494 <param name="fit_EMG" value="false"/>
20495 </section>
20496 </section>
20497 <section name="DIAScoring">
20498 <param name="dia_extraction_window" value="0.05"/>
20499 <param name="dia_extraction_unit" value="Th"/>
20500 <param name="dia_centroided" value="false"/>
20501 <param name="dia_byseries_intensity_min" value="300.0"/>
20502 <param name="dia_byseries_ppm_diff" value="10.0"/>
20503 <param name="dia_nr_isotopes" value="4"/>
20504 <param name="dia_nr_charges" value="4"/>
20505 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20506 </section>
20507 <section name="EMGScoring">
20508 <param name="max_iteration" value="10"/>
20509 </section>
20510 <section name="Scores">
20511 <param name="use_shape_score" value="true"/>
20512 <param name="use_coelution_score" value="true"/>
20513 <param name="use_rt_score" value="true"/>
20514 <param name="use_library_score" value="true"/>
20515 <param name="use_intensity_score" value="true"/>
20516 <param name="use_nr_peaks_score" value="true"/>
20517 <param name="use_total_xic_score" value="true"/>
20518 <param name="use_total_mi_score" value="false"/>
20519 <param name="use_sn_score" value="true"/>
20520 <param name="use_mi_score" value="true"/>
20521 <param name="use_dia_scores" value="true"/>
20522 <param name="use_ms1_correlation" value="false"/>
20523 <param name="use_sonar_scores" value="false"/>
20524 <param name="use_ion_mobility_scores" value="false"/>
20525 <param name="use_ms1_fullscan" value="false"/>
20526 <param name="use_ms1_mi" value="true"/>
20527 <param name="use_uis_scores" value="false"/>
20528 </section>
20529 </section>
20530 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20531 <output name="ctd_out" ftype="xml">
20532 <assert_contents>
20533 <is_valid_xml/>
20534 </assert_contents>
20535 </output>
20536 </test>
20537 <test expect_num_outputs="3">
20538 <conditional name="adv_opts_cond">
20539 <param name="adv_opts_selector" value="advanced"/>
20540 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20541 <param name="sort_swath_maps" value="false"/>
20542 <param name="enable_ms1" value="true"/>
20543 <param name="enable_ipf" value="true"/>
20544 <param name="out_chrom_type" value="mzML"/>
20545 <param name="min_upper_edge_dist" value="0.0"/>
20546 <param name="extra_rt_extraction_window" value="0.0"/>
20547 <param name="mz_extraction_window_unit" value="ppm"/>
20548 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20549 <param name="use_ms1_ion_mobility" value="true"/>
20550 <param name="matching_window_only" value="false"/>
20551 <param name="irt_mz_extraction_window" value="50.0"/>
20552 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20553 <param name="irt_im_extraction_window" value="-1.0"/>
20554 <param name="min_rsq" value="0.95"/>
20555 <param name="min_coverage" value="0.6"/>
20556 <param name="split_file_input" value="false"/>
20557 <param name="use_elution_model_score" value="false"/>
20558 <param name="readOptions" value="cacheWorkingInMemory"/>
20559 <param name="mz_correction_function" value="none"/>
20560 <param name="extraction_function" value="tophat"/>
20561 <param name="batchSize" value="1000"/>
20562 <param name="ms1_isotopes" value="3"/>
20563 <param name="force" value="false"/>
20564 <param name="test" value="false"/>
20565 </conditional>
20566 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20567 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20568 <param name="tr_type" value=""/>
20569 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20570 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20571 <param name="sonar" value="false"/>
20572 <param name="rt_extraction_window" value="600.0"/>
20573 <param name="ion_mobility_window" value="-1.0"/>
20574 <param name="mz_extraction_window" value="50.0"/>
20575 <param name="mz_extraction_window_ms1" value="50.0"/>
20576 <param name="im_extraction_window_ms1" value="-1.0"/>
20577 <section name="Debugging"/>
20578 <section name="Calibration">
20579 <param name="ms1_im_calibration" value="false"/>
20580 <param name="im_correction_function" value="linear"/>
20581 <param name="debug_im_file" value=""/>
20582 <param name="debug_mz_file" value=""/>
20583 </section>
20584 <section name="Library">
20585 <param name="retentionTimeInterpretation" value="iRT"/>
20586 <param name="override_group_label_check" value="false"/>
20587 <param name="force_invalid_mods" value="false"/>
20588 </section>
20589 <section name="RTNormalization">
20590 <param name="alignmentMethod" value="linear"/>
20591 <param name="outlierMethod" value="iter_residual"/>
20592 <param name="useIterativeChauvenet" value="false"/>
20593 <param name="RANSACMaxIterations" value="1000"/>
20594 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20595 <param name="RANSACSamplingSize" value="10"/>
20596 <param name="estimateBestPeptides" value="false"/>
20597 <param name="InitialQualityCutoff" value="0.5"/>
20598 <param name="OverallQualityCutoff" value="5.5"/>
20599 <param name="NrRTBins" value="10"/>
20600 <param name="MinPeptidesPerBin" value="1"/>
20601 <param name="MinBinsFilled" value="8"/>
20602 <section name="lowess">
20603 <param name="span" value="0.05"/>
20604 </section>
20605 <section name="b_spline">
20606 <param name="num_nodes" value="5"/>
20607 </section>
20608 </section>
20609 <section name="Scoring">
20610 <param name="stop_report_after_feature" value="5"/>
20611 <param name="rt_normalization_factor" value="100.0"/>
20612 <param name="quantification_cutoff" value="0.0"/>
20613 <param name="write_convex_hull" value="false"/>
20614 <param name="spectrum_addition_method" value="simple"/>
20615 <param name="add_up_spectra" value="1"/>
20616 <param name="spacing_for_spectra_resampling" value="0.005"/>
20617 <param name="uis_threshold_sn" value="-1"/>
20618 <param name="uis_threshold_peak_area" value="0"/>
20619 <param name="scoring_model" value="default"/>
20620 <param name="im_extra_drift" value="0.0"/>
20621 <param name="strict" value="true"/>
20622 <section name="TransitionGroupPicker">
20623 <param name="stop_after_feature" value="-1"/>
20624 <param name="min_peak_width" value="-1.0"/>
20625 <param name="peak_integration" value="original"/>
20626 <param name="background_subtraction" value="none"/>
20627 <param name="recalculate_peaks" value="true"/>
20628 <param name="use_precursors" value="false"/>
20629 <param name="use_consensus" value="true"/>
20630 <param name="recalculate_peaks_max_z" value="0.75"/>
20631 <param name="minimal_quality" value="-1.5"/>
20632 <param name="resample_boundary" value="15.0"/>
20633 <param name="compute_peak_quality" value="false"/>
20634 <param name="compute_peak_shape_metrics" value="false"/>
20635 <param name="compute_total_mi" value="false"/>
20636 <param name="boundary_selection_method" value="largest"/>
20637 <section name="PeakPickerMRM">
20638 <param name="sgolay_frame_length" value="11"/>
20639 <param name="sgolay_polynomial_order" value="3"/>
20640 <param name="gauss_width" value="30.0"/>
20641 <param name="use_gauss" value="false"/>
20642 <param name="peak_width" value="-1.0"/>
20643 <param name="signal_to_noise" value="0.1"/>
20644 <param name="write_sn_log_messages" value="false"/>
20645 <param name="remove_overlapping_peaks" value="true"/>
20646 <param name="method" value="corrected"/>
20647 </section>
20648 <section name="PeakIntegrator">
20649 <param name="integration_type" value="intensity_sum"/>
20650 <param name="baseline_type" value="base_to_base"/>
20651 <param name="fit_EMG" value="false"/>
20652 </section>
20653 </section>
20654 <section name="DIAScoring">
20655 <param name="dia_extraction_window" value="0.05"/>
20656 <param name="dia_extraction_unit" value="Th"/>
20657 <param name="dia_centroided" value="false"/>
20658 <param name="dia_byseries_intensity_min" value="300.0"/>
20659 <param name="dia_byseries_ppm_diff" value="10.0"/>
20660 <param name="dia_nr_isotopes" value="4"/>
20661 <param name="dia_nr_charges" value="4"/>
20662 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20663 </section>
20664 <section name="EMGScoring">
20665 <param name="max_iteration" value="10"/>
20666 </section>
20667 <section name="Scores">
20668 <param name="use_shape_score" value="true"/>
20669 <param name="use_coelution_score" value="true"/>
20670 <param name="use_rt_score" value="true"/>
20671 <param name="use_library_score" value="true"/>
20672 <param name="use_intensity_score" value="true"/>
20673 <param name="use_nr_peaks_score" value="true"/>
20674 <param name="use_total_xic_score" value="true"/>
20675 <param name="use_total_mi_score" value="false"/>
20676 <param name="use_sn_score" value="true"/>
20677 <param name="use_mi_score" value="true"/>
20678 <param name="use_dia_scores" value="true"/>
20679 <param name="use_ms1_correlation" value="false"/>
20680 <param name="use_sonar_scores" value="false"/>
20681 <param name="use_ion_mobility_scores" value="false"/>
20682 <param name="use_ms1_fullscan" value="false"/>
20683 <param name="use_ms1_mi" value="true"/>
20684 <param name="use_uis_scores" value="false"/>
20685 </section>
20686 </section>
20687 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20688 <output name="ctd_out" ftype="xml">
20689 <assert_contents>
20690 <is_valid_xml/>
20691 </assert_contents>
20692 </output>
20693 </test>
20694 <test expect_num_outputs="3">
20695 <conditional name="adv_opts_cond">
20696 <param name="adv_opts_selector" value="advanced"/>
20697 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20698 <param name="sort_swath_maps" value="false"/>
20699 <param name="enable_ms1" value="true"/>
20700 <param name="enable_ipf" value="true"/>
20701 <param name="out_chrom_type" value="mzML"/>
20702 <param name="min_upper_edge_dist" value="0.0"/>
20703 <param name="extra_rt_extraction_window" value="0.0"/>
20704 <param name="mz_extraction_window_unit" value="ppm"/>
20705 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20706 <param name="use_ms1_ion_mobility" value="true"/>
20707 <param name="matching_window_only" value="false"/>
20708 <param name="irt_mz_extraction_window" value="50.0"/>
20709 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20710 <param name="irt_im_extraction_window" value="-1.0"/>
20711 <param name="min_rsq" value="0.95"/>
20712 <param name="min_coverage" value="0.6"/>
20713 <param name="split_file_input" value="false"/>
20714 <param name="use_elution_model_score" value="false"/>
20715 <param name="readOptions" value="normal"/>
20716 <param name="mz_correction_function" value="none"/>
20717 <param name="extraction_function" value="tophat"/>
20718 <param name="batchSize" value="1000"/>
20719 <param name="ms1_isotopes" value="3"/>
20720 <param name="force" value="false"/>
20721 <param name="test" value="false"/>
20722 </conditional>
20723 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20724 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20725 <param name="tr_type" value=""/>
20726 <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
20727 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20728 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20729 <param name="sonar" value="false"/>
20730 <param name="rt_extraction_window" value="600.0"/>
20731 <param name="ion_mobility_window" value="-1.0"/>
20732 <param name="mz_extraction_window" value="50.0"/>
20733 <param name="mz_extraction_window_ms1" value="50.0"/>
20734 <param name="im_extraction_window_ms1" value="-1.0"/>
20735 <section name="Debugging"/>
20736 <section name="Calibration">
20737 <param name="ms1_im_calibration" value="false"/>
20738 <param name="im_correction_function" value="linear"/>
20739 <param name="debug_im_file" value=""/>
20740 <param name="debug_mz_file" value=""/>
20741 </section>
20742 <section name="Library">
20743 <param name="retentionTimeInterpretation" value="iRT"/>
20744 <param name="override_group_label_check" value="false"/>
20745 <param name="force_invalid_mods" value="false"/>
20746 </section>
20747 <section name="RTNormalization">
20748 <param name="alignmentMethod" value="linear"/>
20749 <param name="outlierMethod" value="iter_residual"/>
20750 <param name="useIterativeChauvenet" value="false"/>
20751 <param name="RANSACMaxIterations" value="1000"/>
20752 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20753 <param name="RANSACSamplingSize" value="10"/>
20754 <param name="estimateBestPeptides" value="false"/>
20755 <param name="InitialQualityCutoff" value="0.5"/>
20756 <param name="OverallQualityCutoff" value="5.5"/>
20757 <param name="NrRTBins" value="10"/>
20758 <param name="MinPeptidesPerBin" value="1"/>
20759 <param name="MinBinsFilled" value="8"/>
20760 <section name="lowess">
20761 <param name="span" value="0.05"/>
20762 </section>
20763 <section name="b_spline">
20764 <param name="num_nodes" value="5"/>
20765 </section>
20766 </section>
20767 <section name="Scoring">
20768 <param name="stop_report_after_feature" value="5"/>
20769 <param name="rt_normalization_factor" value="100.0"/>
20770 <param name="quantification_cutoff" value="0.0"/>
20771 <param name="write_convex_hull" value="false"/>
20772 <param name="spectrum_addition_method" value="simple"/>
20773 <param name="add_up_spectra" value="1"/>
20774 <param name="spacing_for_spectra_resampling" value="0.005"/>
20775 <param name="uis_threshold_sn" value="-1"/>
20776 <param name="uis_threshold_peak_area" value="0"/>
20777 <param name="scoring_model" value="default"/>
20778 <param name="im_extra_drift" value="0.0"/>
20779 <param name="strict" value="true"/>
20780 <section name="TransitionGroupPicker">
20781 <param name="stop_after_feature" value="-1"/>
20782 <param name="min_peak_width" value="-1.0"/>
20783 <param name="peak_integration" value="original"/>
20784 <param name="background_subtraction" value="none"/>
20785 <param name="recalculate_peaks" value="true"/>
20786 <param name="use_precursors" value="false"/>
20787 <param name="use_consensus" value="true"/>
20788 <param name="recalculate_peaks_max_z" value="0.75"/>
20789 <param name="minimal_quality" value="-1.5"/>
20790 <param name="resample_boundary" value="15.0"/>
20791 <param name="compute_peak_quality" value="false"/>
20792 <param name="compute_peak_shape_metrics" value="false"/>
20793 <param name="compute_total_mi" value="false"/>
20794 <param name="boundary_selection_method" value="largest"/>
20795 <section name="PeakPickerMRM">
20796 <param name="sgolay_frame_length" value="11"/>
20797 <param name="sgolay_polynomial_order" value="3"/>
20798 <param name="gauss_width" value="30.0"/>
20799 <param name="use_gauss" value="false"/>
20800 <param name="peak_width" value="-1.0"/>
20801 <param name="signal_to_noise" value="0.1"/>
20802 <param name="write_sn_log_messages" value="false"/>
20803 <param name="remove_overlapping_peaks" value="true"/>
20804 <param name="method" value="corrected"/>
20805 </section>
20806 <section name="PeakIntegrator">
20807 <param name="integration_type" value="intensity_sum"/>
20808 <param name="baseline_type" value="base_to_base"/>
20809 <param name="fit_EMG" value="false"/>
20810 </section>
20811 </section>
20812 <section name="DIAScoring">
20813 <param name="dia_extraction_window" value="0.05"/>
20814 <param name="dia_extraction_unit" value="Th"/>
20815 <param name="dia_centroided" value="false"/>
20816 <param name="dia_byseries_intensity_min" value="300.0"/>
20817 <param name="dia_byseries_ppm_diff" value="10.0"/>
20818 <param name="dia_nr_isotopes" value="4"/>
20819 <param name="dia_nr_charges" value="4"/>
20820 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20821 </section>
20822 <section name="EMGScoring">
20823 <param name="max_iteration" value="10"/>
20824 </section>
20825 <section name="Scores">
20826 <param name="use_shape_score" value="true"/>
20827 <param name="use_coelution_score" value="true"/>
20828 <param name="use_rt_score" value="true"/>
20829 <param name="use_library_score" value="true"/>
20830 <param name="use_intensity_score" value="true"/>
20831 <param name="use_nr_peaks_score" value="true"/>
20832 <param name="use_total_xic_score" value="true"/>
20833 <param name="use_total_mi_score" value="false"/>
20834 <param name="use_sn_score" value="true"/>
20835 <param name="use_mi_score" value="true"/>
20836 <param name="use_dia_scores" value="true"/>
20837 <param name="use_ms1_correlation" value="false"/>
20838 <param name="use_sonar_scores" value="false"/>
20839 <param name="use_ion_mobility_scores" value="false"/>
20840 <param name="use_ms1_fullscan" value="false"/>
20841 <param name="use_ms1_mi" value="true"/>
20842 <param name="use_uis_scores" value="false"/>
20843 </section>
20844 </section>
20845 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20846 <output name="ctd_out" ftype="xml">
20847 <assert_contents>
20848 <is_valid_xml/>
20849 </assert_contents>
20850 </output>
20851 </test>
20852 <test expect_num_outputs="3">
20853 <conditional name="adv_opts_cond">
20854 <param name="adv_opts_selector" value="advanced"/>
20855 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20856 <param name="sort_swath_maps" value="false"/>
20857 <param name="enable_ms1" value="true"/>
20858 <param name="enable_ipf" value="true"/>
20859 <param name="out_chrom_type" value="mzML"/>
20860 <param name="min_upper_edge_dist" value="0.0"/>
20861 <param name="extra_rt_extraction_window" value="0.0"/>
20862 <param name="mz_extraction_window_unit" value="ppm"/>
20863 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20864 <param name="use_ms1_ion_mobility" value="true"/>
20865 <param name="matching_window_only" value="false"/>
20866 <param name="irt_mz_extraction_window" value="50.0"/>
20867 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20868 <param name="irt_im_extraction_window" value="-1.0"/>
20869 <param name="min_rsq" value="0.95"/>
20870 <param name="min_coverage" value="0.6"/>
20871 <param name="split_file_input" value="false"/>
20872 <param name="use_elution_model_score" value="false"/>
20873 <param name="readOptions" value="normal"/>
20874 <param name="mz_correction_function" value="none"/>
20875 <param name="extraction_function" value="tophat"/>
20876 <param name="batchSize" value="1000"/>
20877 <param name="ms1_isotopes" value="3"/>
20878 <param name="force" value="true"/>
20879 <param name="test" value="false"/>
20880 </conditional>
20881 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20882 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20883 <param name="tr_type" value=""/>
20884 <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
20885 <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
20886 <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20887 <param name="sonar" value="false"/>
20888 <param name="rt_extraction_window" value="600.0"/>
20889 <param name="ion_mobility_window" value="-1.0"/>
20890 <param name="mz_extraction_window" value="50.0"/>
20891 <param name="mz_extraction_window_ms1" value="50.0"/>
20892 <param name="im_extraction_window_ms1" value="-1.0"/>
20893 <section name="Debugging"/>
20894 <section name="Calibration">
20895 <param name="ms1_im_calibration" value="false"/>
20896 <param name="im_correction_function" value="linear"/>
20897 <param name="debug_im_file" value=""/>
20898 <param name="debug_mz_file" value=""/>
20899 </section>
20900 <section name="Library">
20901 <param name="retentionTimeInterpretation" value="iRT"/>
20902 <param name="override_group_label_check" value="false"/>
20903 <param name="force_invalid_mods" value="false"/>
20904 </section>
20905 <section name="RTNormalization">
20906 <param name="alignmentMethod" value="linear"/>
20907 <param name="outlierMethod" value="iter_residual"/>
20908 <param name="useIterativeChauvenet" value="false"/>
20909 <param name="RANSACMaxIterations" value="1000"/>
20910 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20911 <param name="RANSACSamplingSize" value="10"/>
20912 <param name="estimateBestPeptides" value="false"/>
20913 <param name="InitialQualityCutoff" value="0.5"/>
20914 <param name="OverallQualityCutoff" value="5.5"/>
20915 <param name="NrRTBins" value="10"/>
20916 <param name="MinPeptidesPerBin" value="1"/>
20917 <param name="MinBinsFilled" value="8"/>
20918 <section name="lowess">
20919 <param name="span" value="0.05"/>
20920 </section>
20921 <section name="b_spline">
20922 <param name="num_nodes" value="5"/>
20923 </section>
20924 </section>
20925 <section name="Scoring">
20926 <param name="stop_report_after_feature" value="5"/>
20927 <param name="rt_normalization_factor" value="100.0"/>
20928 <param name="quantification_cutoff" value="0.0"/>
20929 <param name="write_convex_hull" value="false"/>
20930 <param name="spectrum_addition_method" value="simple"/>
20931 <param name="add_up_spectra" value="1"/>
20932 <param name="spacing_for_spectra_resampling" value="0.005"/>
20933 <param name="uis_threshold_sn" value="-1"/>
20934 <param name="uis_threshold_peak_area" value="0"/>
20935 <param name="scoring_model" value="default"/>
20936 <param name="im_extra_drift" value="0.0"/>
20937 <param name="strict" value="true"/>
20938 <section name="TransitionGroupPicker">
20939 <param name="stop_after_feature" value="-1"/>
20940 <param name="min_peak_width" value="-1.0"/>
20941 <param name="peak_integration" value="original"/>
20942 <param name="background_subtraction" value="none"/>
20943 <param name="recalculate_peaks" value="true"/>
20944 <param name="use_precursors" value="false"/>
20945 <param name="use_consensus" value="true"/>
20946 <param name="recalculate_peaks_max_z" value="0.75"/>
20947 <param name="minimal_quality" value="-1.5"/>
20948 <param name="resample_boundary" value="15.0"/>
20949 <param name="compute_peak_quality" value="false"/>
20950 <param name="compute_peak_shape_metrics" value="false"/>
20951 <param name="compute_total_mi" value="false"/>
20952 <param name="boundary_selection_method" value="largest"/>
20953 <section name="PeakPickerMRM">
20954 <param name="sgolay_frame_length" value="11"/>
20955 <param name="sgolay_polynomial_order" value="3"/>
20956 <param name="gauss_width" value="30.0"/>
20957 <param name="use_gauss" value="false"/>
20958 <param name="peak_width" value="-1.0"/>
20959 <param name="signal_to_noise" value="0.1"/>
20960 <param name="write_sn_log_messages" value="false"/>
20961 <param name="remove_overlapping_peaks" value="true"/>
20962 <param name="method" value="corrected"/>
20963 </section>
20964 <section name="PeakIntegrator">
20965 <param name="integration_type" value="intensity_sum"/>
20966 <param name="baseline_type" value="base_to_base"/>
20967 <param name="fit_EMG" value="false"/>
20968 </section>
20969 </section>
20970 <section name="DIAScoring">
20971 <param name="dia_extraction_window" value="0.05"/>
20972 <param name="dia_extraction_unit" value="Th"/>
20973 <param name="dia_centroided" value="false"/>
20974 <param name="dia_byseries_intensity_min" value="300.0"/>
20975 <param name="dia_byseries_ppm_diff" value="10.0"/>
20976 <param name="dia_nr_isotopes" value="4"/>
20977 <param name="dia_nr_charges" value="4"/>
20978 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20979 </section>
20980 <section name="EMGScoring">
20981 <param name="max_iteration" value="10"/>
20982 </section>
20983 <section name="Scores">
20984 <param name="use_shape_score" value="true"/>
20985 <param name="use_coelution_score" value="true"/>
20986 <param name="use_rt_score" value="true"/>
20987 <param name="use_library_score" value="true"/>
20988 <param name="use_intensity_score" value="true"/>
20989 <param name="use_nr_peaks_score" value="true"/>
20990 <param name="use_total_xic_score" value="true"/>
20991 <param name="use_total_mi_score" value="false"/>
20992 <param name="use_sn_score" value="true"/>
20993 <param name="use_mi_score" value="true"/>
20994 <param name="use_dia_scores" value="true"/>
20995 <param name="use_ms1_correlation" value="false"/>
20996 <param name="use_sonar_scores" value="false"/>
20997 <param name="use_ion_mobility_scores" value="false"/>
20998 <param name="use_ms1_fullscan" value="false"/>
20999 <param name="use_ms1_mi" value="true"/>
21000 <param name="use_uis_scores" value="false"/>
21001 </section>
21002 </section>
21003 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21004 <output name="ctd_out" ftype="xml">
21005 <assert_contents>
21006 <is_valid_xml/>
21007 </assert_contents>
21008 </output>
21009 </test>
21010 <test expect_num_outputs="3">
21011 <conditional name="adv_opts_cond">
21012 <param name="adv_opts_selector" value="advanced"/>
21013 <param name="sort_swath_maps" value="false"/>
21014 <param name="enable_ms1" value="false"/>
21015 <param name="enable_ipf" value="true"/>
21016 <param name="out_chrom_type" value="mzML"/>
21017 <param name="min_upper_edge_dist" value="0.0"/>
21018 <param name="extra_rt_extraction_window" value="0.0"/>
21019 <param name="mz_extraction_window_unit" value="ppm"/>
21020 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21021 <param name="use_ms1_ion_mobility" value="true"/>
21022 <param name="matching_window_only" value="false"/>
21023 <param name="irt_mz_extraction_window" value="550.0"/>
21024 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21025 <param name="irt_im_extraction_window" value="-1.0"/>
21026 <param name="min_rsq" value="0.95"/>
21027 <param name="min_coverage" value="0.6"/>
21028 <param name="split_file_input" value="false"/>
21029 <param name="use_elution_model_score" value="false"/>
21030 <param name="readOptions" value="normal"/>
21031 <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
21032 <param name="extraction_function" value="tophat"/>
21033 <param name="batchSize" value="1000"/>
21034 <param name="ms1_isotopes" value="3"/>
21035 <param name="force" value="false"/>
21036 <param name="test" value="false"/>
21037 </conditional>
21038 <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
21039 <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
21040 <param name="tr_type" value=""/>
21041 <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
21042 <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21043 <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21044 <param name="sonar" value="true"/>
21045 <param name="rt_extraction_window" value="-1.0"/>
21046 <param name="ion_mobility_window" value="-1.0"/>
21047 <param name="mz_extraction_window" value="0.2"/>
21048 <param name="mz_extraction_window_ms1" value="50.0"/>
21049 <param name="im_extraction_window_ms1" value="-1.0"/>
21050 <section name="Debugging"/>
21051 <section name="Calibration">
21052 <param name="ms1_im_calibration" value="false"/>
21053 <param name="im_correction_function" value="linear"/>
21054 <param name="debug_im_file" value=""/>
21055 <param name="debug_mz_file" value=""/>
21056 </section>
21057 <section name="Library">
21058 <param name="retentionTimeInterpretation" value="iRT"/>
21059 <param name="override_group_label_check" value="false"/>
21060 <param name="force_invalid_mods" value="false"/>
21061 </section>
21062 <section name="RTNormalization">
21063 <param name="alignmentMethod" value="linear"/>
21064 <param name="outlierMethod" value="none"/>
21065 <param name="useIterativeChauvenet" value="false"/>
21066 <param name="RANSACMaxIterations" value="1000"/>
21067 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21068 <param name="RANSACSamplingSize" value="10"/>
21069 <param name="estimateBestPeptides" value="false"/>
21070 <param name="InitialQualityCutoff" value="0.5"/>
21071 <param name="OverallQualityCutoff" value="5.5"/>
21072 <param name="NrRTBins" value="10"/>
21073 <param name="MinPeptidesPerBin" value="1"/>
21074 <param name="MinBinsFilled" value="8"/>
21075 <section name="lowess">
21076 <param name="span" value="0.05"/>
21077 </section>
21078 <section name="b_spline">
21079 <param name="num_nodes" value="5"/>
21080 </section>
21081 </section>
21082 <section name="Scoring">
21083 <param name="stop_report_after_feature" value="5"/>
21084 <param name="rt_normalization_factor" value="100.0"/>
21085 <param name="quantification_cutoff" value="0.0"/>
21086 <param name="write_convex_hull" value="false"/>
21087 <param name="spectrum_addition_method" value="simple"/>
21088 <param name="add_up_spectra" value="1"/>
21089 <param name="spacing_for_spectra_resampling" value="0.005"/>
21090 <param name="uis_threshold_sn" value="-1"/>
21091 <param name="uis_threshold_peak_area" value="0"/>
21092 <param name="scoring_model" value="default"/>
21093 <param name="im_extra_drift" value="0.0"/>
21094 <param name="strict" value="true"/>
21095 <section name="TransitionGroupPicker">
21096 <param name="stop_after_feature" value="-1"/>
21097 <param name="min_peak_width" value="-1.0"/>
21098 <param name="peak_integration" value="original"/>
21099 <param name="background_subtraction" value="none"/>
21100 <param name="recalculate_peaks" value="true"/>
21101 <param name="use_precursors" value="false"/>
21102 <param name="use_consensus" value="true"/>
21103 <param name="recalculate_peaks_max_z" value="0.75"/>
21104 <param name="minimal_quality" value="-1.5"/>
21105 <param name="resample_boundary" value="15.0"/>
21106 <param name="compute_peak_quality" value="false"/>
21107 <param name="compute_peak_shape_metrics" value="false"/>
21108 <param name="compute_total_mi" value="false"/>
21109 <param name="boundary_selection_method" value="largest"/>
21110 <section name="PeakPickerMRM">
21111 <param name="sgolay_frame_length" value="11"/>
21112 <param name="sgolay_polynomial_order" value="3"/>
21113 <param name="gauss_width" value="30.0"/>
21114 <param name="use_gauss" value="false"/>
21115 <param name="peak_width" value="-1.0"/>
21116 <param name="signal_to_noise" value="0.1"/>
21117 <param name="write_sn_log_messages" value="false"/>
21118 <param name="remove_overlapping_peaks" value="true"/>
21119 <param name="method" value="corrected"/>
21120 </section>
21121 <section name="PeakIntegrator">
21122 <param name="integration_type" value="intensity_sum"/>
21123 <param name="baseline_type" value="base_to_base"/>
21124 <param name="fit_EMG" value="false"/>
21125 </section>
21126 </section>
21127 <section name="DIAScoring">
21128 <param name="dia_extraction_window" value="0.05"/>
21129 <param name="dia_extraction_unit" value="Th"/>
21130 <param name="dia_centroided" value="false"/>
21131 <param name="dia_byseries_intensity_min" value="300.0"/>
21132 <param name="dia_byseries_ppm_diff" value="10.0"/>
21133 <param name="dia_nr_isotopes" value="4"/>
21134 <param name="dia_nr_charges" value="4"/>
21135 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21136 </section>
21137 <section name="EMGScoring">
21138 <param name="max_iteration" value="10"/>
21139 </section>
21140 <section name="Scores">
21141 <param name="use_shape_score" value="true"/>
21142 <param name="use_coelution_score" value="true"/>
21143 <param name="use_rt_score" value="true"/>
21144 <param name="use_library_score" value="true"/>
21145 <param name="use_intensity_score" value="true"/>
21146 <param name="use_nr_peaks_score" value="true"/>
21147 <param name="use_total_xic_score" value="true"/>
21148 <param name="use_total_mi_score" value="false"/>
21149 <param name="use_sn_score" value="true"/>
21150 <param name="use_mi_score" value="true"/>
21151 <param name="use_dia_scores" value="true"/>
21152 <param name="use_ms1_correlation" value="false"/>
21153 <param name="use_sonar_scores" value="true"/>
21154 <param name="use_ion_mobility_scores" value="false"/>
21155 <param name="use_ms1_fullscan" value="false"/>
21156 <param name="use_ms1_mi" value="true"/>
21157 <param name="use_uis_scores" value="false"/>
21158 </section>
21159 </section>
21160 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21161 <output name="ctd_out" ftype="xml">
21162 <assert_contents>
21163 <is_valid_xml/>
21164 </assert_contents>
21165 </output>
21166 </test>
21167 <test expect_num_outputs="3">
21168 <conditional name="adv_opts_cond">
21169 <param name="adv_opts_selector" value="advanced"/>
21170 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21171 <param name="sort_swath_maps" value="false"/>
21172 <param name="enable_ms1" value="true"/>
21173 <param name="enable_ipf" value="true"/>
21174 <param name="out_chrom_type" value="mzML"/>
21175 <param name="min_upper_edge_dist" value="0.0"/>
21176 <param name="extra_rt_extraction_window" value="0.0"/>
21177 <param name="mz_extraction_window_unit" value="ppm"/>
21178 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21179 <param name="use_ms1_ion_mobility" value="true"/>
21180 <param name="matching_window_only" value="false"/>
21181 <param name="irt_mz_extraction_window" value="50.0"/>
21182 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21183 <param name="irt_im_extraction_window" value="-1.0"/>
21184 <param name="min_rsq" value="0.95"/>
21185 <param name="min_coverage" value="0.6"/>
21186 <param name="split_file_input" value="false"/>
21187 <param name="use_elution_model_score" value="false"/>
21188 <param name="readOptions" value="normal"/>
21189 <param name="mz_correction_function" value="none"/>
21190 <param name="extraction_function" value="tophat"/>
21191 <param name="batchSize" value="1000"/>
21192 <param name="ms1_isotopes" value="3"/>
21193 <param name="force" value="false"/>
21194 <param name="test" value="false"/>
21195 </conditional>
21196 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21197 <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
21198 <param name="tr_type" value="pqp"/>
21199 <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
21200 <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21201 <param name="sonar" value="false"/>
21202 <param name="rt_extraction_window" value="600.0"/>
21203 <param name="ion_mobility_window" value="-1.0"/>
21204 <param name="mz_extraction_window" value="50.0"/>
21205 <param name="mz_extraction_window_ms1" value="50.0"/>
21206 <param name="im_extraction_window_ms1" value="-1.0"/>
21207 <section name="Debugging"/>
21208 <section name="Calibration">
21209 <param name="ms1_im_calibration" value="false"/>
21210 <param name="im_correction_function" value="linear"/>
21211 <param name="debug_im_file" value=""/>
21212 <param name="debug_mz_file" value=""/>
21213 </section>
21214 <section name="Library">
21215 <param name="retentionTimeInterpretation" value="iRT"/>
21216 <param name="override_group_label_check" value="false"/>
21217 <param name="force_invalid_mods" value="false"/>
21218 </section>
21219 <section name="RTNormalization">
21220 <param name="alignmentMethod" value="linear"/>
21221 <param name="outlierMethod" value="iter_residual"/>
21222 <param name="useIterativeChauvenet" value="false"/>
21223 <param name="RANSACMaxIterations" value="1000"/>
21224 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21225 <param name="RANSACSamplingSize" value="10"/>
21226 <param name="estimateBestPeptides" value="false"/>
21227 <param name="InitialQualityCutoff" value="0.5"/>
21228 <param name="OverallQualityCutoff" value="5.5"/>
21229 <param name="NrRTBins" value="10"/>
21230 <param name="MinPeptidesPerBin" value="1"/>
21231 <param name="MinBinsFilled" value="8"/>
21232 <section name="lowess">
21233 <param name="span" value="0.05"/>
21234 </section>
21235 <section name="b_spline">
21236 <param name="num_nodes" value="5"/>
21237 </section>
21238 </section>
21239 <section name="Scoring">
21240 <param name="stop_report_after_feature" value="5"/>
21241 <param name="rt_normalization_factor" value="100.0"/>
21242 <param name="quantification_cutoff" value="0.0"/>
21243 <param name="write_convex_hull" value="false"/>
21244 <param name="spectrum_addition_method" value="simple"/>
21245 <param name="add_up_spectra" value="1"/>
21246 <param name="spacing_for_spectra_resampling" value="0.005"/>
21247 <param name="uis_threshold_sn" value="-1"/>
21248 <param name="uis_threshold_peak_area" value="0"/>
21249 <param name="scoring_model" value="default"/>
21250 <param name="im_extra_drift" value="0.0"/>
21251 <param name="strict" value="true"/>
21252 <section name="TransitionGroupPicker">
21253 <param name="stop_after_feature" value="-1"/>
21254 <param name="min_peak_width" value="-1.0"/>
21255 <param name="peak_integration" value="original"/>
21256 <param name="background_subtraction" value="none"/>
21257 <param name="recalculate_peaks" value="true"/>
21258 <param name="use_precursors" value="false"/>
21259 <param name="use_consensus" value="true"/>
21260 <param name="recalculate_peaks_max_z" value="0.75"/>
21261 <param name="minimal_quality" value="-1.5"/>
21262 <param name="resample_boundary" value="15.0"/>
21263 <param name="compute_peak_quality" value="false"/>
21264 <param name="compute_peak_shape_metrics" value="false"/>
21265 <param name="compute_total_mi" value="false"/>
21266 <param name="boundary_selection_method" value="largest"/>
21267 <section name="PeakPickerMRM">
21268 <param name="sgolay_frame_length" value="11"/>
21269 <param name="sgolay_polynomial_order" value="3"/>
21270 <param name="gauss_width" value="30.0"/>
21271 <param name="use_gauss" value="false"/>
21272 <param name="peak_width" value="-1.0"/>
21273 <param name="signal_to_noise" value="0.1"/>
21274 <param name="write_sn_log_messages" value="false"/>
21275 <param name="remove_overlapping_peaks" value="true"/>
21276 <param name="method" value="corrected"/>
21277 </section>
21278 <section name="PeakIntegrator">
21279 <param name="integration_type" value="intensity_sum"/>
21280 <param name="baseline_type" value="base_to_base"/>
21281 <param name="fit_EMG" value="false"/>
21282 </section>
21283 </section>
21284 <section name="DIAScoring">
21285 <param name="dia_extraction_window" value="0.05"/>
21286 <param name="dia_extraction_unit" value="Th"/>
21287 <param name="dia_centroided" value="false"/>
21288 <param name="dia_byseries_intensity_min" value="300.0"/>
21289 <param name="dia_byseries_ppm_diff" value="10.0"/>
21290 <param name="dia_nr_isotopes" value="4"/>
21291 <param name="dia_nr_charges" value="4"/>
21292 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21293 </section>
21294 <section name="EMGScoring">
21295 <param name="max_iteration" value="10"/>
21296 </section>
21297 <section name="Scores">
21298 <param name="use_shape_score" value="true"/>
21299 <param name="use_coelution_score" value="true"/>
21300 <param name="use_rt_score" value="true"/>
21301 <param name="use_library_score" value="true"/>
21302 <param name="use_intensity_score" value="true"/>
21303 <param name="use_nr_peaks_score" value="true"/>
21304 <param name="use_total_xic_score" value="true"/>
21305 <param name="use_total_mi_score" value="false"/>
21306 <param name="use_sn_score" value="true"/>
21307 <param name="use_mi_score" value="true"/>
21308 <param name="use_dia_scores" value="true"/>
21309 <param name="use_ms1_correlation" value="false"/>
21310 <param name="use_sonar_scores" value="false"/>
21311 <param name="use_ion_mobility_scores" value="false"/>
21312 <param name="use_ms1_fullscan" value="false"/>
21313 <param name="use_ms1_mi" value="true"/>
21314 <param name="use_uis_scores" value="false"/>
21315 </section>
21316 </section>
21317 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
21318 <output name="ctd_out" ftype="xml">
21319 <assert_contents>
21320 <is_valid_xml/>
21321 </assert_contents>
21322 </output>
21323 </test>
21324 <test expect_num_outputs="3">
21325 <conditional name="adv_opts_cond">
21326 <param name="adv_opts_selector" value="advanced"/>
21327 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21328 <param name="sort_swath_maps" value="false"/>
21329 <param name="enable_ms1" value="true"/>
21330 <param name="enable_ipf" value="true"/>
21331 <param name="out_chrom_type" value="sqMass"/>
21332 <param name="min_upper_edge_dist" value="0.0"/>
21333 <param name="extra_rt_extraction_window" value="0.0"/>
21334 <param name="mz_extraction_window_unit" value="ppm"/>
21335 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21336 <param name="use_ms1_ion_mobility" value="true"/>
21337 <param name="matching_window_only" value="false"/>
21338 <param name="irt_mz_extraction_window" value="50.0"/>
21339 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21340 <param name="irt_im_extraction_window" value="-1.0"/>
21341 <param name="min_rsq" value="0.95"/>
21342 <param name="min_coverage" value="0.6"/>
21343 <param name="split_file_input" value="false"/>
21344 <param name="use_elution_model_score" value="false"/>
21345 <param name="readOptions" value="normal"/>
21346 <param name="mz_correction_function" value="none"/>
21347 <param name="extraction_function" value="tophat"/>
21348 <param name="batchSize" value="1000"/>
21349 <param name="ms1_isotopes" value="3"/>
21350 <param name="force" value="false"/>
21351 <param name="test" value="false"/>
21352 </conditional>
21353 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21354 <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
21355 <param name="tr_type" value="pqp"/>
21356 <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
21357 <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
21358 <param name="sonar" value="false"/>
21359 <param name="rt_extraction_window" value="600.0"/>
21360 <param name="ion_mobility_window" value="-1.0"/>
21361 <param name="mz_extraction_window" value="50.0"/>
21362 <param name="mz_extraction_window_ms1" value="50.0"/>
21363 <param name="im_extraction_window_ms1" value="-1.0"/>
21364 <section name="Debugging"/>
21365 <section name="Calibration">
21366 <param name="ms1_im_calibration" value="false"/>
21367 <param name="im_correction_function" value="linear"/>
21368 <param name="debug_im_file" value=""/>
21369 <param name="debug_mz_file" value=""/>
21370 </section>
21371 <section name="Library">
21372 <param name="retentionTimeInterpretation" value="iRT"/>
21373 <param name="override_group_label_check" value="false"/>
21374 <param name="force_invalid_mods" value="false"/>
21375 </section>
21376 <section name="RTNormalization">
21377 <param name="alignmentMethod" value="linear"/>
21378 <param name="outlierMethod" value="iter_residual"/>
21379 <param name="useIterativeChauvenet" value="false"/>
21380 <param name="RANSACMaxIterations" value="1000"/>
21381 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21382 <param name="RANSACSamplingSize" value="10"/>
21383 <param name="estimateBestPeptides" value="false"/>
21384 <param name="InitialQualityCutoff" value="0.5"/>
21385 <param name="OverallQualityCutoff" value="5.5"/>
21386 <param name="NrRTBins" value="10"/>
21387 <param name="MinPeptidesPerBin" value="1"/>
21388 <param name="MinBinsFilled" value="8"/>
21389 <section name="lowess">
21390 <param name="span" value="0.05"/>
21391 </section>
21392 <section name="b_spline">
21393 <param name="num_nodes" value="5"/>
21394 </section>
21395 </section>
21396 <section name="Scoring">
21397 <param name="stop_report_after_feature" value="5"/>
21398 <param name="rt_normalization_factor" value="100.0"/>
21399 <param name="quantification_cutoff" value="0.0"/>
21400 <param name="write_convex_hull" value="false"/>
21401 <param name="spectrum_addition_method" value="simple"/>
21402 <param name="add_up_spectra" value="1"/>
21403 <param name="spacing_for_spectra_resampling" value="0.005"/>
21404 <param name="uis_threshold_sn" value="-1"/>
21405 <param name="uis_threshold_peak_area" value="0"/>
21406 <param name="scoring_model" value="default"/>
21407 <param name="im_extra_drift" value="0.0"/>
21408 <param name="strict" value="true"/>
21409 <section name="TransitionGroupPicker">
21410 <param name="stop_after_feature" value="-1"/>
21411 <param name="min_peak_width" value="-1.0"/>
21412 <param name="peak_integration" value="original"/>
21413 <param name="background_subtraction" value="none"/>
21414 <param name="recalculate_peaks" value="true"/>
21415 <param name="use_precursors" value="false"/>
21416 <param name="use_consensus" value="true"/>
21417 <param name="recalculate_peaks_max_z" value="0.75"/>
21418 <param name="minimal_quality" value="-1.5"/>
21419 <param name="resample_boundary" value="15.0"/>
21420 <param name="compute_peak_quality" value="false"/>
21421 <param name="compute_peak_shape_metrics" value="false"/>
21422 <param name="compute_total_mi" value="false"/>
21423 <param name="boundary_selection_method" value="largest"/>
21424 <section name="PeakPickerMRM">
21425 <param name="sgolay_frame_length" value="11"/>
21426 <param name="sgolay_polynomial_order" value="3"/>
21427 <param name="gauss_width" value="30.0"/>
21428 <param name="use_gauss" value="false"/>
21429 <param name="peak_width" value="-1.0"/>
21430 <param name="signal_to_noise" value="0.1"/>
21431 <param name="write_sn_log_messages" value="false"/>
21432 <param name="remove_overlapping_peaks" value="true"/>
21433 <param name="method" value="corrected"/>
21434 </section>
21435 <section name="PeakIntegrator">
21436 <param name="integration_type" value="intensity_sum"/>
21437 <param name="baseline_type" value="base_to_base"/>
21438 <param name="fit_EMG" value="false"/>
21439 </section>
21440 </section>
21441 <section name="DIAScoring">
21442 <param name="dia_extraction_window" value="0.05"/>
21443 <param name="dia_extraction_unit" value="Th"/>
21444 <param name="dia_centroided" value="false"/>
21445 <param name="dia_byseries_intensity_min" value="300.0"/>
21446 <param name="dia_byseries_ppm_diff" value="10.0"/>
21447 <param name="dia_nr_isotopes" value="4"/>
21448 <param name="dia_nr_charges" value="4"/>
21449 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21450 </section>
21451 <section name="EMGScoring">
21452 <param name="max_iteration" value="10"/>
21453 </section>
21454 <section name="Scores">
21455 <param name="use_shape_score" value="true"/>
21456 <param name="use_coelution_score" value="true"/>
21457 <param name="use_rt_score" value="true"/>
21458 <param name="use_library_score" value="true"/>
21459 <param name="use_intensity_score" value="true"/>
21460 <param name="use_nr_peaks_score" value="true"/>
21461 <param name="use_total_xic_score" value="true"/>
21462 <param name="use_total_mi_score" value="false"/>
21463 <param name="use_sn_score" value="true"/>
21464 <param name="use_mi_score" value="true"/>
21465 <param name="use_dia_scores" value="true"/>
21466 <param name="use_ms1_correlation" value="false"/>
21467 <param name="use_sonar_scores" value="false"/>
21468 <param name="use_ion_mobility_scores" value="false"/>
21469 <param name="use_ms1_fullscan" value="false"/>
21470 <param name="use_ms1_mi" value="true"/>
21471 <param name="use_uis_scores" value="false"/>
21472 </section>
21473 </section>
21474 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
21475 <output name="ctd_out" ftype="xml">
21476 <assert_contents>
21477 <is_valid_xml/>
21478 </assert_contents>
21479 </output>
21480 </test>
21481 <test expect_num_outputs="3">
21482 <conditional name="adv_opts_cond">
21483 <param name="adv_opts_selector" value="advanced"/>
21484 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21485 <param name="sort_swath_maps" value="false"/>
21486 <param name="enable_ms1" value="true"/>
21487 <param name="enable_ipf" value="true"/>
21488 <param name="out_chrom_type" value="mzML"/>
21489 <param name="min_upper_edge_dist" value="0.0"/>
21490 <param name="extra_rt_extraction_window" value="0.0"/>
21491 <param name="mz_extraction_window_unit" value="Th"/>
21492 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21493 <param name="use_ms1_ion_mobility" value="true"/>
21494 <param name="matching_window_only" value="false"/>
21495 <param name="irt_mz_extraction_window" value="50.0"/>
21496 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21497 <param name="irt_im_extraction_window" value="-1.0"/>
21498 <param name="min_rsq" value="0.95"/>
21499 <param name="min_coverage" value="0.6"/>
21500 <param name="split_file_input" value="false"/>
21501 <param name="use_elution_model_score" value="false"/>
21502 <param name="readOptions" value="normal"/>
21503 <param name="mz_correction_function" value="none"/>
21504 <param name="extraction_function" value="tophat"/>
21505 <param name="batchSize" value="1000"/>
21506 <param name="ms1_isotopes" value="2"/>
21507 <param name="force" value="false"/>
21508 <param name="test" value="true"/>
21509 </conditional>
21510 <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
21511 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21512 <param name="tr_type" value=""/>
21513 <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21514 <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21515 <param name="sonar" value="false"/>
21516 <param name="rt_extraction_window" value="600.0"/>
21517 <param name="ion_mobility_window" value="-1.0"/>
21518 <param name="mz_extraction_window" value="0.05"/>
21519 <param name="mz_extraction_window_ms1" value="50.0"/>
21520 <param name="im_extraction_window_ms1" value="-1.0"/>
21521 <section name="Debugging"/>
21522 <section name="Calibration">
21523 <param name="ms1_im_calibration" value="false"/>
21524 <param name="im_correction_function" value="linear"/>
21525 <param name="debug_im_file" value=""/>
21526 <param name="debug_mz_file" value=""/>
21527 </section>
21528 <section name="Library">
21529 <param name="retentionTimeInterpretation" value="iRT"/>
21530 <param name="override_group_label_check" value="false"/>
21531 <param name="force_invalid_mods" value="false"/>
21532 </section>
21533 <section name="RTNormalization">
21534 <param name="alignmentMethod" value="linear"/>
21535 <param name="outlierMethod" value="iter_residual"/>
21536 <param name="useIterativeChauvenet" value="false"/>
21537 <param name="RANSACMaxIterations" value="1000"/>
21538 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21539 <param name="RANSACSamplingSize" value="10"/>
21540 <param name="estimateBestPeptides" value="false"/>
21541 <param name="InitialQualityCutoff" value="0.5"/>
21542 <param name="OverallQualityCutoff" value="5.5"/>
21543 <param name="NrRTBins" value="10"/>
21544 <param name="MinPeptidesPerBin" value="1"/>
21545 <param name="MinBinsFilled" value="8"/>
21546 <section name="lowess">
21547 <param name="span" value="0.05"/>
21548 </section>
21549 <section name="b_spline">
21550 <param name="num_nodes" value="5"/>
21551 </section>
21552 </section>
21553 <section name="Scoring">
21554 <param name="stop_report_after_feature" value="5"/>
21555 <param name="rt_normalization_factor" value="100.0"/>
21556 <param name="quantification_cutoff" value="0.0"/>
21557 <param name="write_convex_hull" value="false"/>
21558 <param name="spectrum_addition_method" value="simple"/>
21559 <param name="add_up_spectra" value="1"/>
21560 <param name="spacing_for_spectra_resampling" value="0.005"/>
21561 <param name="uis_threshold_sn" value="-1"/>
21562 <param name="uis_threshold_peak_area" value="0"/>
21563 <param name="scoring_model" value="default"/>
21564 <param name="im_extra_drift" value="0.0"/>
21565 <param name="strict" value="true"/>
21566 <section name="TransitionGroupPicker">
21567 <param name="stop_after_feature" value="-1"/>
21568 <param name="min_peak_width" value="-1.0"/>
21569 <param name="peak_integration" value="original"/>
21570 <param name="background_subtraction" value="none"/>
21571 <param name="recalculate_peaks" value="true"/>
21572 <param name="use_precursors" value="true"/>
21573 <param name="use_consensus" value="true"/>
21574 <param name="recalculate_peaks_max_z" value="0.75"/>
21575 <param name="minimal_quality" value="-1.5"/>
21576 <param name="resample_boundary" value="15.0"/>
21577 <param name="compute_peak_quality" value="false"/>
21578 <param name="compute_peak_shape_metrics" value="false"/>
21579 <param name="compute_total_mi" value="false"/>
21580 <param name="boundary_selection_method" value="largest"/>
21581 <section name="PeakPickerMRM">
21582 <param name="sgolay_frame_length" value="11"/>
21583 <param name="sgolay_polynomial_order" value="3"/>
21584 <param name="gauss_width" value="30.0"/>
21585 <param name="use_gauss" value="false"/>
21586 <param name="peak_width" value="-1.0"/>
21587 <param name="signal_to_noise" value="0.1"/>
21588 <param name="write_sn_log_messages" value="false"/>
21589 <param name="remove_overlapping_peaks" value="true"/>
21590 <param name="method" value="corrected"/>
21591 </section>
21592 <section name="PeakIntegrator">
21593 <param name="integration_type" value="intensity_sum"/>
21594 <param name="baseline_type" value="base_to_base"/>
21595 <param name="fit_EMG" value="false"/>
21596 </section>
21597 </section>
21598 <section name="DIAScoring">
21599 <param name="dia_extraction_window" value="0.05"/>
21600 <param name="dia_extraction_unit" value="Th"/>
21601 <param name="dia_centroided" value="false"/>
21602 <param name="dia_byseries_intensity_min" value="300.0"/>
21603 <param name="dia_byseries_ppm_diff" value="10.0"/>
21604 <param name="dia_nr_isotopes" value="4"/>
21605 <param name="dia_nr_charges" value="4"/>
21606 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21607 </section>
21608 <section name="EMGScoring">
21609 <param name="max_iteration" value="10"/>
21610 </section>
21611 <section name="Scores">
21612 <param name="use_shape_score" value="true"/>
21613 <param name="use_coelution_score" value="true"/>
21614 <param name="use_rt_score" value="true"/>
21615 <param name="use_library_score" value="true"/>
21616 <param name="use_intensity_score" value="true"/>
21617 <param name="use_nr_peaks_score" value="true"/>
21618 <param name="use_total_xic_score" value="true"/>
21619 <param name="use_total_mi_score" value="false"/>
21620 <param name="use_sn_score" value="true"/>
21621 <param name="use_mi_score" value="false"/>
21622 <param name="use_dia_scores" value="true"/>
21623 <param name="use_ms1_correlation" value="false"/>
21624 <param name="use_sonar_scores" value="false"/>
21625 <param name="use_ion_mobility_scores" value="false"/>
21626 <param name="use_ms1_fullscan" value="false"/>
21627 <param name="use_ms1_mi" value="false"/>
21628 <param name="use_uis_scores" value="false"/>
21629 </section>
21630 </section>
21631 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21632 <output name="ctd_out" ftype="xml">
21633 <assert_contents>
21634 <is_valid_xml/>
21635 </assert_contents>
21636 </output>
21637 </test>
21638 <test expect_num_outputs="3">
21639 <conditional name="adv_opts_cond">
21640 <param name="adv_opts_selector" value="advanced"/>
21641 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21642 <param name="sort_swath_maps" value="false"/>
21643 <param name="enable_ms1" value="true"/>
21644 <param name="enable_ipf" value="true"/>
21645 <param name="out_chrom_type" value="mzML"/>
21646 <param name="min_upper_edge_dist" value="0.0"/>
21647 <param name="extra_rt_extraction_window" value="0.0"/>
21648 <param name="mz_extraction_window_unit" value="ppm"/>
21649 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21650 <param name="use_ms1_ion_mobility" value="true"/>
21651 <param name="matching_window_only" value="false"/>
21652 <param name="irt_mz_extraction_window" value="50.0"/>
21653 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21654 <param name="irt_im_extraction_window" value="-1.0"/>
21655 <param name="min_rsq" value="0.95"/>
21656 <param name="min_coverage" value="0.6"/>
21657 <param name="split_file_input" value="false"/>
21658 <param name="use_elution_model_score" value="false"/>
21659 <param name="readOptions" value="workingInMemory"/>
21660 <param name="mz_correction_function" value="none"/>
21661 <param name="extraction_function" value="tophat"/>
21662 <param name="batchSize" value="1000"/>
21663 <param name="ms1_isotopes" value="2"/>
21664 <param name="force" value="false"/>
21665 <param name="test" value="false"/>
21666 </conditional>
21667 <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
21668 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21669 <param name="tr_type" value=""/>
21670 <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21671 <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21672 <param name="sonar" value="false"/>
21673 <param name="rt_extraction_window" value="600.0"/>
21674 <param name="ion_mobility_window" value="-1.0"/>
21675 <param name="mz_extraction_window" value="50.0"/>
21676 <param name="mz_extraction_window_ms1" value="50.0"/>
21677 <param name="im_extraction_window_ms1" value="-1.0"/>
21678 <section name="Debugging"/>
21679 <section name="Calibration">
21680 <param name="ms1_im_calibration" value="false"/>
21681 <param name="im_correction_function" value="linear"/>
21682 <param name="debug_im_file" value=""/>
21683 <param name="debug_mz_file" value=""/>
21684 </section>
21685 <section name="Library">
21686 <param name="retentionTimeInterpretation" value="iRT"/>
21687 <param name="override_group_label_check" value="false"/>
21688 <param name="force_invalid_mods" value="false"/>
21689 </section>
21690 <section name="RTNormalization">
21691 <param name="alignmentMethod" value="linear"/>
21692 <param name="outlierMethod" value="iter_residual"/>
21693 <param name="useIterativeChauvenet" value="false"/>
21694 <param name="RANSACMaxIterations" value="1000"/>
21695 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21696 <param name="RANSACSamplingSize" value="10"/>
21697 <param name="estimateBestPeptides" value="false"/>
21698 <param name="InitialQualityCutoff" value="0.5"/>
21699 <param name="OverallQualityCutoff" value="5.5"/>
21700 <param name="NrRTBins" value="10"/>
21701 <param name="MinPeptidesPerBin" value="1"/>
21702 <param name="MinBinsFilled" value="8"/>
21703 <section name="lowess">
21704 <param name="span" value="0.05"/>
21705 </section>
21706 <section name="b_spline">
21707 <param name="num_nodes" value="5"/>
21708 </section>
21709 </section>
21710 <section name="Scoring">
21711 <param name="stop_report_after_feature" value="5"/>
21712 <param name="rt_normalization_factor" value="100.0"/>
21713 <param name="quantification_cutoff" value="0.0"/>
21714 <param name="write_convex_hull" value="false"/>
21715 <param name="spectrum_addition_method" value="simple"/>
21716 <param name="add_up_spectra" value="1"/>
21717 <param name="spacing_for_spectra_resampling" value="0.005"/>
21718 <param name="uis_threshold_sn" value="-1"/>
21719 <param name="uis_threshold_peak_area" value="0"/>
21720 <param name="scoring_model" value="default"/>
21721 <param name="im_extra_drift" value="0.0"/>
21722 <param name="strict" value="true"/>
21723 <section name="TransitionGroupPicker">
21724 <param name="stop_after_feature" value="-1"/>
21725 <param name="min_peak_width" value="-1.0"/>
21726 <param name="peak_integration" value="original"/>
21727 <param name="background_subtraction" value="none"/>
21728 <param name="recalculate_peaks" value="true"/>
21729 <param name="use_precursors" value="false"/>
21730 <param name="use_consensus" value="true"/>
21731 <param name="recalculate_peaks_max_z" value="0.75"/>
21732 <param name="minimal_quality" value="-1.5"/>
21733 <param name="resample_boundary" value="15.0"/>
21734 <param name="compute_peak_quality" value="false"/>
21735 <param name="compute_peak_shape_metrics" value="false"/>
21736 <param name="compute_total_mi" value="false"/>
21737 <param name="boundary_selection_method" value="largest"/>
21738 <section name="PeakPickerMRM">
21739 <param name="sgolay_frame_length" value="11"/>
21740 <param name="sgolay_polynomial_order" value="3"/>
21741 <param name="gauss_width" value="30.0"/>
21742 <param name="use_gauss" value="false"/>
21743 <param name="peak_width" value="-1.0"/>
21744 <param name="signal_to_noise" value="0.1"/>
21745 <param name="write_sn_log_messages" value="false"/>
21746 <param name="remove_overlapping_peaks" value="true"/>
21747 <param name="method" value="corrected"/>
21748 </section>
21749 <section name="PeakIntegrator">
21750 <param name="integration_type" value="intensity_sum"/>
21751 <param name="baseline_type" value="base_to_base"/>
21752 <param name="fit_EMG" value="false"/>
21753 </section>
21754 </section>
21755 <section name="DIAScoring">
21756 <param name="dia_extraction_window" value="0.05"/>
21757 <param name="dia_extraction_unit" value="Th"/>
21758 <param name="dia_centroided" value="false"/>
21759 <param name="dia_byseries_intensity_min" value="300.0"/>
21760 <param name="dia_byseries_ppm_diff" value="10.0"/>
21761 <param name="dia_nr_isotopes" value="4"/>
21762 <param name="dia_nr_charges" value="4"/>
21763 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21764 </section>
21765 <section name="EMGScoring">
21766 <param name="max_iteration" value="10"/>
21767 </section>
21768 <section name="Scores">
21769 <param name="use_shape_score" value="true"/>
21770 <param name="use_coelution_score" value="true"/>
21771 <param name="use_rt_score" value="true"/>
21772 <param name="use_library_score" value="true"/>
21773 <param name="use_intensity_score" value="true"/>
21774 <param name="use_nr_peaks_score" value="true"/>
21775 <param name="use_total_xic_score" value="true"/>
21776 <param name="use_total_mi_score" value="false"/>
21777 <param name="use_sn_score" value="true"/>
21778 <param name="use_mi_score" value="true"/>
21779 <param name="use_dia_scores" value="true"/>
21780 <param name="use_ms1_correlation" value="false"/>
21781 <param name="use_sonar_scores" value="false"/>
21782 <param name="use_ion_mobility_scores" value="false"/>
21783 <param name="use_ms1_fullscan" value="false"/>
21784 <param name="use_ms1_mi" value="true"/>
21785 <param name="use_uis_scores" value="false"/>
21786 </section>
21787 </section>
21788 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21789 <output name="ctd_out" ftype="xml">
21790 <assert_contents>
21791 <is_valid_xml/>
21792 </assert_contents>
21793 </output>
21794 </test>
21795 <test expect_num_outputs="3">
21796 <conditional name="adv_opts_cond">
21797 <param name="adv_opts_selector" value="advanced"/>
21798 <param name="sort_swath_maps" value="false"/>
21799 <param name="enable_ms1" value="true"/>
21800 <param name="enable_ipf" value="true"/>
21801 <param name="out_chrom_type" value="mzML"/>
21802 <param name="min_upper_edge_dist" value="0.0"/>
21803 <param name="extra_rt_extraction_window" value="0.0"/>
21804 <param name="mz_extraction_window_unit" value="ppm"/>
21805 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21806 <param name="use_ms1_ion_mobility" value="false"/>
21807 <param name="matching_window_only" value="false"/>
21808 <param name="irt_mz_extraction_window" value="50.0"/>
21809 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21810 <param name="irt_im_extraction_window" value="-1.0"/>
21811 <param name="min_rsq" value="0.95"/>
21812 <param name="min_coverage" value="0.6"/>
21813 <param name="split_file_input" value="false"/>
21814 <param name="use_elution_model_score" value="false"/>
21815 <param name="readOptions" value="workingInMemory"/>
21816 <param name="mz_correction_function" value="none"/>
21817 <param name="extraction_function" value="tophat"/>
21818 <param name="batchSize" value="1000"/>
21819 <param name="ms1_isotopes" value="3"/>
21820 <param name="force" value="false"/>
21821 <param name="test" value="false"/>
21822 </conditional>
21823 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21824 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
21825 <param name="tr_type" value=""/>
21826 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
21827 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
21828 <param name="sonar" value="false"/>
21829 <param name="rt_extraction_window" value="600.0"/>
21830 <param name="ion_mobility_window" value="0.05"/>
21831 <param name="mz_extraction_window" value="50.0"/>
21832 <param name="mz_extraction_window_ms1" value="50.0"/>
21833 <param name="im_extraction_window_ms1" value="-1.0"/>
21834 <section name="Debugging"/>
21835 <section name="Calibration">
21836 <param name="ms1_im_calibration" value="false"/>
21837 <param name="im_correction_function" value="linear"/>
21838 <param name="debug_im_file" value=""/>
21839 <param name="debug_mz_file" value=""/>
21840 </section>
21841 <section name="Library">
21842 <param name="retentionTimeInterpretation" value="iRT"/>
21843 <param name="override_group_label_check" value="false"/>
21844 <param name="force_invalid_mods" value="false"/>
21845 </section>
21846 <section name="RTNormalization">
21847 <param name="alignmentMethod" value="linear"/>
21848 <param name="outlierMethod" value="iter_residual"/>
21849 <param name="useIterativeChauvenet" value="false"/>
21850 <param name="RANSACMaxIterations" value="1000"/>
21851 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21852 <param name="RANSACSamplingSize" value="10"/>
21853 <param name="estimateBestPeptides" value="false"/>
21854 <param name="InitialQualityCutoff" value="0.5"/>
21855 <param name="OverallQualityCutoff" value="5.5"/>
21856 <param name="NrRTBins" value="10"/>
21857 <param name="MinPeptidesPerBin" value="1"/>
21858 <param name="MinBinsFilled" value="8"/>
21859 <section name="lowess">
21860 <param name="span" value="0.05"/>
21861 </section>
21862 <section name="b_spline">
21863 <param name="num_nodes" value="5"/>
21864 </section>
21865 </section>
21866 <section name="Scoring">
21867 <param name="stop_report_after_feature" value="5"/>
21868 <param name="rt_normalization_factor" value="100.0"/>
21869 <param name="quantification_cutoff" value="0.0"/>
21870 <param name="write_convex_hull" value="false"/>
21871 <param name="spectrum_addition_method" value="simple"/>
21872 <param name="add_up_spectra" value="1"/>
21873 <param name="spacing_for_spectra_resampling" value="0.005"/>
21874 <param name="uis_threshold_sn" value="-1"/>
21875 <param name="uis_threshold_peak_area" value="0"/>
21876 <param name="scoring_model" value="default"/>
21877 <param name="im_extra_drift" value="0.0"/>
21878 <param name="strict" value="true"/>
21879 <section name="TransitionGroupPicker">
21880 <param name="stop_after_feature" value="-1"/>
21881 <param name="min_peak_width" value="-1.0"/>
21882 <param name="peak_integration" value="original"/>
21883 <param name="background_subtraction" value="none"/>
21884 <param name="recalculate_peaks" value="true"/>
21885 <param name="use_precursors" value="false"/>
21886 <param name="use_consensus" value="true"/>
21887 <param name="recalculate_peaks_max_z" value="0.75"/>
21888 <param name="minimal_quality" value="-1.5"/>
21889 <param name="resample_boundary" value="15.0"/>
21890 <param name="compute_peak_quality" value="false"/>
21891 <param name="compute_peak_shape_metrics" value="false"/>
21892 <param name="compute_total_mi" value="false"/>
21893 <param name="boundary_selection_method" value="largest"/>
21894 <section name="PeakPickerMRM">
21895 <param name="sgolay_frame_length" value="11"/>
21896 <param name="sgolay_polynomial_order" value="3"/>
21897 <param name="gauss_width" value="30.0"/>
21898 <param name="use_gauss" value="false"/>
21899 <param name="peak_width" value="-1.0"/>
21900 <param name="signal_to_noise" value="0.1"/>
21901 <param name="write_sn_log_messages" value="false"/>
21902 <param name="remove_overlapping_peaks" value="true"/>
21903 <param name="method" value="corrected"/>
21904 </section>
21905 <section name="PeakIntegrator">
21906 <param name="integration_type" value="intensity_sum"/>
21907 <param name="baseline_type" value="base_to_base"/>
21908 <param name="fit_EMG" value="false"/>
21909 </section>
21910 </section>
21911 <section name="DIAScoring">
21912 <param name="dia_extraction_window" value="0.05"/>
21913 <param name="dia_extraction_unit" value="Th"/>
21914 <param name="dia_centroided" value="false"/>
21915 <param name="dia_byseries_intensity_min" value="300.0"/>
21916 <param name="dia_byseries_ppm_diff" value="10.0"/>
21917 <param name="dia_nr_isotopes" value="4"/>
21918 <param name="dia_nr_charges" value="4"/>
21919 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21920 </section>
21921 <section name="EMGScoring">
21922 <param name="max_iteration" value="10"/>
21923 </section>
21924 <section name="Scores">
21925 <param name="use_shape_score" value="true"/>
21926 <param name="use_coelution_score" value="true"/>
21927 <param name="use_rt_score" value="true"/>
21928 <param name="use_library_score" value="true"/>
21929 <param name="use_intensity_score" value="true"/>
21930 <param name="use_nr_peaks_score" value="true"/>
21931 <param name="use_total_xic_score" value="true"/>
21932 <param name="use_total_mi_score" value="false"/>
21933 <param name="use_sn_score" value="true"/>
21934 <param name="use_mi_score" value="true"/>
21935 <param name="use_dia_scores" value="true"/>
21936 <param name="use_ms1_correlation" value="false"/>
21937 <param name="use_sonar_scores" value="false"/>
21938 <param name="use_ion_mobility_scores" value="true"/>
21939 <param name="use_ms1_fullscan" value="false"/>
21940 <param name="use_ms1_mi" value="true"/>
21941 <param name="use_uis_scores" value="false"/>
21942 </section>
21943 </section>
21944 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21945 <output name="ctd_out" ftype="xml">
21946 <assert_contents>
21947 <is_valid_xml/>
21948 </assert_contents>
21949 </output>
21950 </test>
21951 <test expect_num_outputs="3">
21952 <conditional name="adv_opts_cond">
21953 <param name="adv_opts_selector" value="advanced"/>
21954 <param name="sort_swath_maps" value="false"/>
21955 <param name="enable_ms1" value="true"/>
21956 <param name="enable_ipf" value="true"/>
21957 <param name="out_chrom_type" value="mzML"/>
21958 <param name="min_upper_edge_dist" value="0.0"/>
21959 <param name="extra_rt_extraction_window" value="0.0"/>
21960 <param name="mz_extraction_window_unit" value="ppm"/>
21961 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21962 <param name="use_ms1_ion_mobility" value="false"/>
21963 <param name="matching_window_only" value="false"/>
21964 <param name="irt_mz_extraction_window" value="50.0"/>
21965 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21966 <param name="irt_im_extraction_window" value="-1.0"/>
21967 <param name="min_rsq" value="0.95"/>
21968 <param name="min_coverage" value="0.6"/>
21969 <param name="split_file_input" value="false"/>
21970 <param name="use_elution_model_score" value="false"/>
21971 <param name="readOptions" value="cache"/>
21972 <param name="mz_correction_function" value="none"/>
21973 <param name="extraction_function" value="tophat"/>
21974 <param name="batchSize" value="1000"/>
21975 <param name="ms1_isotopes" value="3"/>
21976 <param name="force" value="false"/>
21977 <param name="test" value="false"/>
21978 </conditional>
21979 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21980 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
21981 <param name="tr_type" value=""/>
21982 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
21983 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
21984 <param name="sonar" value="false"/>
21985 <param name="rt_extraction_window" value="600.0"/>
21986 <param name="ion_mobility_window" value="0.05"/>
21987 <param name="mz_extraction_window" value="50.0"/>
21988 <param name="mz_extraction_window_ms1" value="50.0"/>
21989 <param name="im_extraction_window_ms1" value="-1.0"/>
21990 <section name="Debugging"/>
21991 <section name="Calibration">
21992 <param name="ms1_im_calibration" value="false"/>
21993 <param name="im_correction_function" value="linear"/>
21994 <param name="debug_im_file" value=""/>
21995 <param name="debug_mz_file" value=""/>
21996 </section>
21997 <section name="Library">
21998 <param name="retentionTimeInterpretation" value="iRT"/>
21999 <param name="override_group_label_check" value="false"/>
22000 <param name="force_invalid_mods" value="false"/>
22001 </section>
22002 <section name="RTNormalization">
22003 <param name="alignmentMethod" value="linear"/>
22004 <param name="outlierMethod" value="iter_residual"/>
22005 <param name="useIterativeChauvenet" value="false"/>
22006 <param name="RANSACMaxIterations" value="1000"/>
22007 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22008 <param name="RANSACSamplingSize" value="10"/>
22009 <param name="estimateBestPeptides" value="false"/>
22010 <param name="InitialQualityCutoff" value="0.5"/>
22011 <param name="OverallQualityCutoff" value="5.5"/>
22012 <param name="NrRTBins" value="10"/>
22013 <param name="MinPeptidesPerBin" value="1"/>
22014 <param name="MinBinsFilled" value="8"/>
22015 <section name="lowess">
22016 <param name="span" value="0.05"/>
22017 </section>
22018 <section name="b_spline">
22019 <param name="num_nodes" value="5"/>
22020 </section>
22021 </section>
22022 <section name="Scoring">
22023 <param name="stop_report_after_feature" value="5"/>
22024 <param name="rt_normalization_factor" value="100.0"/>
22025 <param name="quantification_cutoff" value="0.0"/>
22026 <param name="write_convex_hull" value="false"/>
22027 <param name="spectrum_addition_method" value="simple"/>
22028 <param name="add_up_spectra" value="1"/>
22029 <param name="spacing_for_spectra_resampling" value="0.005"/>
22030 <param name="uis_threshold_sn" value="-1"/>
22031 <param name="uis_threshold_peak_area" value="0"/>
22032 <param name="scoring_model" value="default"/>
22033 <param name="im_extra_drift" value="0.0"/>
22034 <param name="strict" value="true"/>
22035 <section name="TransitionGroupPicker">
22036 <param name="stop_after_feature" value="-1"/>
22037 <param name="min_peak_width" value="-1.0"/>
22038 <param name="peak_integration" value="original"/>
22039 <param name="background_subtraction" value="none"/>
22040 <param name="recalculate_peaks" value="true"/>
22041 <param name="use_precursors" value="false"/>
22042 <param name="use_consensus" value="true"/>
22043 <param name="recalculate_peaks_max_z" value="0.75"/>
22044 <param name="minimal_quality" value="-1.5"/>
22045 <param name="resample_boundary" value="15.0"/>
22046 <param name="compute_peak_quality" value="false"/>
22047 <param name="compute_peak_shape_metrics" value="false"/>
22048 <param name="compute_total_mi" value="false"/>
22049 <param name="boundary_selection_method" value="largest"/>
22050 <section name="PeakPickerMRM">
22051 <param name="sgolay_frame_length" value="11"/>
22052 <param name="sgolay_polynomial_order" value="3"/>
22053 <param name="gauss_width" value="30.0"/>
22054 <param name="use_gauss" value="false"/>
22055 <param name="peak_width" value="-1.0"/>
22056 <param name="signal_to_noise" value="0.1"/>
22057 <param name="write_sn_log_messages" value="false"/>
22058 <param name="remove_overlapping_peaks" value="true"/>
22059 <param name="method" value="corrected"/>
22060 </section>
22061 <section name="PeakIntegrator">
22062 <param name="integration_type" value="intensity_sum"/>
22063 <param name="baseline_type" value="base_to_base"/>
22064 <param name="fit_EMG" value="false"/>
22065 </section>
22066 </section>
22067 <section name="DIAScoring">
22068 <param name="dia_extraction_window" value="0.05"/>
22069 <param name="dia_extraction_unit" value="Th"/>
22070 <param name="dia_centroided" value="false"/>
22071 <param name="dia_byseries_intensity_min" value="300.0"/>
22072 <param name="dia_byseries_ppm_diff" value="10.0"/>
22073 <param name="dia_nr_isotopes" value="4"/>
22074 <param name="dia_nr_charges" value="4"/>
22075 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22076 </section>
22077 <section name="EMGScoring">
22078 <param name="max_iteration" value="10"/>
22079 </section>
22080 <section name="Scores">
22081 <param name="use_shape_score" value="true"/>
22082 <param name="use_coelution_score" value="true"/>
22083 <param name="use_rt_score" value="true"/>
22084 <param name="use_library_score" value="true"/>
22085 <param name="use_intensity_score" value="true"/>
22086 <param name="use_nr_peaks_score" value="true"/>
22087 <param name="use_total_xic_score" value="true"/>
22088 <param name="use_total_mi_score" value="false"/>
22089 <param name="use_sn_score" value="true"/>
22090 <param name="use_mi_score" value="true"/>
22091 <param name="use_dia_scores" value="true"/>
22092 <param name="use_ms1_correlation" value="false"/>
22093 <param name="use_sonar_scores" value="false"/>
22094 <param name="use_ion_mobility_scores" value="true"/>
22095 <param name="use_ms1_fullscan" value="false"/>
22096 <param name="use_ms1_mi" value="true"/>
22097 <param name="use_uis_scores" value="false"/>
22098 </section>
22099 </section>
22100 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
22101 <output name="ctd_out" ftype="xml">
22102 <assert_contents>
22103 <is_valid_xml/>
22104 </assert_contents>
22105 </output>
22106 </test>
22107 <test expect_num_outputs="3">
22108 <conditional name="adv_opts_cond">
22109 <param name="adv_opts_selector" value="advanced"/>
22110 <param name="sort_swath_maps" value="false"/>
22111 <param name="enable_ms1" value="true"/>
22112 <param name="enable_ipf" value="true"/>
22113 <param name="out_chrom_type" value="mzML"/>
22114 <param name="min_upper_edge_dist" value="0.0"/>
22115 <param name="extra_rt_extraction_window" value="0.0"/>
22116 <param name="mz_extraction_window_unit" value="ppm"/>
22117 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22118 <param name="use_ms1_ion_mobility" value="false"/>
22119 <param name="matching_window_only" value="false"/>
22120 <param name="irt_mz_extraction_window" value="50.0"/>
22121 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22122 <param name="irt_im_extraction_window" value="-1.0"/>
22123 <param name="min_rsq" value="0.95"/>
22124 <param name="min_coverage" value="0.6"/>
22125 <param name="split_file_input" value="false"/>
22126 <param name="use_elution_model_score" value="false"/>
22127 <param name="readOptions" value="workingInMemory"/>
22128 <param name="mz_correction_function" value="none"/>
22129 <param name="extraction_function" value="tophat"/>
22130 <param name="batchSize" value="1000"/>
22131 <param name="ms1_isotopes" value="3"/>
22132 <param name="force" value="false"/>
22133 <param name="test" value="false"/>
22134 </conditional>
22135 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
22136 <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
22137 <param name="tr_type" value="pqp"/>
22138 <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22139 <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22140 <param name="sonar" value="false"/>
22141 <param name="rt_extraction_window" value="600.0"/>
22142 <param name="ion_mobility_window" value="0.05"/>
22143 <param name="mz_extraction_window" value="50.0"/>
22144 <param name="mz_extraction_window_ms1" value="50.0"/>
22145 <param name="im_extraction_window_ms1" value="-1.0"/>
22146 <section name="Debugging"/>
22147 <section name="Calibration">
22148 <param name="ms1_im_calibration" value="false"/>
22149 <param name="im_correction_function" value="linear"/>
22150 <param name="debug_im_file" value=""/>
22151 <param name="debug_mz_file" value=""/>
22152 </section>
22153 <section name="Library">
22154 <param name="retentionTimeInterpretation" value="iRT"/>
22155 <param name="override_group_label_check" value="false"/>
22156 <param name="force_invalid_mods" value="false"/>
22157 </section>
22158 <section name="RTNormalization">
22159 <param name="alignmentMethod" value="linear"/>
22160 <param name="outlierMethod" value="iter_residual"/>
22161 <param name="useIterativeChauvenet" value="false"/>
22162 <param name="RANSACMaxIterations" value="1000"/>
22163 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22164 <param name="RANSACSamplingSize" value="10"/>
22165 <param name="estimateBestPeptides" value="false"/>
22166 <param name="InitialQualityCutoff" value="0.5"/>
22167 <param name="OverallQualityCutoff" value="5.5"/>
22168 <param name="NrRTBins" value="10"/>
22169 <param name="MinPeptidesPerBin" value="1"/>
22170 <param name="MinBinsFilled" value="8"/>
22171 <section name="lowess">
22172 <param name="span" value="0.05"/>
22173 </section>
22174 <section name="b_spline">
22175 <param name="num_nodes" value="5"/>
22176 </section>
22177 </section>
22178 <section name="Scoring">
22179 <param name="stop_report_after_feature" value="5"/>
22180 <param name="rt_normalization_factor" value="100.0"/>
22181 <param name="quantification_cutoff" value="0.0"/>
22182 <param name="write_convex_hull" value="false"/>
22183 <param name="spectrum_addition_method" value="simple"/>
22184 <param name="add_up_spectra" value="1"/>
22185 <param name="spacing_for_spectra_resampling" value="0.005"/>
22186 <param name="uis_threshold_sn" value="-1"/>
22187 <param name="uis_threshold_peak_area" value="0"/>
22188 <param name="scoring_model" value="default"/>
22189 <param name="im_extra_drift" value="0.0"/>
22190 <param name="strict" value="true"/>
22191 <section name="TransitionGroupPicker">
22192 <param name="stop_after_feature" value="-1"/>
22193 <param name="min_peak_width" value="-1.0"/>
22194 <param name="peak_integration" value="original"/>
22195 <param name="background_subtraction" value="none"/>
22196 <param name="recalculate_peaks" value="true"/>
22197 <param name="use_precursors" value="false"/>
22198 <param name="use_consensus" value="true"/>
22199 <param name="recalculate_peaks_max_z" value="0.75"/>
22200 <param name="minimal_quality" value="-1.5"/>
22201 <param name="resample_boundary" value="15.0"/>
22202 <param name="compute_peak_quality" value="false"/>
22203 <param name="compute_peak_shape_metrics" value="false"/>
22204 <param name="compute_total_mi" value="false"/>
22205 <param name="boundary_selection_method" value="largest"/>
22206 <section name="PeakPickerMRM">
22207 <param name="sgolay_frame_length" value="11"/>
22208 <param name="sgolay_polynomial_order" value="3"/>
22209 <param name="gauss_width" value="30.0"/>
22210 <param name="use_gauss" value="false"/>
22211 <param name="peak_width" value="-1.0"/>
22212 <param name="signal_to_noise" value="0.1"/>
22213 <param name="write_sn_log_messages" value="false"/>
22214 <param name="remove_overlapping_peaks" value="true"/>
22215 <param name="method" value="corrected"/>
22216 </section>
22217 <section name="PeakIntegrator">
22218 <param name="integration_type" value="intensity_sum"/>
22219 <param name="baseline_type" value="base_to_base"/>
22220 <param name="fit_EMG" value="false"/>
22221 </section>
22222 </section>
22223 <section name="DIAScoring">
22224 <param name="dia_extraction_window" value="0.05"/>
22225 <param name="dia_extraction_unit" value="Th"/>
22226 <param name="dia_centroided" value="false"/>
22227 <param name="dia_byseries_intensity_min" value="300.0"/>
22228 <param name="dia_byseries_ppm_diff" value="10.0"/>
22229 <param name="dia_nr_isotopes" value="4"/>
22230 <param name="dia_nr_charges" value="4"/>
22231 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22232 </section>
22233 <section name="EMGScoring">
22234 <param name="max_iteration" value="10"/>
22235 </section>
22236 <section name="Scores">
22237 <param name="use_shape_score" value="true"/>
22238 <param name="use_coelution_score" value="true"/>
22239 <param name="use_rt_score" value="true"/>
22240 <param name="use_library_score" value="true"/>
22241 <param name="use_intensity_score" value="true"/>
22242 <param name="use_nr_peaks_score" value="true"/>
22243 <param name="use_total_xic_score" value="true"/>
22244 <param name="use_total_mi_score" value="false"/>
22245 <param name="use_sn_score" value="true"/>
22246 <param name="use_mi_score" value="true"/>
22247 <param name="use_dia_scores" value="true"/>
22248 <param name="use_ms1_correlation" value="false"/>
22249 <param name="use_sonar_scores" value="false"/>
22250 <param name="use_ion_mobility_scores" value="false"/>
22251 <param name="use_ms1_fullscan" value="false"/>
22252 <param name="use_ms1_mi" value="true"/>
22253 <param name="use_uis_scores" value="false"/>
22254 </section>
22255 </section>
22256 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
22257 <output name="ctd_out" ftype="xml">
22258 <assert_contents>
22259 <is_valid_xml/>
22260 </assert_contents>
22261 </output>
22262 </test>
22263 <test expect_num_outputs="2">
22264 <conditional name="adv_opts_cond">
22265 <param name="adv_opts_selector" value="advanced"/>
22266 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
22267 <param name="sort_swath_maps" value="false"/>
22268 <param name="enable_ms1" value="true"/>
22269 <param name="enable_ipf" value="true"/>
22270 <param name="min_upper_edge_dist" value="0.0"/>
22271 <param name="extra_rt_extraction_window" value="0.0"/>
22272 <param name="mz_extraction_window_unit" value="Th"/>
22273 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22274 <param name="use_ms1_ion_mobility" value="true"/>
22275 <param name="matching_window_only" value="false"/>
22276 <param name="irt_mz_extraction_window" value="50.0"/>
22277 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22278 <param name="irt_im_extraction_window" value="-1.0"/>
22279 <param name="min_rsq" value="0.95"/>
22280 <param name="min_coverage" value="0.6"/>
22281 <param name="split_file_input" value="false"/>
22282 <param name="use_elution_model_score" value="false"/>
22283 <param name="readOptions" value="normal"/>
22284 <param name="mz_correction_function" value="none"/>
22285 <param name="extraction_function" value="tophat"/>
22286 <param name="batchSize" value="1000"/>
22287 <param name="ms1_isotopes" value="0"/>
22288 <param name="force" value="false"/>
22289 <param name="test" value="true"/>
22290 </conditional>
22291 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
22292 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
22293 <param name="tr_type" value=""/>
22294 <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22295 <param name="sonar" value="false"/>
22296 <param name="rt_extraction_window" value="600.0"/>
22297 <param name="ion_mobility_window" value="-1.0"/>
22298 <param name="mz_extraction_window" value="0.05"/>
22299 <param name="mz_extraction_window_ms1" value="50.0"/>
22300 <param name="im_extraction_window_ms1" value="-1.0"/>
22301 <section name="Debugging"/>
22302 <section name="Calibration">
22303 <param name="ms1_im_calibration" value="false"/>
22304 <param name="im_correction_function" value="linear"/>
22305 <param name="debug_im_file" value=""/>
22306 <param name="debug_mz_file" value=""/>
22307 </section>
22308 <section name="Library">
22309 <param name="retentionTimeInterpretation" value="iRT"/>
22310 <param name="override_group_label_check" value="false"/>
22311 <param name="force_invalid_mods" value="false"/>
22312 </section>
22313 <section name="RTNormalization">
22314 <param name="alignmentMethod" value="linear"/>
22315 <param name="outlierMethod" value="iter_residual"/>
22316 <param name="useIterativeChauvenet" value="false"/>
22317 <param name="RANSACMaxIterations" value="1000"/>
22318 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22319 <param name="RANSACSamplingSize" value="10"/>
22320 <param name="estimateBestPeptides" value="false"/>
22321 <param name="InitialQualityCutoff" value="0.5"/>
22322 <param name="OverallQualityCutoff" value="5.5"/>
22323 <param name="NrRTBins" value="10"/>
22324 <param name="MinPeptidesPerBin" value="1"/>
22325 <param name="MinBinsFilled" value="8"/>
22326 <section name="lowess">
22327 <param name="span" value="0.05"/>
22328 </section>
22329 <section name="b_spline">
22330 <param name="num_nodes" value="5"/>
22331 </section>
22332 </section>
22333 <section name="Scoring">
22334 <param name="stop_report_after_feature" value="5"/>
22335 <param name="rt_normalization_factor" value="100.0"/>
22336 <param name="quantification_cutoff" value="0.0"/>
22337 <param name="write_convex_hull" value="false"/>
22338 <param name="spectrum_addition_method" value="simple"/>
22339 <param name="add_up_spectra" value="1"/>
22340 <param name="spacing_for_spectra_resampling" value="0.005"/>
22341 <param name="uis_threshold_sn" value="-1"/>
22342 <param name="uis_threshold_peak_area" value="0"/>
22343 <param name="scoring_model" value="default"/>
22344 <param name="im_extra_drift" value="0.0"/>
22345 <param name="strict" value="true"/>
22346 <section name="TransitionGroupPicker">
22347 <param name="stop_after_feature" value="-1"/>
22348 <param name="min_peak_width" value="-1.0"/>
22349 <param name="peak_integration" value="original"/>
22350 <param name="background_subtraction" value="none"/>
22351 <param name="recalculate_peaks" value="true"/>
22352 <param name="use_precursors" value="false"/>
22353 <param name="use_consensus" value="true"/>
22354 <param name="recalculate_peaks_max_z" value="0.75"/>
22355 <param name="minimal_quality" value="-1.5"/>
22356 <param name="resample_boundary" value="15.0"/>
22357 <param name="compute_peak_quality" value="true"/>
22358 <param name="compute_peak_shape_metrics" value="false"/>
22359 <param name="compute_total_mi" value="false"/>
22360 <param name="boundary_selection_method" value="largest"/>
22361 <section name="PeakPickerMRM">
22362 <param name="sgolay_frame_length" value="11"/>
22363 <param name="sgolay_polynomial_order" value="3"/>
22364 <param name="gauss_width" value="30.0"/>
22365 <param name="use_gauss" value="false"/>
22366 <param name="peak_width" value="-1.0"/>
22367 <param name="signal_to_noise" value="0.1"/>
22368 <param name="write_sn_log_messages" value="false"/>
22369 <param name="remove_overlapping_peaks" value="true"/>
22370 <param name="method" value="corrected"/>
22371 </section>
22372 <section name="PeakIntegrator">
22373 <param name="integration_type" value="intensity_sum"/>
22374 <param name="baseline_type" value="base_to_base"/>
22375 <param name="fit_EMG" value="false"/>
22376 </section>
22377 </section>
22378 <section name="DIAScoring">
22379 <param name="dia_extraction_window" value="0.05"/>
22380 <param name="dia_extraction_unit" value="Th"/>
22381 <param name="dia_centroided" value="false"/>
22382 <param name="dia_byseries_intensity_min" value="300.0"/>
22383 <param name="dia_byseries_ppm_diff" value="10.0"/>
22384 <param name="dia_nr_isotopes" value="4"/>
22385 <param name="dia_nr_charges" value="4"/>
22386 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22387 </section>
22388 <section name="EMGScoring">
22389 <param name="max_iteration" value="10"/>
22390 </section>
22391 <section name="Scores">
22392 <param name="use_shape_score" value="true"/>
22393 <param name="use_coelution_score" value="true"/>
22394 <param name="use_rt_score" value="true"/>
22395 <param name="use_library_score" value="true"/>
22396 <param name="use_intensity_score" value="true"/>
22397 <param name="use_nr_peaks_score" value="true"/>
22398 <param name="use_total_xic_score" value="true"/>
22399 <param name="use_total_mi_score" value="false"/>
22400 <param name="use_sn_score" value="true"/>
22401 <param name="use_mi_score" value="false"/>
22402 <param name="use_dia_scores" value="true"/>
22403 <param name="use_ms1_correlation" value="false"/>
22404 <param name="use_sonar_scores" value="false"/>
22405 <param name="use_ion_mobility_scores" value="false"/>
22406 <param name="use_ms1_fullscan" value="false"/>
22407 <param name="use_ms1_mi" value="true"/>
22408 <param name="use_uis_scores" value="false"/>
22409 </section>
22410 </section>
22411 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
22412 <output name="ctd_out" ftype="xml">
22413 <assert_contents>
22414 <is_valid_xml/>
22415 </assert_contents>
22416 </output>
22417 </test>
22418 <test expect_num_outputs="2">
22419 <conditional name="adv_opts_cond">
22420 <param name="adv_opts_selector" value="advanced"/>
22421 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
22422 <param name="sort_swath_maps" value="false"/>
22423 <param name="enable_ms1" value="true"/>
22424 <param name="enable_ipf" value="true"/>
22425 <param name="min_upper_edge_dist" value="0.0"/>
22426 <param name="extra_rt_extraction_window" value="0.0"/>
22427 <param name="mz_extraction_window_unit" value="Th"/>
22428 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22429 <param name="use_ms1_ion_mobility" value="true"/>
22430 <param name="matching_window_only" value="false"/>
22431 <param name="irt_mz_extraction_window" value="50.0"/>
22432 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22433 <param name="irt_im_extraction_window" value="-1.0"/>
22434 <param name="min_rsq" value="0.95"/>
22435 <param name="min_coverage" value="0.6"/>
22436 <param name="split_file_input" value="false"/>
22437 <param name="use_elution_model_score" value="false"/>
22438 <param name="readOptions" value="normal"/>
22439 <param name="mz_correction_function" value="none"/>
22440 <param name="extraction_function" value="tophat"/>
22441 <param name="batchSize" value="1000"/>
22442 <param name="ms1_isotopes" value="0"/>
22443 <param name="force" value="false"/>
22444 <param name="test" value="true"/>
22445 </conditional>
22446 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
22447 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
22448 <param name="tr_type" value=""/>
22449 <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22450 <param name="sonar" value="false"/>
22451 <param name="rt_extraction_window" value="600.0"/>
22452 <param name="ion_mobility_window" value="-1.0"/>
22453 <param name="mz_extraction_window" value="0.05"/>
22454 <param name="mz_extraction_window_ms1" value="50.0"/>
22455 <param name="im_extraction_window_ms1" value="-1.0"/>
22456 <section name="Debugging"/>
22457 <section name="Calibration">
22458 <param name="ms1_im_calibration" value="false"/>
22459 <param name="im_correction_function" value="linear"/>
22460 <param name="debug_im_file" value=""/>
22461 <param name="debug_mz_file" value=""/>
22462 </section>
22463 <section name="Library">
22464 <param name="retentionTimeInterpretation" value="iRT"/>
22465 <param name="override_group_label_check" value="false"/>
22466 <param name="force_invalid_mods" value="false"/>
22467 </section>
22468 <section name="RTNormalization">
22469 <param name="alignmentMethod" value="linear"/>
22470 <param name="outlierMethod" value="iter_residual"/>
22471 <param name="useIterativeChauvenet" value="false"/>
22472 <param name="RANSACMaxIterations" value="1000"/>
22473 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22474 <param name="RANSACSamplingSize" value="10"/>
22475 <param name="estimateBestPeptides" value="false"/>
22476 <param name="InitialQualityCutoff" value="0.5"/>
22477 <param name="OverallQualityCutoff" value="5.5"/>
22478 <param name="NrRTBins" value="10"/>
22479 <param name="MinPeptidesPerBin" value="1"/>
22480 <param name="MinBinsFilled" value="8"/>
22481 <section name="lowess">
22482 <param name="span" value="0.05"/>
22483 </section>
22484 <section name="b_spline">
22485 <param name="num_nodes" value="5"/>
22486 </section>
22487 </section>
22488 <section name="Scoring">
22489 <param name="stop_report_after_feature" value="5"/>
22490 <param name="rt_normalization_factor" value="100.0"/>
22491 <param name="quantification_cutoff" value="0.0"/>
22492 <param name="write_convex_hull" value="false"/>
22493 <param name="spectrum_addition_method" value="simple"/>
22494 <param name="add_up_spectra" value="1"/>
22495 <param name="spacing_for_spectra_resampling" value="0.005"/>
22496 <param name="uis_threshold_sn" value="-1"/>
22497 <param name="uis_threshold_peak_area" value="0"/>
22498 <param name="scoring_model" value="default"/>
22499 <param name="im_extra_drift" value="0.0"/>
22500 <param name="strict" value="true"/>
22501 <section name="TransitionGroupPicker">
22502 <param name="stop_after_feature" value="-1"/>
22503 <param name="min_peak_width" value="-1.0"/>
22504 <param name="peak_integration" value="original"/>
22505 <param name="background_subtraction" value="none"/>
22506 <param name="recalculate_peaks" value="true"/>
22507 <param name="use_precursors" value="false"/>
22508 <param name="use_consensus" value="true"/>
22509 <param name="recalculate_peaks_max_z" value="0.75"/>
22510 <param name="minimal_quality" value="-1.5"/>
22511 <param name="resample_boundary" value="15.0"/>
22512 <param name="compute_peak_quality" value="true"/>
22513 <param name="compute_peak_shape_metrics" value="false"/>
22514 <param name="compute_total_mi" value="false"/>
22515 <param name="boundary_selection_method" value="largest"/>
22516 <section name="PeakPickerMRM">
22517 <param name="sgolay_frame_length" value="11"/>
22518 <param name="sgolay_polynomial_order" value="3"/>
22519 <param name="gauss_width" value="30.0"/>
22520 <param name="use_gauss" value="false"/>
22521 <param name="peak_width" value="-1.0"/>
22522 <param name="signal_to_noise" value="0.1"/>
22523 <param name="write_sn_log_messages" value="false"/>
22524 <param name="remove_overlapping_peaks" value="true"/>
22525 <param name="method" value="corrected"/>
22526 </section>
22527 <section name="PeakIntegrator">
22528 <param name="integration_type" value="intensity_sum"/>
22529 <param name="baseline_type" value="base_to_base"/>
22530 <param name="fit_EMG" value="false"/>
22531 </section>
22532 </section>
22533 <section name="DIAScoring">
22534 <param name="dia_extraction_window" value="0.05"/>
22535 <param name="dia_extraction_unit" value="Th"/>
22536 <param name="dia_centroided" value="false"/>
22537 <param name="dia_byseries_intensity_min" value="300.0"/>
22538 <param name="dia_byseries_ppm_diff" value="10.0"/>
22539 <param name="dia_nr_isotopes" value="4"/>
22540 <param name="dia_nr_charges" value="4"/>
22541 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22542 </section>
22543 <section name="EMGScoring">
22544 <param name="max_iteration" value="10"/>
22545 </section>
22546 <section name="Scores">
22547 <param name="use_shape_score" value="true"/>
22548 <param name="use_coelution_score" value="true"/>
22549 <param name="use_rt_score" value="true"/>
22550 <param name="use_library_score" value="true"/>
22551 <param name="use_intensity_score" value="true"/>
22552 <param name="use_nr_peaks_score" value="true"/>
22553 <param name="use_total_xic_score" value="true"/>
22554 <param name="use_total_mi_score" value="false"/>
22555 <param name="use_sn_score" value="true"/>
22556 <param name="use_mi_score" value="true"/>
22557 <param name="use_dia_scores" value="true"/>
22558 <param name="use_ms1_correlation" value="false"/>
22559 <param name="use_sonar_scores" value="false"/>
22560 <param name="use_ion_mobility_scores" value="false"/>
22561 <param name="use_ms1_fullscan" value="false"/>
22562 <param name="use_ms1_mi" value="false"/>
22563 <param name="use_uis_scores" value="false"/>
22564 </section>
22565 </section>
22566 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
22567 <output name="ctd_out" ftype="xml">
22568 <assert_contents>
22569 <is_valid_xml/>
22570 </assert_contents>
22571 </output>
22572 </test>
22573 <test expect_num_outputs="2">
22574 <conditional name="adv_opts_cond">
22575 <param name="adv_opts_selector" value="advanced"/>
22576 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
22577 <param name="sort_swath_maps" value="false"/>
22578 <param name="enable_ms1" value="true"/>
22579 <param name="enable_ipf" value="true"/>
22580 <param name="min_upper_edge_dist" value="0.0"/>
22581 <param name="extra_rt_extraction_window" value="0.0"/>
22582 <param name="mz_extraction_window_unit" value="Th"/>
22583 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22584 <param name="use_ms1_ion_mobility" value="true"/>
22585 <param name="matching_window_only" value="false"/>
22586 <param name="irt_mz_extraction_window" value="50.0"/>
22587 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22588 <param name="irt_im_extraction_window" value="-1.0"/>
22589 <param name="min_rsq" value="0.95"/>
22590 <param name="min_coverage" value="0.6"/>
22591 <param name="split_file_input" value="false"/>
22592 <param name="use_elution_model_score" value="false"/>
22593 <param name="readOptions" value="normal"/>
22594 <param name="mz_correction_function" value="none"/>
22595 <param name="extraction_function" value="tophat"/>
22596 <param name="batchSize" value="1000"/>
22597 <param name="ms1_isotopes" value="0"/>
22598 <param name="force" value="false"/>
22599 <param name="test" value="true"/>
22600 </conditional>
22601 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
22602 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
22603 <param name="tr_type" value=""/>
22604 <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22605 <param name="sonar" value="false"/>
22606 <param name="rt_extraction_window" value="600.0"/>
22607 <param name="ion_mobility_window" value="-1.0"/>
22608 <param name="mz_extraction_window" value="0.05"/>
22609 <param name="mz_extraction_window_ms1" value="50.0"/>
22610 <param name="im_extraction_window_ms1" value="-1.0"/>
22611 <section name="Debugging"/>
22612 <section name="Calibration">
22613 <param name="ms1_im_calibration" value="false"/>
22614 <param name="im_correction_function" value="linear"/>
22615 <param name="debug_im_file" value=""/>
22616 <param name="debug_mz_file" value=""/>
22617 </section>
22618 <section name="Library">
22619 <param name="retentionTimeInterpretation" value="iRT"/>
22620 <param name="override_group_label_check" value="false"/>
22621 <param name="force_invalid_mods" value="false"/>
22622 </section>
22623 <section name="RTNormalization">
22624 <param name="alignmentMethod" value="linear"/>
22625 <param name="outlierMethod" value="iter_residual"/>
22626 <param name="useIterativeChauvenet" value="false"/>
22627 <param name="RANSACMaxIterations" value="1000"/>
22628 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22629 <param name="RANSACSamplingSize" value="10"/>
22630 <param name="estimateBestPeptides" value="false"/>
22631 <param name="InitialQualityCutoff" value="0.5"/>
22632 <param name="OverallQualityCutoff" value="5.5"/>
22633 <param name="NrRTBins" value="10"/>
22634 <param name="MinPeptidesPerBin" value="1"/>
22635 <param name="MinBinsFilled" value="8"/>
22636 <section name="lowess">
22637 <param name="span" value="0.05"/>
22638 </section>
22639 <section name="b_spline">
22640 <param name="num_nodes" value="5"/>
22641 </section>
22642 </section>
22643 <section name="Scoring">
22644 <param name="stop_report_after_feature" value="5"/>
22645 <param name="rt_normalization_factor" value="100.0"/>
22646 <param name="quantification_cutoff" value="0.0"/>
22647 <param name="write_convex_hull" value="false"/>
22648 <param name="spectrum_addition_method" value="simple"/>
22649 <param name="add_up_spectra" value="1"/>
22650 <param name="spacing_for_spectra_resampling" value="0.005"/>
22651 <param name="uis_threshold_sn" value="-1"/>
22652 <param name="uis_threshold_peak_area" value="0"/>
22653 <param name="scoring_model" value="default"/>
22654 <param name="im_extra_drift" value="0.0"/>
22655 <param name="strict" value="true"/>
22656 <section name="TransitionGroupPicker">
22657 <param name="stop_after_feature" value="-1"/>
22658 <param name="min_peak_width" value="-1.0"/>
22659 <param name="peak_integration" value="original"/>
22660 <param name="background_subtraction" value="none"/>
22661 <param name="recalculate_peaks" value="true"/>
22662 <param name="use_precursors" value="false"/>
22663 <param name="use_consensus" value="true"/>
22664 <param name="recalculate_peaks_max_z" value="0.75"/>
22665 <param name="minimal_quality" value="-1.5"/>
22666 <param name="resample_boundary" value="15.0"/>
22667 <param name="compute_peak_quality" value="true"/>
22668 <param name="compute_peak_shape_metrics" value="false"/>
22669 <param name="compute_total_mi" value="false"/>
22670 <param name="boundary_selection_method" value="largest"/>
22671 <section name="PeakPickerMRM">
22672 <param name="sgolay_frame_length" value="11"/>
22673 <param name="sgolay_polynomial_order" value="3"/>
22674 <param name="gauss_width" value="30.0"/>
22675 <param name="use_gauss" value="false"/>
22676 <param name="peak_width" value="-1.0"/>
22677 <param name="signal_to_noise" value="0.1"/>
22678 <param name="write_sn_log_messages" value="false"/>
22679 <param name="remove_overlapping_peaks" value="true"/>
22680 <param name="method" value="corrected"/>
22681 </section>
22682 <section name="PeakIntegrator">
22683 <param name="integration_type" value="intensity_sum"/>
22684 <param name="baseline_type" value="base_to_base"/>
22685 <param name="fit_EMG" value="false"/>
22686 </section>
22687 </section>
22688 <section name="DIAScoring">
22689 <param name="dia_extraction_window" value="0.05"/>
22690 <param name="dia_extraction_unit" value="Th"/>
22691 <param name="dia_centroided" value="false"/>
22692 <param name="dia_byseries_intensity_min" value="300.0"/>
22693 <param name="dia_byseries_ppm_diff" value="10.0"/>
22694 <param name="dia_nr_isotopes" value="4"/>
22695 <param name="dia_nr_charges" value="4"/>
22696 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22697 </section>
22698 <section name="EMGScoring">
22699 <param name="max_iteration" value="10"/>
22700 </section>
22701 <section name="Scores">
22702 <param name="use_shape_score" value="true"/>
22703 <param name="use_coelution_score" value="true"/>
22704 <param name="use_rt_score" value="true"/>
22705 <param name="use_library_score" value="true"/>
22706 <param name="use_intensity_score" value="true"/>
22707 <param name="use_nr_peaks_score" value="true"/>
22708 <param name="use_total_xic_score" value="true"/>
22709 <param name="use_total_mi_score" value="true"/>
22710 <param name="use_sn_score" value="true"/>
22711 <param name="use_mi_score" value="true"/>
22712 <param name="use_dia_scores" value="true"/>
22713 <param name="use_ms1_correlation" value="false"/>
22714 <param name="use_sonar_scores" value="false"/>
22715 <param name="use_ion_mobility_scores" value="false"/>
22716 <param name="use_ms1_fullscan" value="false"/>
22717 <param name="use_ms1_mi" value="false"/>
22718 <param name="use_uis_scores" value="false"/>
22719 </section>
22720 </section>
22721 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
22722 <output name="ctd_out" ftype="xml">
22723 <assert_contents>
22724 <is_valid_xml/>
22725 </assert_contents>
22726 </output>
22727 </test>
22728 <test expect_num_outputs="4">
22729 <conditional name="adv_opts_cond">
22730 <param name="adv_opts_selector" value="advanced"/>
22731 <param name="sort_swath_maps" value="false"/>
22732 <param name="enable_ms1" value="true"/>
22733 <param name="enable_ipf" value="true"/>
22734 <param name="out_chrom_type" value="mzML"/>
22735 <param name="min_upper_edge_dist" value="0.0"/>
22736 <param name="extra_rt_extraction_window" value="0.0"/>
22737 <param name="mz_extraction_window_unit" value="Th"/>
22738 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22739 <param name="use_ms1_ion_mobility" value="true"/>
22740 <param name="matching_window_only" value="false"/>
22741 <param name="irt_mz_extraction_window" value="50.0"/>
22742 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22743 <param name="irt_im_extraction_window" value="-1.0"/>
22744 <param name="min_rsq" value="0.95"/>
22745 <param name="min_coverage" value="0.6"/>
22746 <param name="split_file_input" value="false"/>
22747 <param name="use_elution_model_score" value="false"/>
22748 <param name="readOptions" value="normal"/>
22749 <param name="mz_correction_function" value="none"/>
22750 <param name="extraction_function" value="tophat"/>
22751 <param name="batchSize" value="1000"/>
22752 <param name="ms1_isotopes" value="0"/>
22753 <param name="force" value="false"/>
22754 <param name="test" value="true"/>
22755 </conditional>
22756 <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
22757 <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
22758 <param name="tr_type" value=""/>
22759 <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
22760 <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22761 <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22762 <param name="sonar" value="false"/>
22763 <param name="rt_extraction_window" value="600.0"/>
22764 <param name="ion_mobility_window" value="-1.0"/>
22765 <param name="mz_extraction_window" value="0.05"/>
22766 <param name="mz_extraction_window_ms1" value="50.0"/>
22767 <param name="im_extraction_window_ms1" value="-1.0"/>
22768 <section name="Debugging"/>
22769 <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
22770 <section name="Calibration">
22771 <param name="ms1_im_calibration" value="false"/>
22772 <param name="im_correction_function" value="linear"/>
22773 <param name="debug_im_file" value=""/>
22774 <param name="debug_mz_file" value=""/>
22775 </section>
22776 <section name="Library">
22777 <param name="retentionTimeInterpretation" value="iRT"/>
22778 <param name="override_group_label_check" value="false"/>
22779 <param name="force_invalid_mods" value="false"/>
22780 </section>
22781 <section name="RTNormalization">
22782 <param name="alignmentMethod" value="linear"/>
22783 <param name="outlierMethod" value="iter_residual"/>
22784 <param name="useIterativeChauvenet" value="false"/>
22785 <param name="RANSACMaxIterations" value="1000"/>
22786 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22787 <param name="RANSACSamplingSize" value="10"/>
22788 <param name="estimateBestPeptides" value="false"/>
22789 <param name="InitialQualityCutoff" value="0.5"/>
22790 <param name="OverallQualityCutoff" value="5.5"/>
22791 <param name="NrRTBins" value="10"/>
22792 <param name="MinPeptidesPerBin" value="1"/>
22793 <param name="MinBinsFilled" value="8"/>
22794 <section name="lowess">
22795 <param name="span" value="0.6666666666666666"/>
22796 </section>
22797 <section name="b_spline">
22798 <param name="num_nodes" value="5"/>
22799 </section>
22800 </section>
22801 <section name="Scoring">
22802 <param name="stop_report_after_feature" value="5"/>
22803 <param name="rt_normalization_factor" value="100.0"/>
22804 <param name="quantification_cutoff" value="0.0"/>
22805 <param name="write_convex_hull" value="false"/>
22806 <param name="spectrum_addition_method" value="simple"/>
22807 <param name="add_up_spectra" value="1"/>
22808 <param name="spacing_for_spectra_resampling" value="0.005"/>
22809 <param name="uis_threshold_sn" value="-1"/>
22810 <param name="uis_threshold_peak_area" value="0"/>
22811 <param name="scoring_model" value="default"/>
22812 <param name="im_extra_drift" value="0.0"/>
22813 <param name="strict" value="true"/>
22814 <section name="TransitionGroupPicker">
22815 <param name="stop_after_feature" value="-1"/>
22816 <param name="min_peak_width" value="-1.0"/>
22817 <param name="peak_integration" value="original"/>
22818 <param name="background_subtraction" value="none"/>
22819 <param name="recalculate_peaks" value="true"/>
22820 <param name="use_precursors" value="false"/>
22821 <param name="use_consensus" value="true"/>
22822 <param name="recalculate_peaks_max_z" value="0.75"/>
22823 <param name="minimal_quality" value="-1.5"/>
22824 <param name="resample_boundary" value="15.0"/>
22825 <param name="compute_peak_quality" value="true"/>
22826 <param name="compute_peak_shape_metrics" value="false"/>
22827 <param name="compute_total_mi" value="false"/>
22828 <param name="boundary_selection_method" value="largest"/>
22829 <section name="PeakPickerMRM">
22830 <param name="sgolay_frame_length" value="11"/>
22831 <param name="sgolay_polynomial_order" value="3"/>
22832 <param name="gauss_width" value="30.0"/>
22833 <param name="use_gauss" value="false"/>
22834 <param name="peak_width" value="-1.0"/>
22835 <param name="signal_to_noise" value="0.1"/>
22836 <param name="write_sn_log_messages" value="false"/>
22837 <param name="remove_overlapping_peaks" value="true"/>
22838 <param name="method" value="corrected"/>
22839 </section>
22840 <section name="PeakIntegrator">
22841 <param name="integration_type" value="intensity_sum"/>
22842 <param name="baseline_type" value="base_to_base"/>
22843 <param name="fit_EMG" value="false"/>
22844 </section>
22845 </section>
22846 <section name="DIAScoring">
22847 <param name="dia_extraction_window" value="0.05"/>
22848 <param name="dia_extraction_unit" value="Th"/>
22849 <param name="dia_centroided" value="false"/>
22850 <param name="dia_byseries_intensity_min" value="300.0"/>
22851 <param name="dia_byseries_ppm_diff" value="10.0"/>
22852 <param name="dia_nr_isotopes" value="4"/>
22853 <param name="dia_nr_charges" value="4"/>
22854 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22855 </section>
22856 <section name="EMGScoring">
22857 <param name="max_iteration" value="10"/>
22858 </section>
22859 <section name="Scores">
22860 <param name="use_shape_score" value="true"/>
22861 <param name="use_coelution_score" value="true"/>
22862 <param name="use_rt_score" value="true"/>
22863 <param name="use_library_score" value="true"/>
22864 <param name="use_intensity_score" value="true"/>
22865 <param name="use_nr_peaks_score" value="true"/>
22866 <param name="use_total_xic_score" value="true"/>
22867 <param name="use_total_mi_score" value="true"/>
22868 <param name="use_sn_score" value="true"/>
22869 <param name="use_mi_score" value="true"/>
22870 <param name="use_dia_scores" value="true"/>
22871 <param name="use_ms1_correlation" value="false"/>
22872 <param name="use_sonar_scores" value="false"/>
22873 <param name="use_ion_mobility_scores" value="false"/>
22874 <param name="use_ms1_fullscan" value="false"/>
22875 <param name="use_ms1_mi" value="false"/>
22876 <param name="use_uis_scores" value="false"/>
22877 </section>
22878 </section>
22879 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
22880 <output name="ctd_out" ftype="xml">
22881 <assert_contents>
22882 <is_valid_xml/>
22883 </assert_contents>
22884 </output>
22885 </test>
22886 <test expect_num_outputs="3">
22887 <conditional name="adv_opts_cond">
22888 <param name="adv_opts_selector" value="advanced"/>
22889 <param name="sort_swath_maps" value="false"/>
22890 <param name="enable_ms1" value="true"/>
22891 <param name="enable_ipf" value="true"/>
22892 <param name="out_chrom_type" value="mzML"/>
22893 <param name="min_upper_edge_dist" value="0.0"/>
22894 <param name="extra_rt_extraction_window" value="0.0"/>
22895 <param name="mz_extraction_window_unit" value="ppm"/>
22896 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22897 <param name="use_ms1_ion_mobility" value="true"/>
22898 <param name="matching_window_only" value="true"/>
22899 <param name="irt_mz_extraction_window" value="50.0"/>
22900 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22901 <param name="irt_im_extraction_window" value="-1.0"/>
22902 <param name="min_rsq" value="0.95"/>
22903 <param name="min_coverage" value="0.6"/>
22904 <param name="split_file_input" value="false"/>
22905 <param name="use_elution_model_score" value="false"/>
22906 <param name="readOptions" value="workingInMemory"/>
22907 <param name="mz_correction_function" value="none"/>
22908 <param name="extraction_function" value="tophat"/>
22909 <param name="batchSize" value="1000"/>
22910 <param name="ms1_isotopes" value="3"/>
22911 <param name="force" value="false"/>
22912 <param name="test" value="false"/>
22913 </conditional>
22914 <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
22915 <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
22916 <param name="tr_type" value=""/>
22917 <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22918 <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22919 <param name="sonar" value="false"/>
22920 <param name="rt_extraction_window" value="600.0"/>
22921 <param name="ion_mobility_window" value="-1.0"/>
22922 <param name="mz_extraction_window" value="50.0"/>
22923 <param name="mz_extraction_window_ms1" value="50.0"/>
22924 <param name="im_extraction_window_ms1" value="-1.0"/>
22925 <section name="Debugging"/>
22926 <section name="Calibration">
22927 <param name="ms1_im_calibration" value="false"/>
22928 <param name="im_correction_function" value="linear"/>
22929 <param name="debug_im_file" value=""/>
22930 <param name="debug_mz_file" value=""/>
22931 </section>
22932 <section name="Library">
22933 <param name="retentionTimeInterpretation" value="iRT"/>
22934 <param name="override_group_label_check" value="false"/>
22935 <param name="force_invalid_mods" value="false"/>
22936 </section>
22937 <section name="RTNormalization">
22938 <param name="alignmentMethod" value="linear"/>
22939 <param name="outlierMethod" value="iter_residual"/>
22940 <param name="useIterativeChauvenet" value="false"/>
22941 <param name="RANSACMaxIterations" value="1000"/>
22942 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22943 <param name="RANSACSamplingSize" value="10"/>
22944 <param name="estimateBestPeptides" value="false"/>
22945 <param name="InitialQualityCutoff" value="0.5"/>
22946 <param name="OverallQualityCutoff" value="5.5"/>
22947 <param name="NrRTBins" value="10"/>
22948 <param name="MinPeptidesPerBin" value="1"/>
22949 <param name="MinBinsFilled" value="8"/>
22950 <section name="lowess">
22951 <param name="span" value="0.05"/>
22952 </section>
22953 <section name="b_spline">
22954 <param name="num_nodes" value="5"/>
22955 </section>
22956 </section>
22957 <section name="Scoring">
22958 <param name="stop_report_after_feature" value="5"/>
22959 <param name="rt_normalization_factor" value="100.0"/>
22960 <param name="quantification_cutoff" value="0.0"/>
22961 <param name="write_convex_hull" value="false"/>
22962 <param name="spectrum_addition_method" value="simple"/>
22963 <param name="add_up_spectra" value="1"/>
22964 <param name="spacing_for_spectra_resampling" value="0.005"/>
22965 <param name="uis_threshold_sn" value="-1"/>
22966 <param name="uis_threshold_peak_area" value="0"/>
22967 <param name="scoring_model" value="default"/>
22968 <param name="im_extra_drift" value="0.0"/>
22969 <param name="strict" value="true"/>
22970 <section name="TransitionGroupPicker">
22971 <param name="stop_after_feature" value="-1"/>
22972 <param name="min_peak_width" value="-1.0"/>
22973 <param name="peak_integration" value="original"/>
22974 <param name="background_subtraction" value="none"/>
22975 <param name="recalculate_peaks" value="true"/>
22976 <param name="use_precursors" value="false"/>
22977 <param name="use_consensus" value="true"/>
22978 <param name="recalculate_peaks_max_z" value="0.75"/>
22979 <param name="minimal_quality" value="-1.5"/>
22980 <param name="resample_boundary" value="15.0"/>
22981 <param name="compute_peak_quality" value="false"/>
22982 <param name="compute_peak_shape_metrics" value="false"/>
22983 <param name="compute_total_mi" value="false"/>
22984 <param name="boundary_selection_method" value="largest"/>
22985 <section name="PeakPickerMRM">
22986 <param name="sgolay_frame_length" value="11"/>
22987 <param name="sgolay_polynomial_order" value="3"/>
22988 <param name="gauss_width" value="30.0"/>
22989 <param name="use_gauss" value="false"/>
22990 <param name="peak_width" value="-1.0"/>
22991 <param name="signal_to_noise" value="0.1"/>
22992 <param name="write_sn_log_messages" value="false"/>
22993 <param name="remove_overlapping_peaks" value="true"/>
22994 <param name="method" value="corrected"/>
22995 </section>
22996 <section name="PeakIntegrator">
22997 <param name="integration_type" value="intensity_sum"/>
22998 <param name="baseline_type" value="base_to_base"/>
22999 <param name="fit_EMG" value="false"/>
23000 </section>
23001 </section>
23002 <section name="DIAScoring">
23003 <param name="dia_extraction_window" value="0.05"/>
23004 <param name="dia_extraction_unit" value="Th"/>
23005 <param name="dia_centroided" value="false"/>
23006 <param name="dia_byseries_intensity_min" value="300.0"/>
23007 <param name="dia_byseries_ppm_diff" value="10.0"/>
23008 <param name="dia_nr_isotopes" value="4"/>
23009 <param name="dia_nr_charges" value="4"/>
23010 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
23011 </section>
23012 <section name="EMGScoring">
23013 <param name="max_iteration" value="10"/>
23014 </section>
23015 <section name="Scores">
23016 <param name="use_shape_score" value="true"/>
23017 <param name="use_coelution_score" value="true"/>
23018 <param name="use_rt_score" value="true"/>
23019 <param name="use_library_score" value="true"/>
23020 <param name="use_intensity_score" value="true"/>
23021 <param name="use_nr_peaks_score" value="true"/>
23022 <param name="use_total_xic_score" value="true"/>
23023 <param name="use_total_mi_score" value="false"/>
23024 <param name="use_sn_score" value="true"/>
23025 <param name="use_mi_score" value="true"/>
23026 <param name="use_dia_scores" value="true"/>
23027 <param name="use_ms1_correlation" value="false"/>
23028 <param name="use_sonar_scores" value="false"/>
23029 <param name="use_ion_mobility_scores" value="false"/>
23030 <param name="use_ms1_fullscan" value="false"/>
23031 <param name="use_ms1_mi" value="true"/>
23032 <param name="use_uis_scores" value="false"/>
23033 </section>
23034 </section>
23035 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
23036 <output name="ctd_out" ftype="xml">
23037 <assert_contents>
23038 <is_valid_xml/>
23039 </assert_contents>
23040 </output>
23041 </test>
23042 </xml>
23043 <xml name="autotest_PeakPickerHiRes">
23044 <test expect_num_outputs="2">
23045 <conditional name="adv_opts_cond">
23046 <param name="adv_opts_selector" value="advanced"/>
23047 <param name="processOption" value="inmemory"/>
23048 <param name="force" value="false"/>
23049 <param name="test" value="true"/>
23050 </conditional>
23051 <param name="in" value="PeakPickerHiRes_input.mzML"/>
23052 <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23053 <section name="algorithm">
23054 <param name="signal_to_noise" value="1.0"/>
23055 <param name="spacing_difference_gap" value="4.0"/>
23056 <param name="spacing_difference" value="1.5"/>
23057 <param name="missing" value="1"/>
23058 <param name="ms_levels" value="1"/>
23059 <param name="report_FWHM" value="true"/>
23060 <param name="report_FWHM_unit" value="relative"/>
23061 <section name="SignalToNoise">
23062 <param name="max_intensity" value="-1"/>
23063 <param name="auto_max_stdev_factor" value="3.0"/>
23064 <param name="auto_max_percentile" value="95"/>
23065 <param name="auto_mode" value="0"/>
23066 <param name="win_len" value="200.0"/>
23067 <param name="bin_count" value="30"/>
23068 <param name="min_required_elements" value="10"/>
23069 <param name="noise_for_empty_window" value="1e+20"/>
23070 <param name="write_log_messages" value="true"/>
23071 </section>
23072 </section>
23073 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23074 <output name="ctd_out" ftype="xml">
23075 <assert_contents>
23076 <is_valid_xml/>
23077 </assert_contents>
23078 </output>
23079 </test>
23080 <test expect_num_outputs="2">
23081 <conditional name="adv_opts_cond">
23082 <param name="adv_opts_selector" value="advanced"/>
23083 <param name="processOption" value="inmemory"/>
23084 <param name="force" value="false"/>
23085 <param name="test" value="true"/>
23086 </conditional>
23087 <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
23088 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23089 <section name="algorithm">
23090 <param name="signal_to_noise" value="1.0"/>
23091 <param name="spacing_difference_gap" value="4.0"/>
23092 <param name="spacing_difference" value="1.5"/>
23093 <param name="missing" value="1"/>
23094 <param name="ms_levels" value="1"/>
23095 <param name="report_FWHM" value="true"/>
23096 <param name="report_FWHM_unit" value="relative"/>
23097 <section name="SignalToNoise">
23098 <param name="max_intensity" value="-1"/>
23099 <param name="auto_max_stdev_factor" value="3.0"/>
23100 <param name="auto_max_percentile" value="95"/>
23101 <param name="auto_mode" value="0"/>
23102 <param name="win_len" value="200.0"/>
23103 <param name="bin_count" value="30"/>
23104 <param name="min_required_elements" value="10"/>
23105 <param name="noise_for_empty_window" value="1e+20"/>
23106 <param name="write_log_messages" value="true"/>
23107 </section>
23108 </section>
23109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23110 <output name="ctd_out" ftype="xml">
23111 <assert_contents>
23112 <is_valid_xml/>
23113 </assert_contents>
23114 </output>
23115 </test>
23116 <test expect_num_outputs="2">
23117 <conditional name="adv_opts_cond">
23118 <param name="adv_opts_selector" value="advanced"/>
23119 <param name="processOption" value="lowmemory"/>
23120 <param name="force" value="false"/>
23121 <param name="test" value="true"/>
23122 </conditional>
23123 <param name="in" value="PeakPickerHiRes_input.mzML"/>
23124 <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23125 <section name="algorithm">
23126 <param name="signal_to_noise" value="1.0"/>
23127 <param name="spacing_difference_gap" value="4.0"/>
23128 <param name="spacing_difference" value="1.5"/>
23129 <param name="missing" value="1"/>
23130 <param name="ms_levels" value="1"/>
23131 <param name="report_FWHM" value="true"/>
23132 <param name="report_FWHM_unit" value="relative"/>
23133 <section name="SignalToNoise">
23134 <param name="max_intensity" value="-1"/>
23135 <param name="auto_max_stdev_factor" value="3.0"/>
23136 <param name="auto_max_percentile" value="95"/>
23137 <param name="auto_mode" value="0"/>
23138 <param name="win_len" value="200.0"/>
23139 <param name="bin_count" value="30"/>
23140 <param name="min_required_elements" value="10"/>
23141 <param name="noise_for_empty_window" value="1e+20"/>
23142 <param name="write_log_messages" value="true"/>
23143 </section>
23144 </section>
23145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23146 <output name="ctd_out" ftype="xml">
23147 <assert_contents>
23148 <is_valid_xml/>
23149 </assert_contents>
23150 </output>
23151 </test>
23152 <test expect_num_outputs="2">
23153 <conditional name="adv_opts_cond">
23154 <param name="adv_opts_selector" value="advanced"/>
23155 <param name="processOption" value="lowmemory"/>
23156 <param name="force" value="false"/>
23157 <param name="test" value="true"/>
23158 </conditional>
23159 <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
23160 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23161 <section name="algorithm">
23162 <param name="signal_to_noise" value="1.0"/>
23163 <param name="spacing_difference_gap" value="4.0"/>
23164 <param name="spacing_difference" value="1.5"/>
23165 <param name="missing" value="1"/>
23166 <param name="ms_levels" value="1"/>
23167 <param name="report_FWHM" value="true"/>
23168 <param name="report_FWHM_unit" value="relative"/>
23169 <section name="SignalToNoise">
23170 <param name="max_intensity" value="-1"/>
23171 <param name="auto_max_stdev_factor" value="3.0"/>
23172 <param name="auto_max_percentile" value="95"/>
23173 <param name="auto_mode" value="0"/>
23174 <param name="win_len" value="200.0"/>
23175 <param name="bin_count" value="30"/>
23176 <param name="min_required_elements" value="10"/>
23177 <param name="noise_for_empty_window" value="1e+20"/>
23178 <param name="write_log_messages" value="true"/>
23179 </section>
23180 </section>
23181 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23182 <output name="ctd_out" ftype="xml">
23183 <assert_contents>
23184 <is_valid_xml/>
23185 </assert_contents>
23186 </output>
23187 </test>
23188 <test expect_num_outputs="2">
23189 <conditional name="adv_opts_cond">
23190 <param name="adv_opts_selector" value="advanced"/>
23191 <param name="processOption" value="inmemory"/>
23192 <param name="force" value="false"/>
23193 <param name="test" value="true"/>
23194 </conditional>
23195 <param name="in" value="PeakPickerHiRes_5_input.mzML"/>
23196 <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23197 <section name="algorithm">
23198 <param name="signal_to_noise" value="0.0"/>
23199 <param name="spacing_difference_gap" value="4.0"/>
23200 <param name="spacing_difference" value="1.5"/>
23201 <param name="missing" value="1"/>
23202 <param name="ms_levels" value=""/>
23203 <param name="report_FWHM" value="false"/>
23204 <param name="report_FWHM_unit" value="relative"/>
23205 <section name="SignalToNoise">
23206 <param name="max_intensity" value="-1"/>
23207 <param name="auto_max_stdev_factor" value="3.0"/>
23208 <param name="auto_max_percentile" value="95"/>
23209 <param name="auto_mode" value="0"/>
23210 <param name="win_len" value="200.0"/>
23211 <param name="bin_count" value="30"/>
23212 <param name="min_required_elements" value="10"/>
23213 <param name="noise_for_empty_window" value="1e+20"/>
23214 <param name="write_log_messages" value="true"/>
23215 </section>
23216 </section>
23217 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23218 <output name="ctd_out" ftype="xml">
23219 <assert_contents>
23220 <is_valid_xml/>
23221 </assert_contents>
23222 </output>
23223 </test>
23224 </xml>
23225 <xml name="autotest_PeakPickerIterative">
23226 <test expect_num_outputs="2">
23227 <conditional name="adv_opts_cond">
23228 <param name="adv_opts_selector" value="advanced"/>
23229 <param name="force" value="false"/>
23230 <param name="test" value="true"/>
23231 </conditional>
23232 <param name="in" value="PeakPickerIterative_1_input.mzML"/>
23233 <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23234 <section name="algorithm">
23235 <param name="signal_to_noise_" value="1.0"/>
23236 <param name="peak_width" value="0.04"/>
23237 <param name="spacing_difference" value="1.5"/>
23238 <param name="sn_bin_count_" value="30"/>
23239 <param name="nr_iterations_" value="5"/>
23240 <param name="sn_win_len_" value="20.0"/>
23241 <param name="check_width_internally" value="false"/>
23242 <param name="ms1_only" value="false"/>
23243 <param name="clear_meta_data" value="false"/>
23244 </section>
23245 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23246 <output name="ctd_out" ftype="xml">
23247 <assert_contents>
23248 <is_valid_xml/>
23249 </assert_contents>
23250 </output>
23251 </test>
23252 <test expect_num_outputs="2">
23253 <conditional name="adv_opts_cond">
23254 <param name="adv_opts_selector" value="advanced"/>
23255 <param name="force" value="false"/>
23256 <param name="test" value="true"/>
23257 </conditional>
23258 <param name="in" value="PeakPickerIterative_2_input.mzML"/>
23259 <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23260 <section name="algorithm">
23261 <param name="signal_to_noise_" value="0.0"/>
23262 <param name="peak_width" value="0.04"/>
23263 <param name="spacing_difference" value="2.5"/>
23264 <param name="sn_bin_count_" value="30"/>
23265 <param name="nr_iterations_" value="5"/>
23266 <param name="sn_win_len_" value="20.0"/>
23267 <param name="check_width_internally" value="true"/>
23268 <param name="ms1_only" value="false"/>
23269 <param name="clear_meta_data" value="false"/>
23270 </section>
23271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23272 <output name="ctd_out" ftype="xml">
23273 <assert_contents>
23274 <is_valid_xml/>
23275 </assert_contents>
23276 </output>
23277 </test>
23278 </xml>
23279 <xml name="autotest_PeakPickerWavelet">
23280 <test expect_num_outputs="2">
23281 <conditional name="adv_opts_cond">
23282 <param name="adv_opts_selector" value="advanced"/>
23283 <param name="write_peak_meta_data" value="true"/>
23284 <param name="force" value="false"/>
23285 <param name="test" value="true"/>
23286 </conditional>
23287 <param name="in" value="PeakPickerWavelet_input.mzML"/>
23288 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23289 <section name="algorithm">
23290 <param name="signal_to_noise" value="3.0"/>
23291 <param name="centroid_percentage" value="0.6"/>
23292 <param name="peak_width" value="0.2"/>
23293 <param name="estimate_peak_width" value="false"/>
23294 <param name="fwhm_lower_bound_factor" value="0.5"/>
23295 <param name="fwhm_upper_bound_factor" value="20.0"/>
23296 <section name="optimization">
23297 <param name="iterations" value="400"/>
23298 <section name="penalties">
23299 <param name="position" value="0.0"/>
23300 <param name="left_width" value="1.0"/>
23301 <param name="right_width" value="1.0"/>
23302 <param name="height" value="1.0"/>
23303 </section>
23304 <section name="2d">
23305 <param name="tolerance_mz" value="2.2"/>
23306 <param name="max_peak_distance" value="1.2"/>
23307 </section>
23308 </section>
23309 <section name="thresholds">
23310 <param name="peak_bound" value="100.0"/>
23311 <param name="peak_bound_ms2_level" value="10.0"/>
23312 <param name="correlation" value="0.5"/>
23313 <param name="noise_level" value="0.1"/>
23314 <param name="search_radius" value="3"/>
23315 </section>
23316 <section name="wavelet_transform">
23317 <param name="spacing" value="0.001"/>
23318 </section>
23319 <section name="deconvolution">
23320 <param name="deconvolution" value="false"/>
23321 <param name="asym_threshold" value="0.3"/>
23322 <param name="left_width" value="2.0"/>
23323 <param name="right_width" value="2.0"/>
23324 <param name="scaling" value="0.12"/>
23325 <section name="fitting">
23326 <param name="fwhm_threshold" value="0.7"/>
23327 <param name="eps_abs" value="9.999999747378752e-06"/>
23328 <param name="eps_rel" value="9.999999747378752e-06"/>
23329 <param name="max_iteration" value="10"/>
23330 <section name="penalties">
23331 <param name="position" value="0.0"/>
23332 <param name="height" value="1.0"/>
23333 <param name="left_width" value="0.0"/>
23334 <param name="right_width" value="0.0"/>
23335 </section>
23336 </section>
23337 </section>
23338 <section name="SignalToNoiseEstimationParameter">
23339 <param name="max_intensity" value="-1"/>
23340 <param name="auto_max_stdev_factor" value="3.0"/>
23341 <param name="auto_max_percentile" value="95"/>
23342 <param name="auto_mode" value="0"/>
23343 <param name="win_len" value="200.0"/>
23344 <param name="bin_count" value="30"/>
23345 <param name="stdev_mp" value="3.0"/>
23346 <param name="min_required_elements" value="10"/>
23347 <param name="noise_for_empty_window" value="1e+20"/>
23348 </section>
23349 </section>
23350 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23351 <output name="ctd_out" ftype="xml">
23352 <assert_contents>
23353 <is_valid_xml/>
23354 </assert_contents>
23355 </output>
23356 </test>
23357 <test expect_num_outputs="2">
23358 <conditional name="adv_opts_cond">
23359 <param name="adv_opts_selector" value="advanced"/>
23360 <param name="write_peak_meta_data" value="true"/>
23361 <param name="force" value="false"/>
23362 <param name="test" value="true"/>
23363 </conditional>
23364 <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
23365 <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23366 <section name="algorithm">
23367 <param name="signal_to_noise" value="2.0"/>
23368 <param name="centroid_percentage" value="0.8"/>
23369 <param name="peak_width" value="0.15"/>
23370 <param name="estimate_peak_width" value="false"/>
23371 <param name="fwhm_lower_bound_factor" value="1.0"/>
23372 <param name="fwhm_upper_bound_factor" value="20.0"/>
23373 <section name="optimization">
23374 <param name="iterations" value="400"/>
23375 <section name="penalties">
23376 <param name="position" value="0.0"/>
23377 <param name="left_width" value="1.0"/>
23378 <param name="right_width" value="1.0"/>
23379 <param name="height" value="1.0"/>
23380 </section>
23381 <section name="2d">
23382 <param name="tolerance_mz" value="2.2"/>
23383 <param name="max_peak_distance" value="1.2"/>
23384 </section>
23385 </section>
23386 <section name="thresholds">
23387 <param name="peak_bound" value="200.0"/>
23388 <param name="peak_bound_ms2_level" value="50.0"/>
23389 <param name="correlation" value="0.5"/>
23390 <param name="noise_level" value="0.1"/>
23391 <param name="search_radius" value="3"/>
23392 </section>
23393 <section name="wavelet_transform">
23394 <param name="spacing" value="0.001"/>
23395 </section>
23396 <section name="deconvolution">
23397 <param name="deconvolution" value="true"/>
23398 <param name="asym_threshold" value="0.3"/>
23399 <param name="left_width" value="2.0"/>
23400 <param name="right_width" value="2.0"/>
23401 <param name="scaling" value="0.1"/>
23402 <section name="fitting">
23403 <param name="fwhm_threshold" value="0.7"/>
23404 <param name="eps_abs" value="9.999999747378752e-06"/>
23405 <param name="eps_rel" value="9.999999747378752e-06"/>
23406 <param name="max_iteration" value="100"/>
23407 <section name="penalties">
23408 <param name="position" value="1.0"/>
23409 <param name="height" value="1.0"/>
23410 <param name="left_width" value="0.0"/>
23411 <param name="right_width" value="0.0"/>
23412 </section>
23413 </section>
23414 </section>
23415 <section name="SignalToNoiseEstimationParameter">
23416 <param name="max_intensity" value="-1"/>
23417 <param name="auto_max_stdev_factor" value="3.0"/>
23418 <param name="auto_max_percentile" value="95"/>
23419 <param name="auto_mode" value="0"/>
23420 <param name="win_len" value="200.0"/>
23421 <param name="bin_count" value="30"/>
23422 <param name="stdev_mp" value="3.0"/>
23423 <param name="min_required_elements" value="10"/>
23424 <param name="noise_for_empty_window" value="1e+20"/>
23425 </section>
23426 </section>
23427 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23428 <output name="ctd_out" ftype="xml">
23429 <assert_contents>
23430 <is_valid_xml/>
23431 </assert_contents>
23432 </output>
23433 </test>
23434 <test expect_num_outputs="2">
23435 <conditional name="adv_opts_cond">
23436 <param name="adv_opts_selector" value="advanced"/>
23437 <param name="write_peak_meta_data" value="true"/>
23438 <param name="force" value="false"/>
23439 <param name="test" value="true"/>
23440 </conditional>
23441 <param name="in" value="PeakPickerWavelet_input.mzML"/>
23442 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23443 <section name="algorithm">
23444 <param name="signal_to_noise" value="3.0"/>
23445 <param name="centroid_percentage" value="0.6"/>
23446 <param name="peak_width" value="0.2"/>
23447 <param name="estimate_peak_width" value="false"/>
23448 <param name="fwhm_lower_bound_factor" value="0.5"/>
23449 <param name="fwhm_upper_bound_factor" value="20.0"/>
23450 <section name="optimization">
23451 <param name="iterations" value="400"/>
23452 <section name="penalties">
23453 <param name="position" value="0.0"/>
23454 <param name="left_width" value="1.0"/>
23455 <param name="right_width" value="1.0"/>
23456 <param name="height" value="1.0"/>
23457 </section>
23458 <section name="2d">
23459 <param name="tolerance_mz" value="2.2"/>
23460 <param name="max_peak_distance" value="1.2"/>
23461 </section>
23462 </section>
23463 <section name="thresholds">
23464 <param name="peak_bound" value="100.0"/>
23465 <param name="peak_bound_ms2_level" value="10.0"/>
23466 <param name="correlation" value="0.5"/>
23467 <param name="noise_level" value="0.1"/>
23468 <param name="search_radius" value="3"/>
23469 </section>
23470 <section name="wavelet_transform">
23471 <param name="spacing" value="0.001"/>
23472 </section>
23473 <section name="deconvolution">
23474 <param name="deconvolution" value="false"/>
23475 <param name="asym_threshold" value="0.3"/>
23476 <param name="left_width" value="2.0"/>
23477 <param name="right_width" value="2.0"/>
23478 <param name="scaling" value="0.12"/>
23479 <section name="fitting">
23480 <param name="fwhm_threshold" value="0.7"/>
23481 <param name="eps_abs" value="9.999999747378752e-06"/>
23482 <param name="eps_rel" value="9.999999747378752e-06"/>
23483 <param name="max_iteration" value="10"/>
23484 <section name="penalties">
23485 <param name="position" value="0.0"/>
23486 <param name="height" value="1.0"/>
23487 <param name="left_width" value="0.0"/>
23488 <param name="right_width" value="0.0"/>
23489 </section>
23490 </section>
23491 </section>
23492 <section name="SignalToNoiseEstimationParameter">
23493 <param name="max_intensity" value="-1"/>
23494 <param name="auto_max_stdev_factor" value="3.0"/>
23495 <param name="auto_max_percentile" value="95"/>
23496 <param name="auto_mode" value="0"/>
23497 <param name="win_len" value="200.0"/>
23498 <param name="bin_count" value="30"/>
23499 <param name="stdev_mp" value="3.0"/>
23500 <param name="min_required_elements" value="10"/>
23501 <param name="noise_for_empty_window" value="1e+20"/>
23502 </section>
23503 </section>
23504 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23505 <output name="ctd_out" ftype="xml">
23506 <assert_contents>
23507 <is_valid_xml/>
23508 </assert_contents>
23509 </output>
23510 </test>
23511 <test expect_num_outputs="2">
23512 <conditional name="adv_opts_cond">
23513 <param name="adv_opts_selector" value="advanced"/>
23514 <param name="write_peak_meta_data" value="false"/>
23515 <param name="force" value="false"/>
23516 <param name="test" value="true"/>
23517 </conditional>
23518 <param name="in" value="PeakPickerWavelet_input.mzML"/>
23519 <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23520 <section name="algorithm">
23521 <param name="signal_to_noise" value="3.0"/>
23522 <param name="centroid_percentage" value="0.6"/>
23523 <param name="peak_width" value="0.2"/>
23524 <param name="estimate_peak_width" value="false"/>
23525 <param name="fwhm_lower_bound_factor" value="0.5"/>
23526 <param name="fwhm_upper_bound_factor" value="20.0"/>
23527 <section name="optimization">
23528 <param name="iterations" value="400"/>
23529 <section name="penalties">
23530 <param name="position" value="0.0"/>
23531 <param name="left_width" value="1.0"/>
23532 <param name="right_width" value="1.0"/>
23533 <param name="height" value="1.0"/>
23534 </section>
23535 <section name="2d">
23536 <param name="tolerance_mz" value="2.2"/>
23537 <param name="max_peak_distance" value="1.2"/>
23538 </section>
23539 </section>
23540 <section name="thresholds">
23541 <param name="peak_bound" value="100.0"/>
23542 <param name="peak_bound_ms2_level" value="10.0"/>
23543 <param name="correlation" value="0.5"/>
23544 <param name="noise_level" value="0.1"/>
23545 <param name="search_radius" value="3"/>
23546 </section>
23547 <section name="wavelet_transform">
23548 <param name="spacing" value="0.001"/>
23549 </section>
23550 <section name="deconvolution">
23551 <param name="deconvolution" value="false"/>
23552 <param name="asym_threshold" value="0.3"/>
23553 <param name="left_width" value="2.0"/>
23554 <param name="right_width" value="2.0"/>
23555 <param name="scaling" value="0.12"/>
23556 <section name="fitting">
23557 <param name="fwhm_threshold" value="0.7"/>
23558 <param name="eps_abs" value="9.999999747378752e-06"/>
23559 <param name="eps_rel" value="9.999999747378752e-06"/>
23560 <param name="max_iteration" value="10"/>
23561 <section name="penalties">
23562 <param name="position" value="0.0"/>
23563 <param name="height" value="1.0"/>
23564 <param name="left_width" value="0.0"/>
23565 <param name="right_width" value="0.0"/>
23566 </section>
23567 </section>
23568 </section>
23569 <section name="SignalToNoiseEstimationParameter">
23570 <param name="max_intensity" value="-1"/>
23571 <param name="auto_max_stdev_factor" value="3.0"/>
23572 <param name="auto_max_percentile" value="95"/>
23573 <param name="auto_mode" value="0"/>
23574 <param name="win_len" value="200.0"/>
23575 <param name="bin_count" value="30"/>
23576 <param name="stdev_mp" value="3.0"/>
23577 <param name="min_required_elements" value="10"/>
23578 <param name="noise_for_empty_window" value="1e+20"/>
23579 </section>
23580 </section>
23581 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23582 <output name="ctd_out" ftype="xml">
23583 <assert_contents>
23584 <is_valid_xml/>
23585 </assert_contents>
23586 </output>
23587 </test>
23588 </xml>
23589 <xml name="autotest_PepNovoAdapter">
23590 </xml>
23591 <xml name="autotest_PeptideIndexer">
23592 <test expect_num_outputs="2">
23593 <conditional name="adv_opts_cond">
23594 <param name="adv_opts_selector" value="advanced"/>
23595 <param name="force" value="false"/>
23596 <param name="test" value="true"/>
23597 </conditional>
23598 <param name="in" value="PeptideIndexer_1.idXML"/>
23599 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23600 <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23601 <param name="decoy_string" value=""/>
23602 <param name="decoy_string_position" value="prefix"/>
23603 <param name="missing_decoy_action" value="error"/>
23604 <param name="write_protein_sequence" value="false"/>
23605 <param name="write_protein_description" value="false"/>
23606 <param name="keep_unreferenced_proteins" value="false"/>
23607 <param name="unmatched_action" value="warn"/>
23608 <param name="aaa_max" value="4"/>
23609 <param name="mismatches_max" value="0"/>
23610 <param name="IL_equivalent" value="false"/>
23611 <section name="enzyme">
23612 <param name="name" value="auto"/>
23613 <param name="specificity" value="none"/>
23614 </section>
23615 <param name="OPTIONAL_OUTPUTS" value="ctd_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="2">
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="PeptideIndexer_1.idXML"/>
23629 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23630 <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23631 <param name="decoy_string" value=""/>
23632 <param name="decoy_string_position" value="prefix"/>
23633 <param name="missing_decoy_action" value="error"/>
23634 <param name="write_protein_sequence" value="true"/>
23635 <param name="write_protein_description" value="false"/>
23636 <param name="keep_unreferenced_proteins" value="false"/>
23637 <param name="unmatched_action" value="warn"/>
23638 <param name="aaa_max" value="4"/>
23639 <param name="mismatches_max" value="0"/>
23640 <param name="IL_equivalent" value="false"/>
23641 <section name="enzyme">
23642 <param name="name" value="auto"/>
23643 <param name="specificity" value="none"/>
23644 </section>
23645 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23646 <output name="ctd_out" ftype="xml">
23647 <assert_contents>
23648 <is_valid_xml/>
23649 </assert_contents>
23650 </output>
23651 </test>
23652 <test expect_num_outputs="2">
23653 <conditional name="adv_opts_cond">
23654 <param name="adv_opts_selector" value="advanced"/>
23655 <param name="force" value="false"/>
23656 <param name="test" value="true"/>
23657 </conditional>
23658 <param name="in" value="PeptideIndexer_1.idXML"/>
23659 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23660 <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23661 <param name="decoy_string" value=""/>
23662 <param name="decoy_string_position" value="prefix"/>
23663 <param name="missing_decoy_action" value="error"/>
23664 <param name="write_protein_sequence" value="false"/>
23665 <param name="write_protein_description" value="false"/>
23666 <param name="keep_unreferenced_proteins" value="true"/>
23667 <param name="unmatched_action" value="warn"/>
23668 <param name="aaa_max" value="4"/>
23669 <param name="mismatches_max" value="0"/>
23670 <param name="IL_equivalent" value="false"/>
23671 <section name="enzyme">
23672 <param name="name" value="auto"/>
23673 <param name="specificity" value="none"/>
23674 </section>
23675 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23676 <output name="ctd_out" ftype="xml">
23677 <assert_contents>
23678 <is_valid_xml/>
23679 </assert_contents>
23680 </output>
23681 </test>
23682 <test expect_num_outputs="2">
23683 <conditional name="adv_opts_cond">
23684 <param name="adv_opts_selector" value="advanced"/>
23685 <param name="force" value="false"/>
23686 <param name="test" value="true"/>
23687 </conditional>
23688 <param name="in" value="PeptideIndexer_1.idXML"/>
23689 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23690 <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23691 <param name="decoy_string" value=""/>
23692 <param name="decoy_string_position" value="prefix"/>
23693 <param name="missing_decoy_action" value="error"/>
23694 <param name="write_protein_sequence" value="true"/>
23695 <param name="write_protein_description" value="false"/>
23696 <param name="keep_unreferenced_proteins" value="false"/>
23697 <param name="unmatched_action" value="warn"/>
23698 <param name="aaa_max" value="0"/>
23699 <param name="mismatches_max" value="0"/>
23700 <param name="IL_equivalent" value="false"/>
23701 <section name="enzyme">
23702 <param name="name" value="auto"/>
23703 <param name="specificity" value="none"/>
23704 </section>
23705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23706 <output name="ctd_out" ftype="xml">
23707 <assert_contents>
23708 <is_valid_xml/>
23709 </assert_contents>
23710 </output>
23711 </test>
23712 <test expect_num_outputs="2">
23713 <conditional name="adv_opts_cond">
23714 <param name="adv_opts_selector" value="advanced"/>
23715 <param name="force" value="false"/>
23716 <param name="test" value="true"/>
23717 </conditional>
23718 <param name="in" value="PeptideIndexer_1.idXML"/>
23719 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23720 <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23721 <param name="decoy_string" value=""/>
23722 <param name="decoy_string_position" value="prefix"/>
23723 <param name="missing_decoy_action" value="error"/>
23724 <param name="write_protein_sequence" value="false"/>
23725 <param name="write_protein_description" value="false"/>
23726 <param name="keep_unreferenced_proteins" value="false"/>
23727 <param name="unmatched_action" value="warn"/>
23728 <param name="aaa_max" value="4"/>
23729 <param name="mismatches_max" value="0"/>
23730 <param name="IL_equivalent" value="false"/>
23731 <section name="enzyme">
23732 <param name="name" value="auto"/>
23733 <param name="specificity" value="none"/>
23734 </section>
23735 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23736 <output name="ctd_out" ftype="xml">
23737 <assert_contents>
23738 <is_valid_xml/>
23739 </assert_contents>
23740 </output>
23741 </test>
23742 <test expect_num_outputs="2">
23743 <conditional name="adv_opts_cond">
23744 <param name="adv_opts_selector" value="advanced"/>
23745 <param name="force" value="false"/>
23746 <param name="test" value="true"/>
23747 </conditional>
23748 <param name="in" value="PeptideIndexer_2.idXML"/>
23749 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23750 <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23751 <param name="decoy_string" value=""/>
23752 <param name="decoy_string_position" value="prefix"/>
23753 <param name="missing_decoy_action" value="error"/>
23754 <param name="write_protein_sequence" value="false"/>
23755 <param name="write_protein_description" value="false"/>
23756 <param name="keep_unreferenced_proteins" value="false"/>
23757 <param name="unmatched_action" value="warn"/>
23758 <param name="aaa_max" value="3"/>
23759 <param name="mismatches_max" value="0"/>
23760 <param name="IL_equivalent" value="false"/>
23761 <section name="enzyme">
23762 <param name="name" value="auto"/>
23763 <param name="specificity" value="none"/>
23764 </section>
23765 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23766 <output name="ctd_out" ftype="xml">
23767 <assert_contents>
23768 <is_valid_xml/>
23769 </assert_contents>
23770 </output>
23771 </test>
23772 <test expect_num_outputs="2">
23773 <conditional name="adv_opts_cond">
23774 <param name="adv_opts_selector" value="advanced"/>
23775 <param name="force" value="false"/>
23776 <param name="test" value="true"/>
23777 </conditional>
23778 <param name="in" value="PeptideIndexer_3.idXML"/>
23779 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23780 <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23781 <param name="decoy_string" value="DECOY_"/>
23782 <param name="decoy_string_position" value="prefix"/>
23783 <param name="missing_decoy_action" value="error"/>
23784 <param name="write_protein_sequence" value="false"/>
23785 <param name="write_protein_description" value="false"/>
23786 <param name="keep_unreferenced_proteins" value="false"/>
23787 <param name="unmatched_action" value="warn"/>
23788 <param name="aaa_max" value="4"/>
23789 <param name="mismatches_max" value="0"/>
23790 <param name="IL_equivalent" value="false"/>
23791 <section name="enzyme">
23792 <param name="name" value="auto"/>
23793 <param name="specificity" value="full"/>
23794 </section>
23795 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23796 <output name="ctd_out" ftype="xml">
23797 <assert_contents>
23798 <is_valid_xml/>
23799 </assert_contents>
23800 </output>
23801 </test>
23802 <test expect_num_outputs="2">
23803 <conditional name="adv_opts_cond">
23804 <param name="adv_opts_selector" value="advanced"/>
23805 <param name="force" value="false"/>
23806 <param name="test" value="true"/>
23807 </conditional>
23808 <param name="in" value="PeptideIndexer_3.idXML"/>
23809 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23810 <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23811 <param name="decoy_string" value=""/>
23812 <param name="decoy_string_position" value="prefix"/>
23813 <param name="missing_decoy_action" value="error"/>
23814 <param name="write_protein_sequence" value="false"/>
23815 <param name="write_protein_description" value="false"/>
23816 <param name="keep_unreferenced_proteins" value="false"/>
23817 <param name="unmatched_action" value="warn"/>
23818 <param name="aaa_max" value="4"/>
23819 <param name="mismatches_max" value="0"/>
23820 <param name="IL_equivalent" value="false"/>
23821 <section name="enzyme">
23822 <param name="name" value="auto"/>
23823 <param name="specificity" value="semi"/>
23824 </section>
23825 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23826 <output name="ctd_out" ftype="xml">
23827 <assert_contents>
23828 <is_valid_xml/>
23829 </assert_contents>
23830 </output>
23831 </test>
23832 <test expect_num_outputs="2">
23833 <conditional name="adv_opts_cond">
23834 <param name="adv_opts_selector" value="advanced"/>
23835 <param name="force" value="false"/>
23836 <param name="test" value="true"/>
23837 </conditional>
23838 <param name="in" value="PeptideIndexer_3.idXML"/>
23839 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23840 <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23841 <param name="decoy_string" value=""/>
23842 <param name="decoy_string_position" value="prefix"/>
23843 <param name="missing_decoy_action" value="error"/>
23844 <param name="write_protein_sequence" value="false"/>
23845 <param name="write_protein_description" value="false"/>
23846 <param name="keep_unreferenced_proteins" value="false"/>
23847 <param name="unmatched_action" value="remove"/>
23848 <param name="aaa_max" value="4"/>
23849 <param name="mismatches_max" value="0"/>
23850 <param name="IL_equivalent" value="false"/>
23851 <section name="enzyme">
23852 <param name="name" value="auto"/>
23853 <param name="specificity" value="none"/>
23854 </section>
23855 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23856 <output name="ctd_out" ftype="xml">
23857 <assert_contents>
23858 <is_valid_xml/>
23859 </assert_contents>
23860 </output>
23861 </test>
23862 <test expect_num_outputs="2">
23863 <conditional name="adv_opts_cond">
23864 <param name="adv_opts_selector" value="advanced"/>
23865 <param name="force" value="false"/>
23866 <param name="test" value="true"/>
23867 </conditional>
23868 <param name="in" value="PeptideIndexer_10_input.idXML"/>
23869 <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
23870 <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23871 <param name="decoy_string" value=""/>
23872 <param name="decoy_string_position" value="prefix"/>
23873 <param name="missing_decoy_action" value="error"/>
23874 <param name="write_protein_sequence" value="true"/>
23875 <param name="write_protein_description" value="false"/>
23876 <param name="keep_unreferenced_proteins" value="false"/>
23877 <param name="unmatched_action" value="error"/>
23878 <param name="aaa_max" value="3"/>
23879 <param name="mismatches_max" value="0"/>
23880 <param name="IL_equivalent" value="true"/>
23881 <section name="enzyme">
23882 <param name="name" value="auto"/>
23883 <param name="specificity" value="auto"/>
23884 </section>
23885 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23886 <output name="ctd_out" ftype="xml">
23887 <assert_contents>
23888 <is_valid_xml/>
23889 </assert_contents>
23890 </output>
23891 </test>
23892 <test expect_num_outputs="2">
23893 <conditional name="adv_opts_cond">
23894 <param name="adv_opts_selector" value="advanced"/>
23895 <param name="force" value="false"/>
23896 <param name="test" value="true"/>
23897 </conditional>
23898 <param name="in" value="PeptideIndexer_1.idXML"/>
23899 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23900 <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23901 <param name="decoy_string" value=""/>
23902 <param name="decoy_string_position" value="prefix"/>
23903 <param name="missing_decoy_action" value="error"/>
23904 <param name="write_protein_sequence" value="false"/>
23905 <param name="write_protein_description" value="false"/>
23906 <param name="keep_unreferenced_proteins" value="false"/>
23907 <param name="unmatched_action" value="warn"/>
23908 <param name="aaa_max" value="4"/>
23909 <param name="mismatches_max" value="0"/>
23910 <param name="IL_equivalent" value="false"/>
23911 <section name="enzyme">
23912 <param name="name" value="auto"/>
23913 <param name="specificity" value="none"/>
23914 </section>
23915 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23916 <output name="ctd_out" ftype="xml">
23917 <assert_contents>
23918 <is_valid_xml/>
23919 </assert_contents>
23920 </output>
23921 </test>
23922 <test expect_num_outputs="2">
23923 <conditional name="adv_opts_cond">
23924 <param name="adv_opts_selector" value="advanced"/>
23925 <param name="force" value="false"/>
23926 <param name="test" value="true"/>
23927 </conditional>
23928 <param name="in" value="empty.idXML"/>
23929 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23930 <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23931 <param name="decoy_string" value=""/>
23932 <param name="decoy_string_position" value="prefix"/>
23933 <param name="missing_decoy_action" value="error"/>
23934 <param name="write_protein_sequence" value="false"/>
23935 <param name="write_protein_description" value="false"/>
23936 <param name="keep_unreferenced_proteins" value="false"/>
23937 <param name="unmatched_action" value="error"/>
23938 <param name="aaa_max" value="4"/>
23939 <param name="mismatches_max" value="0"/>
23940 <param name="IL_equivalent" value="false"/>
23941 <section name="enzyme">
23942 <param name="name" value="auto"/>
23943 <param name="specificity" value="auto"/>
23944 </section>
23945 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23946 <output name="ctd_out" ftype="xml">
23947 <assert_contents>
23948 <is_valid_xml/>
23949 </assert_contents>
23950 </output>
23951 </test>
23952 <test expect_num_outputs="2">
23953 <conditional name="adv_opts_cond">
23954 <param name="adv_opts_selector" value="advanced"/>
23955 <param name="force" value="false"/>
23956 <param name="test" value="true"/>
23957 </conditional>
23958 <param name="in" value="PeptideIndexer_14.idXML"/>
23959 <param name="fasta" value="PeptideIndexer_2.fasta"/>
23960 <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23961 <param name="decoy_string" value=""/>
23962 <param name="decoy_string_position" value="prefix"/>
23963 <param name="missing_decoy_action" value="error"/>
23964 <param name="write_protein_sequence" value="true"/>
23965 <param name="write_protein_description" value="false"/>
23966 <param name="keep_unreferenced_proteins" value="false"/>
23967 <param name="unmatched_action" value="error"/>
23968 <param name="aaa_max" value="4"/>
23969 <param name="mismatches_max" value="0"/>
23970 <param name="IL_equivalent" value="false"/>
23971 <section name="enzyme">
23972 <param name="name" value="auto"/>
23973 <param name="specificity" value="none"/>
23974 </section>
23975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23976 <output name="ctd_out" ftype="xml">
23977 <assert_contents>
23978 <is_valid_xml/>
23979 </assert_contents>
23980 </output>
23981 </test>
23982 </xml>
23983 <xml name="autotest_PercolatorAdapter">
23984 <test expect_num_outputs="2">
23985 <conditional name="adv_opts_cond">
23986 <param name="adv_opts_selector" value="advanced"/>
23987 <param name="generic_feature_set" value="false"/>
23988 <param name="subset_max_train" value="0"/>
23989 <param name="cpos" value="0.0"/>
23990 <param name="cneg" value="0.0"/>
23991 <param name="testFDR" value="0.5"/>
23992 <param name="trainFDR" value="0.5"/>
23993 <param name="maxiter" value="10"/>
23994 <param name="nested_xval_bins" value="1"/>
23995 <param name="quick_validation" value="false"/>
23996 <param name="static" value="false"/>
23997 <param name="default_direction" value=""/>
23998 <param name="verbose" value="2"/>
23999 <param name="unitnorm" value="false"/>
24000 <param name="test_each_iteration" value="false"/>
24001 <param name="override" value="false"/>
24002 <param name="seed" value="1"/>
24003 <param name="doc" value="0"/>
24004 <param name="klammer" value="false"/>
24005 <param name="decoy_pattern" value="random"/>
24006 <param name="post_processing_tdc" value="false"/>
24007 <param name="train_best_positive" value="false"/>
24008 <param name="ipf_max_peakgroup_pep" value="0.7"/>
24009 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
24010 <param name="ipf_min_transition_sn" value="0.0"/>
24011 <param name="force" value="false"/>
24012 <param name="test" value="true"/>
24013 </conditional>
24014 <param name="in" value="PercolatorAdapter_1.idXML"/>
24015 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24016 <param name="out_type" value="idXML"/>
24017 <param name="enzyme" value="trypsin"/>
24018 <param name="peptide_level_fdrs" value="false"/>
24019 <param name="protein_level_fdrs" value="false"/>
24020 <param name="osw_level" value="ms2"/>
24021 <param name="score_type" value="q-value"/>
24022 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24023 <output name="ctd_out" ftype="xml">
24024 <assert_contents>
24025 <is_valid_xml/>
24026 </assert_contents>
24027 </output>
24028 </test>
24029 <test expect_num_outputs="2">
24030 <conditional name="adv_opts_cond">
24031 <param name="adv_opts_selector" value="advanced"/>
24032 <param name="generic_feature_set" value="false"/>
24033 <param name="subset_max_train" value="0"/>
24034 <param name="cpos" value="0.0"/>
24035 <param name="cneg" value="0.0"/>
24036 <param name="testFDR" value="0.01"/>
24037 <param name="trainFDR" value="0.01"/>
24038 <param name="maxiter" value="10"/>
24039 <param name="nested_xval_bins" value="1"/>
24040 <param name="quick_validation" value="false"/>
24041 <param name="static" value="false"/>
24042 <param name="default_direction" value=""/>
24043 <param name="verbose" value="2"/>
24044 <param name="unitnorm" value="false"/>
24045 <param name="test_each_iteration" value="false"/>
24046 <param name="override" value="false"/>
24047 <param name="seed" value="1"/>
24048 <param name="doc" value="0"/>
24049 <param name="klammer" value="false"/>
24050 <param name="decoy_pattern" value="random"/>
24051 <param name="post_processing_tdc" value="false"/>
24052 <param name="train_best_positive" value="false"/>
24053 <param name="ipf_max_peakgroup_pep" value="0.7"/>
24054 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
24055 <param name="ipf_min_transition_sn" value="0.0"/>
24056 <param name="force" value="false"/>
24057 <param name="test" value="true"/>
24058 </conditional>
24059 <param name="in_osw" value="PercolatorAdapter_2.osw"/>
24060 <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
24061 <param name="out_type" value="osw"/>
24062 <param name="enzyme" value="trypsin"/>
24063 <param name="peptide_level_fdrs" value="false"/>
24064 <param name="protein_level_fdrs" value="false"/>
24065 <param name="osw_level" value="ms1"/>
24066 <param name="score_type" value="q-value"/>
24067 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24068 <output name="ctd_out" ftype="xml">
24069 <assert_contents>
24070 <is_valid_xml/>
24071 </assert_contents>
24072 </output>
24073 </test>
24074 <test expect_num_outputs="2">
24075 <conditional name="adv_opts_cond">
24076 <param name="adv_opts_selector" value="advanced"/>
24077 <param name="generic_feature_set" value="false"/>
24078 <param name="subset_max_train" value="0"/>
24079 <param name="cpos" value="0.0"/>
24080 <param name="cneg" value="0.0"/>
24081 <param name="testFDR" value="0.01"/>
24082 <param name="trainFDR" value="0.01"/>
24083 <param name="maxiter" value="10"/>
24084 <param name="nested_xval_bins" value="1"/>
24085 <param name="quick_validation" value="false"/>
24086 <param name="static" value="false"/>
24087 <param name="default_direction" value=""/>
24088 <param name="verbose" value="2"/>
24089 <param name="unitnorm" value="false"/>
24090 <param name="test_each_iteration" value="false"/>
24091 <param name="override" value="false"/>
24092 <param name="seed" value="1"/>
24093 <param name="doc" value="0"/>
24094 <param name="klammer" value="false"/>
24095 <param name="decoy_pattern" value="random"/>
24096 <param name="post_processing_tdc" value="false"/>
24097 <param name="train_best_positive" value="false"/>
24098 <param name="ipf_max_peakgroup_pep" value="0.7"/>
24099 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
24100 <param name="ipf_min_transition_sn" value="0.0"/>
24101 <param name="force" value="false"/>
24102 <param name="test" value="true"/>
24103 </conditional>
24104 <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/>
24105 <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
24106 <param name="out_type" value="osw"/>
24107 <param name="enzyme" value="trypsin"/>
24108 <param name="peptide_level_fdrs" value="false"/>
24109 <param name="protein_level_fdrs" value="false"/>
24110 <param name="osw_level" value="ms2"/>
24111 <param name="score_type" value="q-value"/>
24112 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24113 <output name="ctd_out" ftype="xml">
24114 <assert_contents>
24115 <is_valid_xml/>
24116 </assert_contents>
24117 </output>
24118 </test>
24119 <test expect_num_outputs="2">
24120 <conditional name="adv_opts_cond">
24121 <param name="adv_opts_selector" value="advanced"/>
24122 <param name="generic_feature_set" value="false"/>
24123 <param name="subset_max_train" value="0"/>
24124 <param name="cpos" value="0.0"/>
24125 <param name="cneg" value="0.0"/>
24126 <param name="testFDR" value="0.01"/>
24127 <param name="trainFDR" value="0.01"/>
24128 <param name="maxiter" value="10"/>
24129 <param name="nested_xval_bins" value="1"/>
24130 <param name="quick_validation" value="false"/>
24131 <param name="static" value="false"/>
24132 <param name="default_direction" value=""/>
24133 <param name="verbose" value="2"/>
24134 <param name="unitnorm" value="false"/>
24135 <param name="test_each_iteration" value="false"/>
24136 <param name="override" value="false"/>
24137 <param name="seed" value="1"/>
24138 <param name="doc" value="0"/>
24139 <param name="klammer" value="false"/>
24140 <param name="decoy_pattern" value="random"/>
24141 <param name="post_processing_tdc" value="false"/>
24142 <param name="train_best_positive" value="false"/>
24143 <param name="ipf_max_peakgroup_pep" value="0.7"/>
24144 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
24145 <param name="ipf_min_transition_sn" value="0.0"/>
24146 <param name="force" value="false"/>
24147 <param name="test" value="true"/>
24148 </conditional>
24149 <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/>
24150 <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
24151 <param name="out_type" value="osw"/>
24152 <param name="enzyme" value="trypsin"/>
24153 <param name="peptide_level_fdrs" value="false"/>
24154 <param name="protein_level_fdrs" value="false"/>
24155 <param name="osw_level" value="transition"/>
24156 <param name="score_type" value="q-value"/>
24157 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24158 <output name="ctd_out" ftype="xml">
24159 <assert_contents>
24160 <is_valid_xml/>
24161 </assert_contents>
24162 </output>
24163 </test>
24164 <test expect_num_outputs="3">
24165 <conditional name="adv_opts_cond">
24166 <param name="adv_opts_selector" value="advanced"/>
24167 <param name="generic_feature_set" value="false"/>
24168 <param name="subset_max_train" value="0"/>
24169 <param name="cpos" value="0.0"/>
24170 <param name="cneg" value="0.0"/>
24171 <param name="testFDR" value="0.5"/>
24172 <param name="trainFDR" value="0.5"/>
24173 <param name="maxiter" value="10"/>
24174 <param name="nested_xval_bins" value="1"/>
24175 <param name="quick_validation" value="false"/>
24176 <param name="static" value="false"/>
24177 <param name="default_direction" value=""/>
24178 <param name="verbose" value="2"/>
24179 <param name="unitnorm" value="false"/>
24180 <param name="test_each_iteration" value="false"/>
24181 <param name="override" value="false"/>
24182 <param name="seed" value="1"/>
24183 <param name="doc" value="0"/>
24184 <param name="klammer" value="false"/>
24185 <param name="decoy_pattern" value="random"/>
24186 <param name="post_processing_tdc" value="false"/>
24187 <param name="train_best_positive" value="false"/>
24188 <param name="ipf_max_peakgroup_pep" value="0.7"/>
24189 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
24190 <param name="ipf_min_transition_sn" value="0.0"/>
24191 <param name="force" value="false"/>
24192 <param name="test" value="true"/>
24193 </conditional>
24194 <param name="in" value="PercolatorAdapter_1.idXML"/>
24195 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24196 <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
24197 <param name="out_type" value="idXML"/>
24198 <param name="enzyme" value="trypsin"/>
24199 <param name="peptide_level_fdrs" value="false"/>
24200 <param name="protein_level_fdrs" value="false"/>
24201 <param name="osw_level" value="ms2"/>
24202 <param name="score_type" value="q-value"/>
24203 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/>
24204 <output name="ctd_out" ftype="xml">
24205 <assert_contents>
24206 <is_valid_xml/>
24207 </assert_contents>
24208 </output>
24209 </test>
24210 </xml>
24211 <xml name="autotest_PhosphoScoring">
24212 </xml>
24213 <xml name="autotest_PrecursorIonSelector">
24214 <test expect_num_outputs="2">
24215 <conditional name="adv_opts_cond">
24216 <param name="adv_opts_selector" value="advanced"/>
24217 <param name="solver" value="GLPK"/>
24218 <param name="force" value="false"/>
24219 <param name="test" value="true"/>
24220 </conditional>
24221 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
24222 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
24223 <param name="num_precursors" value="1"/>
24224 <param name="load_preprocessing" value="false"/>
24225 <param name="store_preprocessing" value="false"/>
24226 <param name="simulation" value="true"/>
24227 <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
24228 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
24229 <param name="fixed_modifications" value=""/>
24230 <section name="algorithm">
24231 <param name="type" value="IPS"/>
24232 <param name="max_iteration" value="10"/>
24233 <param name="rt_bin_capacity" value="10"/>
24234 <param name="step_size" value="1"/>
24235 <param name="peptide_min_prob" value="0.2"/>
24236 <param name="sequential_spectrum_order" value="false"/>
24237 <section name="MIPFormulation">
24238 <section name="thresholds">
24239 <param name="min_protein_probability" value="0.2"/>
24240 <param name="min_protein_id_probability" value="0.95"/>
24241 <param name="min_pt_weight" value="0.5"/>
24242 <param name="min_mz" value="500.0"/>
24243 <param name="max_mz" value="5000.0"/>
24244 <param name="min_pred_pep_prob" value="0.5"/>
24245 <param name="min_rt_weight" value="0.5"/>
24246 <param name="use_peptide_rule" value="true"/>
24247 <param name="min_peptide_ids" value="2"/>
24248 <param name="min_peptide_probability" value="0.95"/>
24249 </section>
24250 <section name="combined_ilp">
24251 <param name="k1" value="0.2"/>
24252 <param name="k2" value="0.2"/>
24253 <param name="k3" value="0.4"/>
24254 <param name="scale_matching_probs" value="true"/>
24255 </section>
24256 <section name="feature_based">
24257 <param name="no_intensity_normalization" value="false"/>
24258 <param name="max_number_precursors_per_feature" value="1"/>
24259 </section>
24260 </section>
24261 <section name="Preprocessing">
24262 <param name="precursor_mass_tolerance" value="0.9"/>
24263 <param name="precursor_mass_tolerance_unit" value="Da"/>
24264 <param name="preprocessed_db_path" value=""/>
24265 <param name="preprocessed_db_pred_rt_path" value=""/>
24266 <param name="preprocessed_db_pred_dt_path" value=""/>
24267 <param name="max_peptides_per_run" value="100000"/>
24268 <param name="missed_cleavages" value="1"/>
24269 <param name="taxonomy" value=""/>
24270 <param name="store_peptide_sequences" value="false"/>
24271 <section name="rt_settings">
24272 <param name="min_rt" value="960.0"/>
24273 <param name="max_rt" value="3840.0"/>
24274 <param name="rt_step_size" value="30.0"/>
24275 <param name="gauss_mean" value="-1.0"/>
24276 <param name="gauss_sigma" value="3.0"/>
24277 </section>
24278 </section>
24279 </section>
24280 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
24281 <output name="ctd_out" ftype="xml">
24282 <assert_contents>
24283 <is_valid_xml/>
24284 </assert_contents>
24285 </output>
24286 </test>
24287 <test expect_num_outputs="2">
24288 <conditional name="adv_opts_cond">
24289 <param name="adv_opts_selector" value="advanced"/>
24290 <param name="solver" value="GLPK"/>
24291 <param name="force" value="false"/>
24292 <param name="test" value="true"/>
24293 </conditional>
24294 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
24295 <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
24296 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
24297 <param name="num_precursors" value="1"/>
24298 <param name="load_preprocessing" value="false"/>
24299 <param name="store_preprocessing" value="false"/>
24300 <param name="simulation" value="false"/>
24301 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
24302 <param name="fixed_modifications" value=""/>
24303 <section name="algorithm">
24304 <param name="type" value="IPS"/>
24305 <param name="max_iteration" value="10"/>
24306 <param name="rt_bin_capacity" value="10"/>
24307 <param name="step_size" value="1"/>
24308 <param name="peptide_min_prob" value="0.2"/>
24309 <param name="sequential_spectrum_order" value="false"/>
24310 <section name="MIPFormulation">
24311 <section name="thresholds">
24312 <param name="min_protein_probability" value="0.2"/>
24313 <param name="min_protein_id_probability" value="0.95"/>
24314 <param name="min_pt_weight" value="0.5"/>
24315 <param name="min_mz" value="500.0"/>
24316 <param name="max_mz" value="5000.0"/>
24317 <param name="min_pred_pep_prob" value="0.5"/>
24318 <param name="min_rt_weight" value="0.5"/>
24319 <param name="use_peptide_rule" value="true"/>
24320 <param name="min_peptide_ids" value="2"/>
24321 <param name="min_peptide_probability" value="0.95"/>
24322 </section>
24323 <section name="combined_ilp">
24324 <param name="k1" value="0.2"/>
24325 <param name="k2" value="0.2"/>
24326 <param name="k3" value="0.4"/>
24327 <param name="scale_matching_probs" value="true"/>
24328 </section>
24329 <section name="feature_based">
24330 <param name="no_intensity_normalization" value="false"/>
24331 <param name="max_number_precursors_per_feature" value="1"/>
24332 </section>
24333 </section>
24334 <section name="Preprocessing">
24335 <param name="precursor_mass_tolerance" value="0.9"/>
24336 <param name="precursor_mass_tolerance_unit" value="Da"/>
24337 <param name="preprocessed_db_path" value=""/>
24338 <param name="preprocessed_db_pred_rt_path" value=""/>
24339 <param name="preprocessed_db_pred_dt_path" value=""/>
24340 <param name="max_peptides_per_run" value="100000"/>
24341 <param name="missed_cleavages" value="1"/>
24342 <param name="taxonomy" value=""/>
24343 <param name="store_peptide_sequences" value="false"/>
24344 <section name="rt_settings">
24345 <param name="min_rt" value="960.0"/>
24346 <param name="max_rt" value="3840.0"/>
24347 <param name="rt_step_size" value="30.0"/>
24348 <param name="gauss_mean" value="-1.0"/>
24349 <param name="gauss_sigma" value="3.0"/>
24350 </section>
24351 </section>
24352 </section>
24353 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24354 <output name="ctd_out" ftype="xml">
24355 <assert_contents>
24356 <is_valid_xml/>
24357 </assert_contents>
24358 </output>
24359 </test>
24360 </xml>
24361 <xml name="autotest_PrecursorMassCorrector">
24362 <test expect_num_outputs="2">
24363 <conditional name="adv_opts_cond">
24364 <param name="adv_opts_selector" value="advanced"/>
24365 <param name="max_charge" value="3"/>
24366 <param name="intensity_threshold" value="-1.0"/>
24367 <param name="force" value="false"/>
24368 <param name="test" value="true"/>
24369 </conditional>
24370 <param name="in" value="PrecursorMassCorrector_1_input.mzML"/>
24371 <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
24372 <param name="precursor_mass_tolerance" value="1.5"/>
24373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24374 <output name="ctd_out" ftype="xml">
24375 <assert_contents>
24376 <is_valid_xml/>
24377 </assert_contents>
24378 </output>
24379 </test>
24380 </xml>
24381 <xml name="autotest_ProteinInference">
24382 <test expect_num_outputs="2">
24383 <conditional name="adv_opts_cond">
24384 <param name="adv_opts_selector" value="advanced"/>
24385 <param name="force" value="false"/>
24386 <param name="test" value="true"/>
24387 </conditional>
24388 <param name="in" value="ProteinInference_1_input.idXML"/>
24389 <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24390 <param name="merge_runs" value="all"/>
24391 <param name="annotate_indist_groups" value="true"/>
24392 <section name="Merging">
24393 <param name="annotate_origin" value="false"/>
24394 <param name="allow_disagreeing_settings" value="false"/>
24395 </section>
24396 <section name="Algorithm">
24397 <param name="min_peptides_per_protein" value="1"/>
24398 <param name="score_aggregation_method" value="maximum"/>
24399 <param name="treat_charge_variants_separately" value="true"/>
24400 <param name="treat_modification_variants_separately" value="true"/>
24401 <param name="use_shared_peptides" value="false"/>
24402 <param name="skip_count_annotation" value="false"/>
24403 </section>
24404 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24405 <output name="ctd_out" ftype="xml">
24406 <assert_contents>
24407 <is_valid_xml/>
24408 </assert_contents>
24409 </output>
24410 </test>
24411 </xml>
24412 <xml name="autotest_ProteinQuantifier">
24413 <test expect_num_outputs="3">
24414 <conditional name="adv_opts_cond">
24415 <param name="adv_opts_selector" value="advanced"/>
24416 <param name="force" value="false"/>
24417 <param name="test" value="true"/>
24418 </conditional>
24419 <param name="in" value="ProteinQuantifier_input.featureXML"/>
24420 <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
24421 <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
24422 <param name="top" value="3"/>
24423 <param name="average" value="median"/>
24424 <param name="include_all" value="false"/>
24425 <param name="best_charge_and_fraction" value="false"/>
24426 <param name="greedy_group_resolution" value="false"/>
24427 <param name="ratios" value="false"/>
24428 <param name="ratiosSILAC" value="false"/>
24429 <section name="consensus">
24430 <param name="normalize" value="false"/>
24431 <param name="fix_peptides" value="false"/>
24432 </section>
24433 <section name="format">
24434 <param name="separator" value=""/>
24435 <param name="quoting" value="double"/>
24436 <param name="replacement" value="_"/>
24437 </section>
24438 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
24439 <output name="ctd_out" ftype="xml">
24440 <assert_contents>
24441 <is_valid_xml/>
24442 </assert_contents>
24443 </output>
24444 </test>
24445 <test expect_num_outputs="3">
24446 <conditional name="adv_opts_cond">
24447 <param name="adv_opts_selector" value="advanced"/>
24448 <param name="force" value="false"/>
24449 <param name="test" value="true"/>
24450 </conditional>
24451 <param name="in" value="ProteinQuantifier_input.featureXML"/>
24452 <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
24453 <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
24454 <param name="top" value="2"/>
24455 <param name="average" value="sum"/>
24456 <param name="include_all" value="true"/>
24457 <param name="best_charge_and_fraction" value="true"/>
24458 <param name="greedy_group_resolution" value="false"/>
24459 <param name="ratios" value="false"/>
24460 <param name="ratiosSILAC" value="false"/>
24461 <section name="consensus">
24462 <param name="normalize" value="false"/>
24463 <param name="fix_peptides" value="false"/>
24464 </section>
24465 <section name="format">
24466 <param name="separator" value=""/>
24467 <param name="quoting" value="double"/>
24468 <param name="replacement" value="_"/>
24469 </section>
24470 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
24471 <output name="ctd_out" ftype="xml">
24472 <assert_contents>
24473 <is_valid_xml/>
24474 </assert_contents>
24475 </output>
24476 </test>
24477 <test expect_num_outputs="3">
24478 <conditional name="adv_opts_cond">
24479 <param name="adv_opts_selector" value="advanced"/>
24480 <param name="force" value="false"/>
24481 <param name="test" value="true"/>
24482 </conditional>
24483 <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
24484 <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
24485 <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
24486 <param name="top" value="2"/>
24487 <param name="average" value="mean"/>
24488 <param name="include_all" value="true"/>
24489 <param name="best_charge_and_fraction" value="false"/>
24490 <param name="greedy_group_resolution" value="false"/>
24491 <param name="ratios" value="false"/>
24492 <param name="ratiosSILAC" value="false"/>
24493 <section name="consensus">
24494 <param name="normalize" value="false"/>
24495 <param name="fix_peptides" value="false"/>
24496 </section>
24497 <section name="format">
24498 <param name="separator" value=""/>
24499 <param name="quoting" value="double"/>
24500 <param name="replacement" value="_"/>
24501 </section>
24502 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
24503 <output name="ctd_out" ftype="xml">
24504 <assert_contents>
24505 <is_valid_xml/>
24506 </assert_contents>
24507 </output>
24508 </test>
24509 <test expect_num_outputs="2">
24510 <conditional name="adv_opts_cond">
24511 <param name="adv_opts_selector" value="advanced"/>
24512 <param name="force" value="false"/>
24513 <param name="test" value="true"/>
24514 </conditional>
24515 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24516 <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24517 <param name="top" value="0"/>
24518 <param name="average" value="sum"/>
24519 <param name="include_all" value="false"/>
24520 <param name="best_charge_and_fraction" value="false"/>
24521 <param name="greedy_group_resolution" value="false"/>
24522 <param name="ratios" value="false"/>
24523 <param name="ratiosSILAC" value="false"/>
24524 <section name="consensus">
24525 <param name="normalize" value="false"/>
24526 <param name="fix_peptides" value="false"/>
24527 </section>
24528 <section name="format">
24529 <param name="separator" value=""/>
24530 <param name="quoting" value="double"/>
24531 <param name="replacement" value="_"/>
24532 </section>
24533 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24534 <output name="ctd_out" ftype="xml">
24535 <assert_contents>
24536 <is_valid_xml/>
24537 </assert_contents>
24538 </output>
24539 </test>
24540 <test expect_num_outputs="2">
24541 <conditional name="adv_opts_cond">
24542 <param name="adv_opts_selector" value="advanced"/>
24543 <param name="force" value="false"/>
24544 <param name="test" value="true"/>
24545 </conditional>
24546 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24547 <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24548 <param name="top" value="3"/>
24549 <param name="average" value="sum"/>
24550 <param name="include_all" value="false"/>
24551 <param name="best_charge_and_fraction" value="false"/>
24552 <param name="greedy_group_resolution" value="false"/>
24553 <param name="ratios" value="false"/>
24554 <param name="ratiosSILAC" value="false"/>
24555 <section name="consensus">
24556 <param name="normalize" value="false"/>
24557 <param name="fix_peptides" value="false"/>
24558 </section>
24559 <section name="format">
24560 <param name="separator" value=""/>
24561 <param name="quoting" value="double"/>
24562 <param name="replacement" value="_"/>
24563 </section>
24564 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24565 <output name="ctd_out" ftype="xml">
24566 <assert_contents>
24567 <is_valid_xml/>
24568 </assert_contents>
24569 </output>
24570 </test>
24571 <test expect_num_outputs="2">
24572 <conditional name="adv_opts_cond">
24573 <param name="adv_opts_selector" value="advanced"/>
24574 <param name="force" value="false"/>
24575 <param name="test" value="true"/>
24576 </conditional>
24577 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24578 <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24579 <param name="top" value="3"/>
24580 <param name="average" value="sum"/>
24581 <param name="include_all" value="true"/>
24582 <param name="best_charge_and_fraction" value="false"/>
24583 <param name="greedy_group_resolution" value="false"/>
24584 <param name="ratios" value="false"/>
24585 <param name="ratiosSILAC" value="false"/>
24586 <section name="consensus">
24587 <param name="normalize" value="false"/>
24588 <param name="fix_peptides" value="false"/>
24589 </section>
24590 <section name="format">
24591 <param name="separator" value=""/>
24592 <param name="quoting" value="double"/>
24593 <param name="replacement" value="_"/>
24594 </section>
24595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24596 <output name="ctd_out" ftype="xml">
24597 <assert_contents>
24598 <is_valid_xml/>
24599 </assert_contents>
24600 </output>
24601 </test>
24602 <test expect_num_outputs="2">
24603 <conditional name="adv_opts_cond">
24604 <param name="adv_opts_selector" value="advanced"/>
24605 <param name="force" value="false"/>
24606 <param name="test" value="true"/>
24607 </conditional>
24608 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24609 <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24610 <param name="top" value="0"/>
24611 <param name="average" value="sum"/>
24612 <param name="include_all" value="false"/>
24613 <param name="best_charge_and_fraction" value="false"/>
24614 <param name="greedy_group_resolution" value="false"/>
24615 <param name="ratios" value="false"/>
24616 <param name="ratiosSILAC" value="false"/>
24617 <section name="consensus">
24618 <param name="normalize" value="false"/>
24619 <param name="fix_peptides" value="true"/>
24620 </section>
24621 <section name="format">
24622 <param name="separator" value=""/>
24623 <param name="quoting" value="double"/>
24624 <param name="replacement" value="_"/>
24625 </section>
24626 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24627 <output name="ctd_out" ftype="xml">
24628 <assert_contents>
24629 <is_valid_xml/>
24630 </assert_contents>
24631 </output>
24632 </test>
24633 <test expect_num_outputs="2">
24634 <conditional name="adv_opts_cond">
24635 <param name="adv_opts_selector" value="advanced"/>
24636 <param name="force" value="false"/>
24637 <param name="test" value="true"/>
24638 </conditional>
24639 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24640 <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24641 <param name="top" value="3"/>
24642 <param name="average" value="sum"/>
24643 <param name="include_all" value="false"/>
24644 <param name="best_charge_and_fraction" value="false"/>
24645 <param name="greedy_group_resolution" value="false"/>
24646 <param name="ratios" value="false"/>
24647 <param name="ratiosSILAC" value="false"/>
24648 <section name="consensus">
24649 <param name="normalize" value="false"/>
24650 <param name="fix_peptides" value="true"/>
24651 </section>
24652 <section name="format">
24653 <param name="separator" value=""/>
24654 <param name="quoting" value="double"/>
24655 <param name="replacement" value="_"/>
24656 </section>
24657 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24658 <output name="ctd_out" ftype="xml">
24659 <assert_contents>
24660 <is_valid_xml/>
24661 </assert_contents>
24662 </output>
24663 </test>
24664 <test expect_num_outputs="3">
24665 <conditional name="adv_opts_cond">
24666 <param name="adv_opts_selector" value="advanced"/>
24667 <param name="force" value="false"/>
24668 <param name="test" value="true"/>
24669 </conditional>
24670 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24671 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24672 <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24673 <param name="top" value="3"/>
24674 <param name="average" value="sum"/>
24675 <param name="include_all" value="true"/>
24676 <param name="best_charge_and_fraction" value="false"/>
24677 <param name="greedy_group_resolution" value="false"/>
24678 <param name="ratios" value="false"/>
24679 <param name="ratiosSILAC" value="false"/>
24680 <section name="consensus">
24681 <param name="normalize" value="false"/>
24682 <param name="fix_peptides" value="true"/>
24683 </section>
24684 <section name="format">
24685 <param name="separator" value=""/>
24686 <param name="quoting" value="double"/>
24687 <param name="replacement" value="_"/>
24688 </section>
24689 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
24690 <output name="ctd_out" ftype="xml">
24691 <assert_contents>
24692 <is_valid_xml/>
24693 </assert_contents>
24694 </output>
24695 </test>
24696 <test expect_num_outputs="2">
24697 <conditional name="adv_opts_cond">
24698 <param name="adv_opts_selector" value="advanced"/>
24699 <param name="force" value="false"/>
24700 <param name="test" value="true"/>
24701 </conditional>
24702 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24703 <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24704 <param name="top" value="3"/>
24705 <param name="average" value="sum"/>
24706 <param name="include_all" value="true"/>
24707 <param name="best_charge_and_fraction" value="false"/>
24708 <param name="greedy_group_resolution" value="false"/>
24709 <param name="ratios" value="true"/>
24710 <param name="ratiosSILAC" value="false"/>
24711 <section name="consensus">
24712 <param name="normalize" value="false"/>
24713 <param name="fix_peptides" value="true"/>
24714 </section>
24715 <section name="format">
24716 <param name="separator" value=""/>
24717 <param name="quoting" value="double"/>
24718 <param name="replacement" value="_"/>
24719 </section>
24720 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24721 <output name="ctd_out" ftype="xml">
24722 <assert_contents>
24723 <is_valid_xml/>
24724 </assert_contents>
24725 </output>
24726 </test>
24727 <test expect_num_outputs="2">
24728 <conditional name="adv_opts_cond">
24729 <param name="adv_opts_selector" value="advanced"/>
24730 <param name="force" value="false"/>
24731 <param name="test" value="true"/>
24732 </conditional>
24733 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
24734 <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24735 <param name="top" value="3"/>
24736 <param name="average" value="sum"/>
24737 <param name="include_all" value="true"/>
24738 <param name="best_charge_and_fraction" value="false"/>
24739 <param name="greedy_group_resolution" value="false"/>
24740 <param name="ratios" value="false"/>
24741 <param name="ratiosSILAC" value="true"/>
24742 <section name="consensus">
24743 <param name="normalize" value="false"/>
24744 <param name="fix_peptides" value="true"/>
24745 </section>
24746 <section name="format">
24747 <param name="separator" value=""/>
24748 <param name="quoting" value="double"/>
24749 <param name="replacement" value="_"/>
24750 </section>
24751 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24752 <output name="ctd_out" ftype="xml">
24753 <assert_contents>
24754 <is_valid_xml/>
24755 </assert_contents>
24756 </output>
24757 </test>
24758 <test expect_num_outputs="3">
24759 <conditional name="adv_opts_cond">
24760 <param name="adv_opts_selector" value="advanced"/>
24761 <param name="force" value="false"/>
24762 <param name="test" value="true"/>
24763 </conditional>
24764 <param name="in" value="ProteinQuantifier_input.idXML"/>
24765 <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
24766 <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
24767 <param name="top" value="0"/>
24768 <param name="average" value="sum"/>
24769 <param name="include_all" value="false"/>
24770 <param name="best_charge_and_fraction" value="false"/>
24771 <param name="greedy_group_resolution" value="false"/>
24772 <param name="ratios" value="false"/>
24773 <param name="ratiosSILAC" value="false"/>
24774 <section name="consensus">
24775 <param name="normalize" value="false"/>
24776 <param name="fix_peptides" value="false"/>
24777 </section>
24778 <section name="format">
24779 <param name="separator" value=""/>
24780 <param name="quoting" value="double"/>
24781 <param name="replacement" value="_"/>
24782 </section>
24783 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
24784 <output name="ctd_out" ftype="xml">
24785 <assert_contents>
24786 <is_valid_xml/>
24787 </assert_contents>
24788 </output>
24789 </test>
24790 </xml>
24791 <xml name="autotest_ProteinResolver">
24792 <test expect_num_outputs="4">
24793 <conditional name="adv_opts_cond">
24794 <param name="adv_opts_selector" value="advanced"/>
24795 <param name="force" value="false"/>
24796 <param name="test" value="true"/>
24797 </conditional>
24798 <param name="fasta" value="ProteinResolver_1_input.fasta"/>
24799 <param name="in" value="ProteinResolver_1_input.consensusXML"/>
24800 <param name="in_path" value=""/>
24801 <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
24802 <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
24803 <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/>
24804 <section name="resolver">
24805 <param name="missed_cleavages" value="2"/>
24806 <param name="min_length" value="6"/>
24807 <param name="enzyme" value="Trypsin"/>
24808 </section>
24809 <section name="designer">
24810 <param name="experiment" value="ExperimentalSetting"/>
24811 <param name="file" value="File"/>
24812 <param name="separator" value="tab"/>
24813 </section>
24814 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/>
24815 <output name="ctd_out" ftype="xml">
24816 <assert_contents>
24817 <is_valid_xml/>
24818 </assert_contents>
24819 </output>
24820 </test>
24821 </xml>
24822 <xml name="autotest_PSMFeatureExtractor">
24823 </xml>
24824 <xml name="autotest_PTModel">
24825 <test expect_num_outputs="2">
24826 <conditional name="adv_opts_cond">
24827 <param name="adv_opts_selector" value="advanced"/>
24828 <param name="force" value="false"/>
24829 <param name="test" value="true"/>
24830 </conditional>
24831 <param name="in_positive" value="PTModel_1_input_positive.idXML"/>
24832 <param name="in_negative" value="PTModel_1_input_negative.idXML"/>
24833 <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
24834 <param name="c" value="0.5"/>
24835 <param name="svm_type" value="C_SVC"/>
24836 <param name="nu" value="0.5"/>
24837 <param name="kernel_type" value="OLIGO"/>
24838 <param name="degree" value="1"/>
24839 <param name="border_length" value="22"/>
24840 <param name="k_mer_length" value="1"/>
24841 <param name="sigma" value="5.0"/>
24842 <param name="max_positive_count" value="1000"/>
24843 <param name="max_negative_count" value="1000"/>
24844 <param name="redundant" value="false"/>
24845 <param name="additive_cv" value="false"/>
24846 <section name="cv">
24847 <param name="skip_cv" value="true"/>
24848 <param name="number_of_runs" value="10"/>
24849 <param name="number_of_partitions" value="10"/>
24850 <param name="degree_start" value="1"/>
24851 <param name="degree_step_size" value="2"/>
24852 <param name="degree_stop" value="4"/>
24853 <param name="c_start" value="1.0"/>
24854 <param name="c_step_size" value="100.0"/>
24855 <param name="c_stop" value="1000.0"/>
24856 <param name="nu_start" value="0.1"/>
24857 <param name="nu_step_size" value="1.3"/>
24858 <param name="nu_stop" value="0.9"/>
24859 <param name="sigma_start" value="1.0"/>
24860 <param name="sigma_step_size" value="1.3"/>
24861 <param name="sigma_stop" value="15.0"/>
24862 </section>
24863 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24864 <output name="ctd_out" ftype="xml">
24865 <assert_contents>
24866 <is_valid_xml/>
24867 </assert_contents>
24868 </output>
24869 </test>
24870 </xml>
24871 <xml name="autotest_QCCalculator">
24872 </xml>
24873 <xml name="autotest_QCEmbedder">
24874 </xml>
24875 <xml name="autotest_QCExporter">
24876 </xml>
24877 <xml name="autotest_QCExtractor">
24878 </xml>
24879 <xml name="autotest_QCImporter">
24880 </xml>
24881 <xml name="autotest_QCMerger">
24882 </xml>
24883 <xml name="autotest_QCShrinker">
24884 </xml>
24885 <xml name="autotest_QualityControl">
24886 <test expect_num_outputs="3">
24887 <conditional name="adv_opts_cond">
24888 <param name="adv_opts_selector" value="advanced"/>
24889 <param name="force" value="false"/>
24890 <param name="test" value="true"/>
24891 </conditional>
24892 <param name="in_cm" value="QualityControl_1_in.consensusXML"/>
24893 <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/>
24894 <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
24895 <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24896 <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
24897 <param name="in_contaminants" value="QualityControl_1.fasta"/>
24898 <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
24899 <section name="FragmentMassError">
24900 <param name="unit" value="auto"/>
24901 <param name="tolerance" value="20.0"/>
24902 </section>
24903 <section name="MS2_id_rate">
24904 <param name="assume_all_target" value="false"/>
24905 </section>
24906 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
24907 <output name="ctd_out" ftype="xml">
24908 <assert_contents>
24909 <is_valid_xml/>
24910 </assert_contents>
24911 </output>
24912 </test>
24913 </xml>
24914 <xml name="autotest_RNADigestor">
24915 </xml>
24916 <xml name="autotest_RNAMassCalculator">
24917 <test expect_num_outputs="2">
24918 <conditional name="adv_opts_cond">
24919 <param name="adv_opts_selector" value="advanced"/>
24920 <param name="force" value="false"/>
24921 <param name="test" value="true"/>
24922 </conditional>
24923 <param name="in_seq" value="&quot;AUCGGC&quot;"/>
24924 <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/>
24925 <param name="charge" value="-1 -2"/>
24926 <param name="format" value="list"/>
24927 <param name="average_mass" value="false"/>
24928 <param name="fragment_type" value="full"/>
24929 <param name="separator" value=""/>
24930 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24931 <output name="ctd_out" ftype="xml">
24932 <assert_contents>
24933 <is_valid_xml/>
24934 </assert_contents>
24935 </output>
24936 </test>
24937 </xml>
24938 <xml name="autotest_RNPxlSearch">
24939 <test expect_num_outputs="2">
24940 <conditional name="adv_opts_cond">
24941 <param name="adv_opts_selector" value="advanced"/>
24942 <param name="force" value="false"/>
24943 <param name="test" value="true"/>
24944 </conditional>
24945 <param name="in" value="RNPxlSearch_1_input.mzML"/>
24946 <param name="database" value="RNPxlSearch_1_input.fasta"/>
24947 <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24948 <section name="precursor">
24949 <param name="mass_tolerance" value="20.0"/>
24950 <param name="mass_tolerance_unit" value="ppm"/>
24951 <param name="min_charge" value="2"/>
24952 <param name="max_charge" value="5"/>
24953 <param name="isotopes" value="0 1"/>
24954 </section>
24955 <section name="fragment">
24956 <param name="mass_tolerance" value="20.0"/>
24957 <param name="mass_tolerance_unit" value="ppm"/>
24958 </section>
24959 <section name="modifications">
24960 <param name="fixed" value=""/>
24961 <param name="variable" value="Oxidation (M)"/>
24962 <param name="variable_max_per_peptide" value="2"/>
24963 </section>
24964 <section name="peptide">
24965 <param name="min_size" value="6"/>
24966 <param name="max_size" value="1000000"/>
24967 <param name="missed_cleavages" value="1"/>
24968 <param name="enzyme" value="Trypsin"/>
24969 </section>
24970 <section name="report">
24971 <param name="top_hits" value="1"/>
24972 </section>
24973 <section name="RNPxl">
24974 <param name="length" value="2"/>
24975 <param name="sequence" value="GUA"/>
24976 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
24977 <param name="nt_groups" value=""/>
24978 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
24979 <param name="can_cross_link" value="U"/>
24980 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
24981 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
24982 <param name="scoring" value="fast"/>
24983 <param name="decoys" value="false"/>
24984 <param name="CysteineAdduct" value="false"/>
24985 <param name="filter_fractional_mass" value="false"/>
24986 <param name="carbon_labeled_fragments" value="false"/>
24987 <param name="only_xl" value="false"/>
24988 <param name="filter_small_peptide_mass" value="600.0"/>
24989 <param name="marker_ions_tolerance" value="0.05"/>
24990 </section>
24991 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24992 <output name="ctd_out" ftype="xml">
24993 <assert_contents>
24994 <is_valid_xml/>
24995 </assert_contents>
24996 </output>
24997 </test>
24998 <test expect_num_outputs="2">
24999 <conditional name="adv_opts_cond">
25000 <param name="adv_opts_selector" value="advanced"/>
25001 <param name="force" value="false"/>
25002 <param name="test" value="true"/>
25003 </conditional>
25004 <param name="in" value="RNPxlSearch_1_input.mzML"/>
25005 <param name="database" value="RNPxlSearch_1_input.fasta"/>
25006 <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
25007 <section name="precursor">
25008 <param name="mass_tolerance" value="20.0"/>
25009 <param name="mass_tolerance_unit" value="ppm"/>
25010 <param name="min_charge" value="2"/>
25011 <param name="max_charge" value="5"/>
25012 <param name="isotopes" value="0 1"/>
25013 </section>
25014 <section name="fragment">
25015 <param name="mass_tolerance" value="20.0"/>
25016 <param name="mass_tolerance_unit" value="ppm"/>
25017 </section>
25018 <section name="modifications">
25019 <param name="fixed" value=""/>
25020 <param name="variable" value="Oxidation (M)"/>
25021 <param name="variable_max_per_peptide" value="2"/>
25022 </section>
25023 <section name="peptide">
25024 <param name="min_size" value="6"/>
25025 <param name="max_size" value="1000000"/>
25026 <param name="missed_cleavages" value="1"/>
25027 <param name="enzyme" value="Trypsin"/>
25028 </section>
25029 <section name="report">
25030 <param name="top_hits" value="1"/>
25031 </section>
25032 <section name="RNPxl">
25033 <param name="length" value="2"/>
25034 <param name="sequence" value="GUA"/>
25035 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
25036 <param name="nt_groups" value=""/>
25037 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
25038 <param name="can_cross_link" value="U"/>
25039 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
25040 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
25041 <param name="scoring" value="fast"/>
25042 <param name="decoys" value="true"/>
25043 <param name="CysteineAdduct" value="false"/>
25044 <param name="filter_fractional_mass" value="false"/>
25045 <param name="carbon_labeled_fragments" value="false"/>
25046 <param name="only_xl" value="false"/>
25047 <param name="filter_small_peptide_mass" value="600.0"/>
25048 <param name="marker_ions_tolerance" value="0.05"/>
25049 </section>
25050 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25051 <output name="ctd_out" ftype="xml">
25052 <assert_contents>
25053 <is_valid_xml/>
25054 </assert_contents>
25055 </output>
25056 </test>
25057 <test expect_num_outputs="3">
25058 <conditional name="adv_opts_cond">
25059 <param name="adv_opts_selector" value="advanced"/>
25060 <param name="force" value="false"/>
25061 <param name="test" value="true"/>
25062 </conditional>
25063 <param name="in" value="RNPxlSearch_1_input.mzML"/>
25064 <param name="database" value="RNPxlSearch_1_input.fasta"/>
25065 <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
25066 <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
25067 <section name="precursor">
25068 <param name="mass_tolerance" value="10.0"/>
25069 <param name="mass_tolerance_unit" value="ppm"/>
25070 <param name="min_charge" value="2"/>
25071 <param name="max_charge" value="5"/>
25072 <param name="isotopes" value="0 1"/>
25073 </section>
25074 <section name="fragment">
25075 <param name="mass_tolerance" value="10.0"/>
25076 <param name="mass_tolerance_unit" value="ppm"/>
25077 </section>
25078 <section name="modifications">
25079 <param name="fixed" value=""/>
25080 <param name="variable" value=""/>
25081 <param name="variable_max_per_peptide" value="2"/>
25082 </section>
25083 <section name="peptide">
25084 <param name="min_size" value="6"/>
25085 <param name="max_size" value="1000000"/>
25086 <param name="missed_cleavages" value="1"/>
25087 <param name="enzyme" value="Trypsin"/>
25088 </section>
25089 <section name="report">
25090 <param name="top_hits" value="3"/>
25091 </section>
25092 <section name="RNPxl">
25093 <param name="length" value="2"/>
25094 <param name="sequence" value=""/>
25095 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
25096 <param name="nt_groups" value=""/>
25097 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
25098 <param name="can_cross_link" value="U"/>
25099 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
25100 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
25101 <param name="scoring" value="fast"/>
25102 <param name="decoys" value="false"/>
25103 <param name="CysteineAdduct" value="false"/>
25104 <param name="filter_fractional_mass" value="false"/>
25105 <param name="carbon_labeled_fragments" value="false"/>
25106 <param name="only_xl" value="false"/>
25107 <param name="filter_small_peptide_mass" value="600.0"/>
25108 <param name="marker_ions_tolerance" value="0.05"/>
25109 </section>
25110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
25111 <output name="ctd_out" ftype="xml">
25112 <assert_contents>
25113 <is_valid_xml/>
25114 </assert_contents>
25115 </output>
25116 </test>
25117 <test expect_num_outputs="3">
25118 <conditional name="adv_opts_cond">
25119 <param name="adv_opts_selector" value="advanced"/>
25120 <param name="force" value="false"/>
25121 <param name="test" value="true"/>
25122 </conditional>
25123 <param name="in" value="RNPxlSearch_1_input.mzML"/>
25124 <param name="database" value="RNPxlSearch_1_input.fasta"/>
25125 <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
25126 <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
25127 <section name="precursor">
25128 <param name="mass_tolerance" value="10.0"/>
25129 <param name="mass_tolerance_unit" value="ppm"/>
25130 <param name="min_charge" value="2"/>
25131 <param name="max_charge" value="5"/>
25132 <param name="isotopes" value="0 1"/>
25133 </section>
25134 <section name="fragment">
25135 <param name="mass_tolerance" value="10.0"/>
25136 <param name="mass_tolerance_unit" value="ppm"/>
25137 </section>
25138 <section name="modifications">
25139 <param name="fixed" value=""/>
25140 <param name="variable" value=""/>
25141 <param name="variable_max_per_peptide" value="2"/>
25142 </section>
25143 <section name="peptide">
25144 <param name="min_size" value="6"/>
25145 <param name="max_size" value="1000000"/>
25146 <param name="missed_cleavages" value="1"/>
25147 <param name="enzyme" value="Trypsin"/>
25148 </section>
25149 <section name="report">
25150 <param name="top_hits" value="2"/>
25151 </section>
25152 <section name="RNPxl">
25153 <param name="length" value="2"/>
25154 <param name="sequence" value=""/>
25155 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
25156 <param name="nt_groups" value=""/>
25157 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
25158 <param name="can_cross_link" value="U"/>
25159 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
25160 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
25161 <param name="scoring" value="fast"/>
25162 <param name="decoys" value="true"/>
25163 <param name="CysteineAdduct" value="false"/>
25164 <param name="filter_fractional_mass" value="false"/>
25165 <param name="carbon_labeled_fragments" value="false"/>
25166 <param name="only_xl" value="false"/>
25167 <param name="filter_small_peptide_mass" value="600.0"/>
25168 <param name="marker_ions_tolerance" value="0.05"/>
25169 </section>
25170 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
25171 <output name="ctd_out" ftype="xml">
25172 <assert_contents>
25173 <is_valid_xml/>
25174 </assert_contents>
25175 </output>
25176 </test>
25177 </xml>
25178 <xml name="autotest_RNPxlXICFilter">
25179 </xml>
25180 <xml name="autotest_RTEvaluation">
25181 </xml>
25182 <xml name="autotest_RTModel">
25183 <test expect_num_outputs="2">
25184 <conditional name="adv_opts_cond">
25185 <param name="adv_opts_selector" value="advanced"/>
25186 <param name="force" value="false"/>
25187 <param name="test" value="true"/>
25188 </conditional>
25189 <param name="in" value="RTModel_1_input.idXML"/>
25190 <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/>
25191 <param name="svm_type" value="NU_SVR"/>
25192 <param name="nu" value="0.5"/>
25193 <param name="p" value="0.1"/>
25194 <param name="c" value="0.1"/>
25195 <param name="kernel_type" value="POLY"/>
25196 <param name="degree" value="1"/>
25197 <param name="border_length" value="22"/>
25198 <param name="max_std" value="10.0"/>
25199 <param name="k_mer_length" value="1"/>
25200 <param name="sigma" value="5.0"/>
25201 <param name="total_gradient_time" value="3000.0"/>
25202 <param name="first_dim_rt" value="false"/>
25203 <param name="additive_cv" value="false"/>
25204 <section name="cv">
25205 <param name="skip_cv" value="true"/>
25206 <param name="number_of_runs" value="10"/>
25207 <param name="number_of_partitions" value="10"/>
25208 <param name="degree_start" value="1"/>
25209 <param name="degree_step_size" value="2"/>
25210 <param name="degree_stop" value="4"/>
25211 <param name="p_start" value="1.0"/>
25212 <param name="p_step_size" value="10.0"/>
25213 <param name="p_stop" value="1000.0"/>
25214 <param name="c_start" value="1.0"/>
25215 <param name="c_step_size" value="10.0"/>
25216 <param name="c_stop" value="1000.0"/>
25217 <param name="nu_start" value="0.3"/>
25218 <param name="nu_step_size" value="1.2"/>
25219 <param name="nu_stop" value="0.7"/>
25220 <param name="sigma_start" value="1.0"/>
25221 <param name="sigma_step_size" value="1.3"/>
25222 <param name="sigma_stop" value="15.0"/>
25223 </section>
25224 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25225 <output name="ctd_out" ftype="xml">
25226 <assert_contents>
25227 <is_valid_xml/>
25228 </assert_contents>
25229 </output>
25230 </test>
25231 <test expect_num_outputs="2">
25232 <conditional name="adv_opts_cond">
25233 <param name="adv_opts_selector" value="advanced"/>
25234 <param name="force" value="false"/>
25235 <param name="test" value="true"/>
25236 </conditional>
25237 <param name="in_positive" value="RTModel_2_input_positive.idXML"/>
25238 <param name="in_negative" value="RTModel_2_input_negative.idXML"/>
25239 <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
25240 <param name="svm_type" value="NU_SVR"/>
25241 <param name="nu" value="0.5"/>
25242 <param name="p" value="0.1"/>
25243 <param name="c" value="0.5"/>
25244 <param name="kernel_type" value="OLIGO"/>
25245 <param name="degree" value="1"/>
25246 <param name="border_length" value="22"/>
25247 <param name="max_std" value="10.0"/>
25248 <param name="k_mer_length" value="1"/>
25249 <param name="sigma" value="5.0"/>
25250 <param name="total_gradient_time" value="1.0"/>
25251 <param name="first_dim_rt" value="false"/>
25252 <param name="additive_cv" value="false"/>
25253 <section name="cv">
25254 <param name="skip_cv" value="true"/>
25255 <param name="number_of_runs" value="10"/>
25256 <param name="number_of_partitions" value="10"/>
25257 <param name="degree_start" value="1"/>
25258 <param name="degree_step_size" value="2"/>
25259 <param name="degree_stop" value="4"/>
25260 <param name="p_start" value="1.0"/>
25261 <param name="p_step_size" value="10.0"/>
25262 <param name="p_stop" value="1000.0"/>
25263 <param name="c_start" value="1.0"/>
25264 <param name="c_step_size" value="10.0"/>
25265 <param name="c_stop" value="1000.0"/>
25266 <param name="nu_start" value="0.3"/>
25267 <param name="nu_step_size" value="1.2"/>
25268 <param name="nu_stop" value="0.7"/>
25269 <param name="sigma_start" value="1.0"/>
25270 <param name="sigma_step_size" value="1.3"/>
25271 <param name="sigma_stop" value="15.0"/>
25272 </section>
25273 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25274 <output name="ctd_out" ftype="xml">
25275 <assert_contents>
25276 <is_valid_xml/>
25277 </assert_contents>
25278 </output>
25279 </test>
25280 <test expect_num_outputs="2">
25281 <conditional name="adv_opts_cond">
25282 <param name="adv_opts_selector" value="advanced"/>
25283 <param name="force" value="false"/>
25284 <param name="test" value="true"/>
25285 </conditional>
25286 <param name="in" value="RTModel_3_input.idXML"/>
25287 <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
25288 <param name="svm_type" value="NU_SVR"/>
25289 <param name="nu" value="0.5"/>
25290 <param name="p" value="0.1"/>
25291 <param name="c" value="0.001953125"/>
25292 <param name="kernel_type" value="OLIGO"/>
25293 <param name="degree" value="1"/>
25294 <param name="border_length" value="22"/>
25295 <param name="max_std" value="10.0"/>
25296 <param name="k_mer_length" value="1"/>
25297 <param name="sigma" value="1.0"/>
25298 <param name="total_gradient_time" value="1.0"/>
25299 <param name="first_dim_rt" value="false"/>
25300 <param name="additive_cv" value="false"/>
25301 <section name="cv">
25302 <param name="skip_cv" value="false"/>
25303 <param name="number_of_runs" value="1"/>
25304 <param name="number_of_partitions" value="5"/>
25305 <param name="degree_start" value="1"/>
25306 <param name="degree_step_size" value="2"/>
25307 <param name="degree_stop" value="4"/>
25308 <param name="p_start" value="1.0"/>
25309 <param name="p_step_size" value="10.0"/>
25310 <param name="p_stop" value="1000.0"/>
25311 <param name="c_start" value="0.001953125"/>
25312 <param name="c_step_size" value="2.0"/>
25313 <param name="c_stop" value="0.001953125"/>
25314 <param name="nu_start" value="0.4"/>
25315 <param name="nu_step_size" value="1.2"/>
25316 <param name="nu_stop" value="0.4"/>
25317 <param name="sigma_start" value="5.0"/>
25318 <param name="sigma_step_size" value="1.221055"/>
25319 <param name="sigma_stop" value="5.0"/>
25320 </section>
25321 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25322 <output name="ctd_out" ftype="xml">
25323 <assert_contents>
25324 <is_valid_xml/>
25325 </assert_contents>
25326 </output>
25327 </test>
25328 <test expect_num_outputs="2">
25329 <conditional name="adv_opts_cond">
25330 <param name="adv_opts_selector" value="advanced"/>
25331 <param name="force" value="false"/>
25332 <param name="test" value="true"/>
25333 </conditional>
25334 <param name="in" value="RTModel_4_input.txt" ftype="txt"/>
25335 <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
25336 <param name="svm_type" value="NU_SVR"/>
25337 <param name="nu" value="0.5"/>
25338 <param name="p" value="0.1"/>
25339 <param name="c" value="0.001953125"/>
25340 <param name="kernel_type" value="OLIGO"/>
25341 <param name="degree" value="1"/>
25342 <param name="border_length" value="22"/>
25343 <param name="max_std" value="10.0"/>
25344 <param name="k_mer_length" value="1"/>
25345 <param name="sigma" value="1.0"/>
25346 <param name="total_gradient_time" value="1.0"/>
25347 <param name="first_dim_rt" value="false"/>
25348 <param name="additive_cv" value="false"/>
25349 <section name="cv">
25350 <param name="skip_cv" value="false"/>
25351 <param name="number_of_runs" value="1"/>
25352 <param name="number_of_partitions" value="5"/>
25353 <param name="degree_start" value="1"/>
25354 <param name="degree_step_size" value="2"/>
25355 <param name="degree_stop" value="4"/>
25356 <param name="p_start" value="1.0"/>
25357 <param name="p_step_size" value="10.0"/>
25358 <param name="p_stop" value="1000.0"/>
25359 <param name="c_start" value="0.001953125"/>
25360 <param name="c_step_size" value="2.0"/>
25361 <param name="c_stop" value="0.001953125"/>
25362 <param name="nu_start" value="0.4"/>
25363 <param name="nu_step_size" value="1.2"/>
25364 <param name="nu_stop" value="0.4"/>
25365 <param name="sigma_start" value="5.0"/>
25366 <param name="sigma_step_size" value="1.221055"/>
25367 <param name="sigma_stop" value="5.0"/>
25368 </section>
25369 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25370 <output name="ctd_out" ftype="xml">
25371 <assert_contents>
25372 <is_valid_xml/>
25373 </assert_contents>
25374 </output>
25375 </test>
25376 </xml>
25377 <xml name="autotest_SeedListGenerator">
25378 <test expect_num_outputs="2">
25379 <conditional name="adv_opts_cond">
25380 <param name="adv_opts_selector" value="advanced"/>
25381 <param name="force" value="false"/>
25382 <param name="test" value="true"/>
25383 </conditional>
25384 <param name="in" value="PepXMLFile_test.mzML"/>
25385 <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
25386 <param name="use_peptide_mass" value="false"/>
25387 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25388 <output name="ctd_out" ftype="xml">
25389 <assert_contents>
25390 <is_valid_xml/>
25391 </assert_contents>
25392 </output>
25393 </test>
25394 <test expect_num_outputs="2">
25395 <conditional name="adv_opts_cond">
25396 <param name="adv_opts_selector" value="advanced"/>
25397 <param name="force" value="false"/>
25398 <param name="test" value="true"/>
25399 </conditional>
25400 <param name="in" value="IDMapper_1_output.featureXML"/>
25401 <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
25402 <param name="use_peptide_mass" value="false"/>
25403 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25404 <output name="ctd_out" ftype="xml">
25405 <assert_contents>
25406 <is_valid_xml/>
25407 </assert_contents>
25408 </output>
25409 </test>
25410 </xml>
25411 <xml name="autotest_SemanticValidator">
25412 </xml>
25413 <xml name="autotest_SequenceCoverageCalculator">
25414 </xml>
25415 <xml name="autotest_SimpleSearchEngine">
25416 <test expect_num_outputs="2">
25417 <conditional name="adv_opts_cond">
25418 <param name="adv_opts_selector" value="advanced"/>
25419 <param name="force" value="false"/>
25420 <param name="test" value="true"/>
25421 </conditional>
25422 <param name="in" value="SimpleSearchEngine_1.mzML"/>
25423 <param name="database" value="SimpleSearchEngine_1.fasta"/>
25424 <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
25425 <section name="Search">
25426 <param name="enzyme" value="Trypsin"/>
25427 <param name="decoys" value="false"/>
25428 <section name="precursor">
25429 <param name="mass_tolerance" value="5.0"/>
25430 <param name="mass_tolerance_unit" value="ppm"/>
25431 <param name="min_charge" value="2"/>
25432 <param name="max_charge" value="5"/>
25433 <param name="isotopes" value="0 1"/>
25434 </section>
25435 <section name="fragment">
25436 <param name="mass_tolerance" value="0.3"/>
25437 <param name="mass_tolerance_unit" value="Da"/>
25438 </section>
25439 <section name="modifications">
25440 <param name="fixed" value=""/>
25441 <param name="variable" value="Oxidation (M)"/>
25442 <param name="variable_max_per_peptide" value="2"/>
25443 </section>
25444 <section name="annotate">
25445 <param name="PSM" value=""/>
25446 </section>
25447 <section name="peptide">
25448 <param name="min_size" value="7"/>
25449 <param name="max_size" value="40"/>
25450 <param name="missed_cleavages" value="1"/>
25451 <param name="motif" value=""/>
25452 </section>
25453 <section name="report">
25454 <param name="top_hits" value="1"/>
25455 </section>
25456 </section>
25457 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25458 <output name="ctd_out" ftype="xml">
25459 <assert_contents>
25460 <is_valid_xml/>
25461 </assert_contents>
25462 </output>
25463 </test>
25464 </xml>
25465 <xml name="autotest_SiriusAdapter">
25466 <test expect_num_outputs="2">
25467 <conditional name="adv_opts_cond">
25468 <param name="adv_opts_selector" value="advanced"/>
25469 <param name="converter_mode" value="false"/>
25470 <param name="force" value="false"/>
25471 <param name="test" value="true"/>
25472 </conditional>
25473 <param name="in" value="SiriusAdapter_1_input.mzML"/>
25474 <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
25475 <param name="out_workspace_directory" value=""/>
25476 <section name="preprocessing">
25477 <param name="filter_by_num_masstraces" value="1"/>
25478 <param name="precursor_mz_tolerance" value="0.005"/>
25479 <param name="precursor_mz_tolerance_unit" value="Da"/>
25480 <param name="precursor_rt_tolerance" value="5"/>
25481 <param name="isotope_pattern_iterations" value="3"/>
25482 <param name="feature_only" value="false"/>
25483 <param name="no_masstrace_info_isotope_pattern" value="false"/>
25484 </section>
25485 <section name="sirius">
25486 <param name="profile" value="qtof"/>
25487 <param name="candidates" value="5"/>
25488 <param name="database" value="all"/>
25489 <param name="noise" value="0"/>
25490 <param name="ppm_max" value="10"/>
25491 <param name="isotope" value="both"/>
25492 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
25493 <param name="compound_timeout" value="10"/>
25494 <param name="tree_timeout" value="0"/>
25495 <param name="top_n_hits" value="10"/>
25496 <param name="auto_charge" value="true"/>
25497 <param name="ion_tree" value="false"/>
25498 <param name="no_recalibration" value="false"/>
25499 <param name="most_intense_ms2" value="false"/>
25500 </section>
25501 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
25502 <output name="ctd_out" ftype="xml">
25503 <assert_contents>
25504 <is_valid_xml/>
25505 </assert_contents>
25506 </output>
25507 </test>
25508 <test expect_num_outputs="2">
25509 <conditional name="adv_opts_cond">
25510 <param name="adv_opts_selector" value="advanced"/>
25511 <param name="converter_mode" value="false"/>
25512 <param name="force" value="false"/>
25513 <param name="test" value="true"/>
25514 </conditional>
25515 <param name="in" value="SiriusAdapter_2_input.mzML"/>
25516 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
25517 <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
25518 <param name="out_workspace_directory" value=""/>
25519 <section name="preprocessing">
25520 <param name="filter_by_num_masstraces" value="3"/>
25521 <param name="precursor_mz_tolerance" value="0.005"/>
25522 <param name="precursor_mz_tolerance_unit" value="Da"/>
25523 <param name="precursor_rt_tolerance" value="5"/>
25524 <param name="isotope_pattern_iterations" value="3"/>
25525 <param name="feature_only" value="true"/>
25526 <param name="no_masstrace_info_isotope_pattern" value="false"/>
25527 </section>
25528 <section name="sirius">
25529 <param name="profile" value="qtof"/>
25530 <param name="candidates" value="5"/>
25531 <param name="database" value="all"/>
25532 <param name="noise" value="0"/>
25533 <param name="ppm_max" value="10"/>
25534 <param name="isotope" value="both"/>
25535 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
25536 <param name="compound_timeout" value="10"/>
25537 <param name="tree_timeout" value="0"/>
25538 <param name="top_n_hits" value="10"/>
25539 <param name="auto_charge" value="true"/>
25540 <param name="ion_tree" value="false"/>
25541 <param name="no_recalibration" value="false"/>
25542 <param name="most_intense_ms2" value="false"/>
25543 </section>
25544 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
25545 <output name="ctd_out" ftype="xml">
25546 <assert_contents>
25547 <is_valid_xml/>
25548 </assert_contents>
25549 </output>
25550 </test>
25551 <test expect_num_outputs="2">
25552 <conditional name="adv_opts_cond">
25553 <param name="adv_opts_selector" value="advanced"/>
25554 <param name="converter_mode" value="false"/>
25555 <param name="force" value="false"/>
25556 <param name="test" value="true"/>
25557 </conditional>
25558 <param name="in" value="SiriusAdapter_3_input.mzML"/>
25559 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
25560 <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
25561 <param name="out_workspace_directory" value=""/>
25562 <section name="preprocessing">
25563 <param name="filter_by_num_masstraces" value="3"/>
25564 <param name="precursor_mz_tolerance" value="0.005"/>
25565 <param name="precursor_mz_tolerance_unit" value="Da"/>
25566 <param name="precursor_rt_tolerance" value="5"/>
25567 <param name="isotope_pattern_iterations" value="3"/>
25568 <param name="feature_only" value="false"/>
25569 <param name="no_masstrace_info_isotope_pattern" value="false"/>
25570 </section>
25571 <section name="sirius">
25572 <param name="profile" value="qtof"/>
25573 <param name="candidates" value="5"/>
25574 <param name="database" value="all"/>
25575 <param name="noise" value="0"/>
25576 <param name="ppm_max" value="10"/>
25577 <param name="isotope" value="both"/>
25578 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
25579 <param name="compound_timeout" value="10"/>
25580 <param name="tree_timeout" value="0"/>
25581 <param name="top_n_hits" value="10"/>
25582 <param name="auto_charge" value="true"/>
25583 <param name="ion_tree" value="false"/>
25584 <param name="no_recalibration" value="false"/>
25585 <param name="most_intense_ms2" value="false"/>
25586 </section>
25587 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
25588 <output name="ctd_out" ftype="xml">
25589 <assert_contents>
25590 <is_valid_xml/>
25591 </assert_contents>
25592 </output>
25593 </test>
25594 <test expect_num_outputs="2">
25595 <conditional name="adv_opts_cond">
25596 <param name="adv_opts_selector" value="advanced"/>
25597 <param name="converter_mode" value="true"/>
25598 <param name="force" value="false"/>
25599 <param name="test" value="true"/>
25600 </conditional>
25601 <param name="in" value="SiriusAdapter_3_input.mzML"/>
25602 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
25603 <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
25604 <param name="out_workspace_directory" value=""/>
25605 <section name="preprocessing">
25606 <param name="filter_by_num_masstraces" value="1"/>
25607 <param name="precursor_mz_tolerance" value="0.005"/>
25608 <param name="precursor_mz_tolerance_unit" value="Da"/>
25609 <param name="precursor_rt_tolerance" value="5"/>
25610 <param name="isotope_pattern_iterations" value="3"/>
25611 <param name="feature_only" value="false"/>
25612 <param name="no_masstrace_info_isotope_pattern" value="false"/>
25613 </section>
25614 <section name="sirius">
25615 <param name="profile" value="qtof"/>
25616 <param name="candidates" value="5"/>
25617 <param name="database" value="all"/>
25618 <param name="noise" value="0"/>
25619 <param name="ppm_max" value="10"/>
25620 <param name="isotope" value="both"/>
25621 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
25622 <param name="compound_timeout" value="10"/>
25623 <param name="tree_timeout" value="0"/>
25624 <param name="top_n_hits" value="10"/>
25625 <param name="auto_charge" value="false"/>
25626 <param name="ion_tree" value="false"/>
25627 <param name="no_recalibration" value="false"/>
25628 <param name="most_intense_ms2" value="false"/>
25629 </section>
25630 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
25631 <output name="ctd_out" ftype="xml">
25632 <assert_contents>
25633 <is_valid_xml/>
25634 </assert_contents>
25635 </output>
25636 </test>
25637 <test expect_num_outputs="2">
25638 <conditional name="adv_opts_cond">
25639 <param name="adv_opts_selector" value="advanced"/>
25640 <param name="converter_mode" value="true"/>
25641 <param name="force" value="false"/>
25642 <param name="test" value="true"/>
25643 </conditional>
25644 <param name="in" value="SiriusAdapter_4_input.mzML"/>
25645 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
25646 <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
25647 <param name="out_workspace_directory" value=""/>
25648 <section name="preprocessing">
25649 <param name="filter_by_num_masstraces" value="1"/>
25650 <param name="precursor_mz_tolerance" value="0.005"/>
25651 <param name="precursor_mz_tolerance_unit" value="Da"/>
25652 <param name="precursor_rt_tolerance" value="5"/>
25653 <param name="isotope_pattern_iterations" value="3"/>
25654 <param name="feature_only" value="false"/>
25655 <param name="no_masstrace_info_isotope_pattern" value="false"/>
25656 </section>
25657 <section name="sirius">
25658 <param name="profile" value="qtof"/>
25659 <param name="candidates" value="5"/>
25660 <param name="database" value="all"/>
25661 <param name="noise" value="0"/>
25662 <param name="ppm_max" value="10"/>
25663 <param name="isotope" value="both"/>
25664 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
25665 <param name="compound_timeout" value="10"/>
25666 <param name="tree_timeout" value="0"/>
25667 <param name="top_n_hits" value="10"/>
25668 <param name="auto_charge" value="false"/>
25669 <param name="ion_tree" value="false"/>
25670 <param name="no_recalibration" value="false"/>
25671 <param name="most_intense_ms2" value="false"/>
25672 </section>
25673 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
25674 <output name="ctd_out" ftype="xml">
25675 <assert_contents>
25676 <is_valid_xml/>
25677 </assert_contents>
25678 </output>
25679 </test>
25680 <test expect_num_outputs="2">
25681 <conditional name="adv_opts_cond">
25682 <param name="adv_opts_selector" value="advanced"/>
25683 <param name="converter_mode" value="false"/>
25684 <param name="force" value="false"/>
25685 <param name="test" value="true"/>
25686 </conditional>
25687 <param name="in" value="SiriusAdapter_4_input.mzML"/>
25688 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
25689 <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
25690 <param name="out_workspace_directory" value=""/>
25691 <section name="preprocessing">
25692 <param name="filter_by_num_masstraces" value="1"/>
25693 <param name="precursor_mz_tolerance" value="0.005"/>
25694 <param name="precursor_mz_tolerance_unit" value="Da"/>
25695 <param name="precursor_rt_tolerance" value="5"/>
25696 <param name="isotope_pattern_iterations" value="3"/>
25697 <param name="feature_only" value="true"/>
25698 <param name="no_masstrace_info_isotope_pattern" value="false"/>
25699 </section>
25700 <section name="sirius">
25701 <param name="profile" value="qtof"/>
25702 <param name="candidates" value="5"/>
25703 <param name="database" value="all"/>
25704 <param name="noise" value="0"/>
25705 <param name="ppm_max" value="10"/>
25706 <param name="isotope" value="both"/>
25707 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
25708 <param name="compound_timeout" value="10"/>
25709 <param name="tree_timeout" value="0"/>
25710 <param name="top_n_hits" value="10"/>
25711 <param name="auto_charge" value="false"/>
25712 <param name="ion_tree" value="false"/>
25713 <param name="no_recalibration" value="false"/>
25714 <param name="most_intense_ms2" value="false"/>
25715 </section>
25716 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
25717 <output name="ctd_out" ftype="xml">
25718 <assert_contents>
25719 <is_valid_xml/>
25720 </assert_contents>
25721 </output>
25722 </test>
25723 <test expect_num_outputs="3">
25724 <conditional name="adv_opts_cond">
25725 <param name="adv_opts_selector" value="advanced"/>
25726 <param name="converter_mode" value="false"/>
25727 <param name="force" value="false"/>
25728 <param name="test" value="true"/>
25729 </conditional>
25730 <param name="in" value="SiriusAdapter_2_input.mzML"/>
25731 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
25732 <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/>
25733 <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
25734 <param name="out_workspace_directory" value=""/>
25735 <section name="preprocessing">
25736 <param name="filter_by_num_masstraces" value="1"/>
25737 <param name="precursor_mz_tolerance" value="0.005"/>
25738 <param name="precursor_mz_tolerance_unit" value="Da"/>
25739 <param name="precursor_rt_tolerance" value="5"/>
25740 <param name="isotope_pattern_iterations" value="3"/>
25741 <param name="feature_only" value="false"/>
25742 <param name="no_masstrace_info_isotope_pattern" value="false"/>
25743 </section>
25744 <section name="sirius">
25745 <param name="profile" value="qtof"/>
25746 <param name="candidates" value="5"/>
25747 <param name="database" value="pubchem"/>
25748 <param name="noise" value="0"/>
25749 <param name="ppm_max" value="10"/>
25750 <param name="isotope" value="both"/>
25751 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
25752 <param name="compound_timeout" value="10"/>
25753 <param name="tree_timeout" value="0"/>
25754 <param name="top_n_hits" value="10"/>
25755 <param name="auto_charge" value="true"/>
25756 <param name="ion_tree" value="false"/>
25757 <param name="no_recalibration" value="false"/>
25758 <param name="most_intense_ms2" value="false"/>
25759 </section>
25760 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
25761 <output name="ctd_out" ftype="xml">
25762 <assert_contents>
25763 <is_valid_xml/>
25764 </assert_contents>
25765 </output>
25766 </test>
25767 </xml>
25768 <xml name="autotest_SpecLibCreator">
25769 </xml>
25770 <xml name="autotest_SpecLibSearcher">
25771 <test expect_num_outputs="2">
25772 <conditional name="adv_opts_cond">
25773 <param name="adv_opts_selector" value="advanced"/>
25774 <param name="force" value="false"/>
25775 <param name="test" value="true"/>
25776 </conditional>
25777 <param name="in" value="SpecLibSearcher_1.mzML"/>
25778 <param name="lib" value="SpecLibSearcher_1.MSP"/>
25779 <output_collection name="out" count="1"/>
25780 <param name="compare_function" value="ZhangSimilarityScore"/>
25781 <section name="precursor">
25782 <param name="mass_tolerance" value="3.0"/>
25783 <param name="mass_tolerance_unit" value="Da"/>
25784 <param name="min_charge" value="1"/>
25785 <param name="max_charge" value="5"/>
25786 <param name="isotopes" value="0 1"/>
25787 </section>
25788 <section name="fragment">
25789 <param name="mass_tolerance" value="10.0"/>
25790 </section>
25791 <section name="report">
25792 <param name="top_hits" value="10"/>
25793 </section>
25794 <section name="filter">
25795 <param name="remove_peaks_below_threshold" value="2.01"/>
25796 <param name="min_peaks" value="5"/>
25797 <param name="max_peaks" value="150"/>
25798 <param name="cut_peaks_below" value="1000"/>
25799 </section>
25800 <section name="modifications">
25801 <param name="fixed" value=""/>
25802 <param name="variable" value=""/>
25803 <param name="variable_max_per_peptide" value="2"/>
25804 </section>
25805 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25806 <output name="ctd_out" ftype="xml">
25807 <assert_contents>
25808 <is_valid_xml/>
25809 </assert_contents>
25810 </output>
25811 </test>
25812 </xml>
25813 <xml name="autotest_SpectraFilterBernNorm">
25814 </xml>
25815 <xml name="autotest_SpectraFilterMarkerMower">
25816 </xml>
25817 <xml name="autotest_SpectraFilterNLargest">
25818 </xml>
25819 <xml name="autotest_SpectraFilterNormalizer">
25820 </xml>
25821 <xml name="autotest_SpectraFilterParentPeakMower">
25822 </xml>
25823 <xml name="autotest_SpectraFilterScaler">
25824 </xml>
25825 <xml name="autotest_SpectraFilterSqrtMower">
25826 <test expect_num_outputs="2">
25827 <conditional name="adv_opts_cond">
25828 <param name="adv_opts_selector" value="advanced"/>
25829 <param name="force" value="false"/>
25830 <param name="test" value="true"/>
25831 </conditional>
25832 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
25833 <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25834 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25835 <output name="ctd_out" ftype="xml">
25836 <assert_contents>
25837 <is_valid_xml/>
25838 </assert_contents>
25839 </output>
25840 </test>
25841 </xml>
25842 <xml name="autotest_SpectraFilterThresholdMower">
25843 </xml>
25844 <xml name="autotest_SpectraFilterWindowMower">
25845 <test expect_num_outputs="2">
25846 <conditional name="adv_opts_cond">
25847 <param name="adv_opts_selector" value="advanced"/>
25848 <param name="force" value="false"/>
25849 <param name="test" value="true"/>
25850 </conditional>
25851 <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/>
25852 <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25853 <section name="algorithm">
25854 <param name="windowsize" value="50.0"/>
25855 <param name="peakcount" value="2"/>
25856 <param name="movetype" value="slide"/>
25857 </section>
25858 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25859 <output name="ctd_out" ftype="xml">
25860 <assert_contents>
25861 <is_valid_xml/>
25862 </assert_contents>
25863 </output>
25864 </test>
25865 <test expect_num_outputs="2">
25866 <conditional name="adv_opts_cond">
25867 <param name="adv_opts_selector" value="advanced"/>
25868 <param name="force" value="false"/>
25869 <param name="test" value="true"/>
25870 </conditional>
25871 <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/>
25872 <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25873 <section name="algorithm">
25874 <param name="windowsize" value="20.0"/>
25875 <param name="peakcount" value="4"/>
25876 <param name="movetype" value="slide"/>
25877 </section>
25878 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25879 <output name="ctd_out" ftype="xml">
25880 <assert_contents>
25881 <is_valid_xml/>
25882 </assert_contents>
25883 </output>
25884 </test>
25885 </xml>
25886 <xml name="autotest_SpectraMerger">
25887 </xml>
25888 <xml name="autotest_SpectraSTSearchAdapter"/>
25889 <xml name="autotest_StaticModification">
25890 </xml>
25891 <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
25892 </xml>
25893 <xml name="autotest_TargetedFileConverter">
25894 <test expect_num_outputs="2">
25895 <conditional name="adv_opts_cond">
25896 <param name="adv_opts_selector" value="advanced"/>
25897 <param name="legacy_traml_id" value="false"/>
25898 <param name="force" value="false"/>
25899 <param name="test" value="true"/>
25900 </conditional>
25901 <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/>
25902 <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25903 <param name="out_type" value="TraML"/>
25904 <section name="algorithm">
25905 <param name="retentionTimeInterpretation" value="iRT"/>
25906 <param name="override_group_label_check" value="false"/>
25907 <param name="force_invalid_mods" value="false"/>
25908 </section>
25909 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25910 <output name="ctd_out" ftype="xml">
25911 <assert_contents>
25912 <is_valid_xml/>
25913 </assert_contents>
25914 </output>
25915 </test>
25916 <test expect_num_outputs="2">
25917 <conditional name="adv_opts_cond">
25918 <param name="adv_opts_selector" value="advanced"/>
25919 <param name="legacy_traml_id" value="false"/>
25920 <param name="force" value="false"/>
25921 <param name="test" value="true"/>
25922 </conditional>
25923 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
25924 <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25925 <param name="out_type" value="TraML"/>
25926 <section name="algorithm">
25927 <param name="retentionTimeInterpretation" value="minutes"/>
25928 <param name="override_group_label_check" value="false"/>
25929 <param name="force_invalid_mods" value="false"/>
25930 </section>
25931 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25932 <output name="ctd_out" ftype="xml">
25933 <assert_contents>
25934 <is_valid_xml/>
25935 </assert_contents>
25936 </output>
25937 </test>
25938 <test expect_num_outputs="2">
25939 <conditional name="adv_opts_cond">
25940 <param name="adv_opts_selector" value="advanced"/>
25941 <param name="legacy_traml_id" value="false"/>
25942 <param name="force" value="false"/>
25943 <param name="test" value="true"/>
25944 </conditional>
25945 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
25946 <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25947 <param name="out_type" value="TraML"/>
25948 <section name="algorithm">
25949 <param name="retentionTimeInterpretation" value="seconds"/>
25950 <param name="override_group_label_check" value="false"/>
25951 <param name="force_invalid_mods" value="false"/>
25952 </section>
25953 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25954 <output name="ctd_out" ftype="xml">
25955 <assert_contents>
25956 <is_valid_xml/>
25957 </assert_contents>
25958 </output>
25959 </test>
25960 <test expect_num_outputs="2">
25961 <conditional name="adv_opts_cond">
25962 <param name="adv_opts_selector" value="advanced"/>
25963 <param name="legacy_traml_id" value="false"/>
25964 <param name="force" value="false"/>
25965 <param name="test" value="true"/>
25966 </conditional>
25967 <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/>
25968 <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25969 <param name="out_type" value="TraML"/>
25970 <section name="algorithm">
25971 <param name="retentionTimeInterpretation" value="iRT"/>
25972 <param name="override_group_label_check" value="false"/>
25973 <param name="force_invalid_mods" value="false"/>
25974 </section>
25975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25976 <output name="ctd_out" ftype="xml">
25977 <assert_contents>
25978 <is_valid_xml/>
25979 </assert_contents>
25980 </output>
25981 </test>
25982 <test expect_num_outputs="2">
25983 <conditional name="adv_opts_cond">
25984 <param name="adv_opts_selector" value="advanced"/>
25985 <param name="legacy_traml_id" value="false"/>
25986 <param name="force" value="false"/>
25987 <param name="test" value="true"/>
25988 </conditional>
25989 <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/>
25990 <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25991 <param name="out_type" value="TraML"/>
25992 <section name="algorithm">
25993 <param name="retentionTimeInterpretation" value="iRT"/>
25994 <param name="override_group_label_check" value="false"/>
25995 <param name="force_invalid_mods" value="false"/>
25996 </section>
25997 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25998 <output name="ctd_out" ftype="xml">
25999 <assert_contents>
26000 <is_valid_xml/>
26001 </assert_contents>
26002 </output>
26003 </test>
26004 <test expect_num_outputs="2">
26005 <conditional name="adv_opts_cond">
26006 <param name="adv_opts_selector" value="advanced"/>
26007 <param name="legacy_traml_id" value="false"/>
26008 <param name="force" value="false"/>
26009 <param name="test" value="true"/>
26010 </conditional>
26011 <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/>
26012 <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26013 <param name="out_type" value="TraML"/>
26014 <section name="algorithm">
26015 <param name="retentionTimeInterpretation" value="iRT"/>
26016 <param name="override_group_label_check" value="false"/>
26017 <param name="force_invalid_mods" value="false"/>
26018 </section>
26019 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26020 <output name="ctd_out" ftype="xml">
26021 <assert_contents>
26022 <is_valid_xml/>
26023 </assert_contents>
26024 </output>
26025 </test>
26026 <test expect_num_outputs="2">
26027 <conditional name="adv_opts_cond">
26028 <param name="adv_opts_selector" value="advanced"/>
26029 <param name="legacy_traml_id" value="false"/>
26030 <param name="force" value="false"/>
26031 <param name="test" value="true"/>
26032 </conditional>
26033 <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/>
26034 <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26035 <param name="out_type" value="TraML"/>
26036 <section name="algorithm">
26037 <param name="retentionTimeInterpretation" value="iRT"/>
26038 <param name="override_group_label_check" value="false"/>
26039 <param name="force_invalid_mods" value="false"/>
26040 </section>
26041 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26042 <output name="ctd_out" ftype="xml">
26043 <assert_contents>
26044 <is_valid_xml/>
26045 </assert_contents>
26046 </output>
26047 </test>
26048 <test expect_num_outputs="2">
26049 <conditional name="adv_opts_cond">
26050 <param name="adv_opts_selector" value="advanced"/>
26051 <param name="legacy_traml_id" value="false"/>
26052 <param name="force" value="false"/>
26053 <param name="test" value="true"/>
26054 </conditional>
26055 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
26056 <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26057 <param name="out_type" value="TraML"/>
26058 <section name="algorithm">
26059 <param name="retentionTimeInterpretation" value="iRT"/>
26060 <param name="override_group_label_check" value="false"/>
26061 <param name="force_invalid_mods" value="false"/>
26062 </section>
26063 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26064 <output name="ctd_out" ftype="xml">
26065 <assert_contents>
26066 <is_valid_xml/>
26067 </assert_contents>
26068 </output>
26069 </test>
26070 <test expect_num_outputs="2">
26071 <conditional name="adv_opts_cond">
26072 <param name="adv_opts_selector" value="advanced"/>
26073 <param name="legacy_traml_id" value="true"/>
26074 <param name="force" value="false"/>
26075 <param name="test" value="true"/>
26076 </conditional>
26077 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
26078 <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26079 <param name="out_type" value="TraML"/>
26080 <section name="algorithm">
26081 <param name="retentionTimeInterpretation" value="iRT"/>
26082 <param name="override_group_label_check" value="false"/>
26083 <param name="force_invalid_mods" value="false"/>
26084 </section>
26085 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26086 <output name="ctd_out" ftype="xml">
26087 <assert_contents>
26088 <is_valid_xml/>
26089 </assert_contents>
26090 </output>
26091 </test>
26092 <test expect_num_outputs="2">
26093 <conditional name="adv_opts_cond">
26094 <param name="adv_opts_selector" value="advanced"/>
26095 <param name="legacy_traml_id" value="false"/>
26096 <param name="force" value="false"/>
26097 <param name="test" value="true"/>
26098 </conditional>
26099 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
26100 <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26101 <param name="out_type" value="TraML"/>
26102 <section name="algorithm">
26103 <param name="retentionTimeInterpretation" value="iRT"/>
26104 <param name="override_group_label_check" value="false"/>
26105 <param name="force_invalid_mods" value="false"/>
26106 </section>
26107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26108 <output name="ctd_out" ftype="xml">
26109 <assert_contents>
26110 <is_valid_xml/>
26111 </assert_contents>
26112 </output>
26113 </test>
26114 <test expect_num_outputs="2">
26115 <conditional name="adv_opts_cond">
26116 <param name="adv_opts_selector" value="advanced"/>
26117 <param name="legacy_traml_id" value="true"/>
26118 <param name="force" value="false"/>
26119 <param name="test" value="true"/>
26120 </conditional>
26121 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
26122 <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26123 <param name="out_type" value="TraML"/>
26124 <section name="algorithm">
26125 <param name="retentionTimeInterpretation" value="iRT"/>
26126 <param name="override_group_label_check" value="false"/>
26127 <param name="force_invalid_mods" value="false"/>
26128 </section>
26129 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26130 <output name="ctd_out" ftype="xml">
26131 <assert_contents>
26132 <is_valid_xml/>
26133 </assert_contents>
26134 </output>
26135 </test>
26136 <test expect_num_outputs="2">
26137 <conditional name="adv_opts_cond">
26138 <param name="adv_opts_selector" value="advanced"/>
26139 <param name="legacy_traml_id" value="false"/>
26140 <param name="force" value="false"/>
26141 <param name="test" value="true"/>
26142 </conditional>
26143 <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/>
26144 <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
26145 <param name="out_type" value="tsv"/>
26146 <section name="algorithm">
26147 <param name="retentionTimeInterpretation" value="iRT"/>
26148 <param name="override_group_label_check" value="false"/>
26149 <param name="force_invalid_mods" value="false"/>
26150 </section>
26151 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26152 <output name="ctd_out" ftype="xml">
26153 <assert_contents>
26154 <is_valid_xml/>
26155 </assert_contents>
26156 </output>
26157 </test>
26158 <test expect_num_outputs="2">
26159 <conditional name="adv_opts_cond">
26160 <param name="adv_opts_selector" value="advanced"/>
26161 <param name="legacy_traml_id" value="false"/>
26162 <param name="force" value="false"/>
26163 <param name="test" value="true"/>
26164 </conditional>
26165 <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/>
26166 <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26167 <param name="out_type" value="TraML"/>
26168 <section name="algorithm">
26169 <param name="retentionTimeInterpretation" value="iRT"/>
26170 <param name="override_group_label_check" value="false"/>
26171 <param name="force_invalid_mods" value="false"/>
26172 </section>
26173 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26174 <output name="ctd_out" ftype="xml">
26175 <assert_contents>
26176 <is_valid_xml/>
26177 </assert_contents>
26178 </output>
26179 </test>
26180 <test expect_num_outputs="2">
26181 <conditional name="adv_opts_cond">
26182 <param name="adv_opts_selector" value="advanced"/>
26183 <param name="legacy_traml_id" value="false"/>
26184 <param name="force" value="false"/>
26185 <param name="test" value="true"/>
26186 </conditional>
26187 <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/>
26188 <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
26189 <param name="out_type" value="tsv"/>
26190 <section name="algorithm">
26191 <param name="retentionTimeInterpretation" value="iRT"/>
26192 <param name="override_group_label_check" value="true"/>
26193 <param name="force_invalid_mods" value="false"/>
26194 </section>
26195 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26196 <output name="ctd_out" ftype="xml">
26197 <assert_contents>
26198 <is_valid_xml/>
26199 </assert_contents>
26200 </output>
26201 </test>
26202 <test expect_num_outputs="2">
26203 <conditional name="adv_opts_cond">
26204 <param name="adv_opts_selector" value="advanced"/>
26205 <param name="legacy_traml_id" value="false"/>
26206 <param name="force" value="false"/>
26207 <param name="test" value="true"/>
26208 </conditional>
26209 <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/>
26210 <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26211 <param name="out_type" value="TraML"/>
26212 <section name="algorithm">
26213 <param name="retentionTimeInterpretation" value="iRT"/>
26214 <param name="override_group_label_check" value="true"/>
26215 <param name="force_invalid_mods" value="false"/>
26216 </section>
26217 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26218 <output name="ctd_out" ftype="xml">
26219 <assert_contents>
26220 <is_valid_xml/>
26221 </assert_contents>
26222 </output>
26223 </test>
26224 <test expect_num_outputs="2">
26225 <conditional name="adv_opts_cond">
26226 <param name="adv_opts_selector" value="advanced"/>
26227 <param name="legacy_traml_id" value="false"/>
26228 <param name="force" value="false"/>
26229 <param name="test" value="true"/>
26230 </conditional>
26231 <param name="in" value="ConvertTSVToTraML_output.TraML"/>
26232 <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
26233 <param name="out_type" value="tsv"/>
26234 <section name="algorithm">
26235 <param name="retentionTimeInterpretation" value="iRT"/>
26236 <param name="override_group_label_check" value="false"/>
26237 <param name="force_invalid_mods" value="false"/>
26238 </section>
26239 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26240 <output name="ctd_out" ftype="xml">
26241 <assert_contents>
26242 <is_valid_xml/>
26243 </assert_contents>
26244 </output>
26245 </test>
26246 <test expect_num_outputs="2">
26247 <conditional name="adv_opts_cond">
26248 <param name="adv_opts_selector" value="advanced"/>
26249 <param name="legacy_traml_id" value="false"/>
26250 <param name="force" value="false"/>
26251 <param name="test" value="true"/>
26252 </conditional>
26253 <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/>
26254 <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26255 <param name="out_type" value="TraML"/>
26256 <section name="algorithm">
26257 <param name="retentionTimeInterpretation" value="iRT"/>
26258 <param name="override_group_label_check" value="true"/>
26259 <param name="force_invalid_mods" value="false"/>
26260 </section>
26261 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26262 <output name="ctd_out" ftype="xml">
26263 <assert_contents>
26264 <is_valid_xml/>
26265 </assert_contents>
26266 </output>
26267 </test>
26268 <test expect_num_outputs="2">
26269 <conditional name="adv_opts_cond">
26270 <param name="adv_opts_selector" value="advanced"/>
26271 <param name="legacy_traml_id" value="false"/>
26272 <param name="force" value="false"/>
26273 <param name="test" value="true"/>
26274 </conditional>
26275 <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/>
26276 <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26277 <param name="out_type" value="TraML"/>
26278 <section name="algorithm">
26279 <param name="retentionTimeInterpretation" value="iRT"/>
26280 <param name="override_group_label_check" value="false"/>
26281 <param name="force_invalid_mods" value="false"/>
26282 </section>
26283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26284 <output name="ctd_out" ftype="xml">
26285 <assert_contents>
26286 <is_valid_xml/>
26287 </assert_contents>
26288 </output>
26289 </test>
26290 <test expect_num_outputs="2">
26291 <conditional name="adv_opts_cond">
26292 <param name="adv_opts_selector" value="advanced"/>
26293 <param name="legacy_traml_id" value="false"/>
26294 <param name="force" value="false"/>
26295 <param name="test" value="true"/>
26296 </conditional>
26297 <param name="in" value="ConvertTSVToTraML_5_output.TraML"/>
26298 <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
26299 <param name="out_type" value="tsv"/>
26300 <section name="algorithm">
26301 <param name="retentionTimeInterpretation" value="iRT"/>
26302 <param name="override_group_label_check" value="false"/>
26303 <param name="force_invalid_mods" value="false"/>
26304 </section>
26305 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26306 <output name="ctd_out" ftype="xml">
26307 <assert_contents>
26308 <is_valid_xml/>
26309 </assert_contents>
26310 </output>
26311 </test>
26312 <test expect_num_outputs="2">
26313 <conditional name="adv_opts_cond">
26314 <param name="adv_opts_selector" value="advanced"/>
26315 <param name="legacy_traml_id" value="false"/>
26316 <param name="force" value="false"/>
26317 <param name="test" value="true"/>
26318 </conditional>
26319 <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/>
26320 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/>
26321 <param name="out_type" value="traml"/>
26322 <section name="algorithm">
26323 <param name="retentionTimeInterpretation" value="iRT"/>
26324 <param name="override_group_label_check" value="false"/>
26325 <param name="force_invalid_mods" value="false"/>
26326 </section>
26327 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26328 <output name="ctd_out" ftype="xml">
26329 <assert_contents>
26330 <is_valid_xml/>
26331 </assert_contents>
26332 </output>
26333 </test>
26334 </xml>
26335 <xml name="autotest_TextExporter">
26336 <test expect_num_outputs="2">
26337 <conditional name="adv_opts_cond">
26338 <param name="adv_opts_selector" value="advanced"/>
26339 <param name="force" value="false"/>
26340 <param name="test" value="true"/>
26341 </conditional>
26342 <param name="in" value="TextExporter_1_input.featureXML"/>
26343 <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
26344 <param name="separator" value=""/>
26345 <param name="replacement" value="_"/>
26346 <param name="quoting" value="none"/>
26347 <param name="no_ids" value="false"/>
26348 <section name="feature">
26349 <param name="minimal" value="false"/>
26350 <param name="add_metavalues" value="-1"/>
26351 </section>
26352 <section name="id">
26353 <param name="proteins_only" value="false"/>
26354 <param name="peptides_only" value="false"/>
26355 <param name="protein_groups" value="false"/>
26356 <param name="first_dim_rt" value="false"/>
26357 <param name="add_metavalues" value="-1"/>
26358 <param name="add_hit_metavalues" value="-1"/>
26359 <param name="add_protein_hit_metavalues" value="-1"/>
26360 </section>
26361 <section name="consensus">
26362 <param name="sorting_method" value="none"/>
26363 <param name="sort_by_maps" value="false"/>
26364 <param name="sort_by_size" value="false"/>
26365 </section>
26366 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26367 <output name="ctd_out" ftype="xml">
26368 <assert_contents>
26369 <is_valid_xml/>
26370 </assert_contents>
26371 </output>
26372 </test>
26373 <test expect_num_outputs="5">
26374 <conditional name="adv_opts_cond">
26375 <param name="adv_opts_selector" value="advanced"/>
26376 <param name="force" value="false"/>
26377 <param name="test" value="true"/>
26378 </conditional>
26379 <param name="in" value="TextExporter_2_input.consensusXML"/>
26380 <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
26381 <param name="separator" value=""/>
26382 <param name="replacement" value="_"/>
26383 <param name="quoting" value="none"/>
26384 <param name="no_ids" value="true"/>
26385 <section name="feature">
26386 <param name="minimal" value="false"/>
26387 <param name="add_metavalues" value="-1"/>
26388 </section>
26389 <section name="id">
26390 <param name="proteins_only" value="false"/>
26391 <param name="peptides_only" value="false"/>
26392 <param name="protein_groups" value="false"/>
26393 <param name="first_dim_rt" value="false"/>
26394 <param name="add_metavalues" value="-1"/>
26395 <param name="add_hit_metavalues" value="-1"/>
26396 <param name="add_protein_hit_metavalues" value="-1"/>
26397 </section>
26398 <section name="consensus">
26399 <param name="sorting_method" value="RT_then_MZ"/>
26400 <param name="sort_by_maps" value="true"/>
26401 <param name="sort_by_size" value="true"/>
26402 </section>
26403 <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
26404 <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
26405 <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
26406 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
26407 <output name="ctd_out" ftype="xml">
26408 <assert_contents>
26409 <is_valid_xml/>
26410 </assert_contents>
26411 </output>
26412 </test>
26413 <test expect_num_outputs="2">
26414 <conditional name="adv_opts_cond">
26415 <param name="adv_opts_selector" value="advanced"/>
26416 <param name="force" value="false"/>
26417 <param name="test" value="true"/>
26418 </conditional>
26419 <param name="in" value="TextExporter_3_input.idXML"/>
26420 <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
26421 <param name="separator" value=""/>
26422 <param name="replacement" value="_"/>
26423 <param name="quoting" value="none"/>
26424 <param name="no_ids" value="false"/>
26425 <section name="feature">
26426 <param name="minimal" value="false"/>
26427 <param name="add_metavalues" value="-1"/>
26428 </section>
26429 <section name="id">
26430 <param name="proteins_only" value="false"/>
26431 <param name="peptides_only" value="false"/>
26432 <param name="protein_groups" value="false"/>
26433 <param name="first_dim_rt" value="false"/>
26434 <param name="add_metavalues" value="-1"/>
26435 <param name="add_hit_metavalues" value="-1"/>
26436 <param name="add_protein_hit_metavalues" value="-1"/>
26437 </section>
26438 <section name="consensus">
26439 <param name="sorting_method" value="none"/>
26440 <param name="sort_by_maps" value="false"/>
26441 <param name="sort_by_size" value="false"/>
26442 </section>
26443 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26444 <output name="ctd_out" ftype="xml">
26445 <assert_contents>
26446 <is_valid_xml/>
26447 </assert_contents>
26448 </output>
26449 </test>
26450 <test expect_num_outputs="2">
26451 <conditional name="adv_opts_cond">
26452 <param name="adv_opts_selector" value="advanced"/>
26453 <param name="force" value="false"/>
26454 <param name="test" value="true"/>
26455 </conditional>
26456 <param name="in" value="TextExporter_3_input.idXML"/>
26457 <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
26458 <param name="separator" value=""/>
26459 <param name="replacement" value="_"/>
26460 <param name="quoting" value="none"/>
26461 <param name="no_ids" value="false"/>
26462 <section name="feature">
26463 <param name="minimal" value="false"/>
26464 <param name="add_metavalues" value="-1"/>
26465 </section>
26466 <section name="id">
26467 <param name="proteins_only" value="true"/>
26468 <param name="peptides_only" value="false"/>
26469 <param name="protein_groups" value="false"/>
26470 <param name="first_dim_rt" value="false"/>
26471 <param name="add_metavalues" value="-1"/>
26472 <param name="add_hit_metavalues" value="-1"/>
26473 <param name="add_protein_hit_metavalues" value="-1"/>
26474 </section>
26475 <section name="consensus">
26476 <param name="sorting_method" value="none"/>
26477 <param name="sort_by_maps" value="false"/>
26478 <param name="sort_by_size" value="false"/>
26479 </section>
26480 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26481 <output name="ctd_out" ftype="xml">
26482 <assert_contents>
26483 <is_valid_xml/>
26484 </assert_contents>
26485 </output>
26486 </test>
26487 <test expect_num_outputs="2">
26488 <conditional name="adv_opts_cond">
26489 <param name="adv_opts_selector" value="advanced"/>
26490 <param name="force" value="false"/>
26491 <param name="test" value="true"/>
26492 </conditional>
26493 <param name="in" value="TextExporter_5_input.idXML"/>
26494 <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
26495 <param name="separator" value=""/>
26496 <param name="replacement" value="_"/>
26497 <param name="quoting" value="none"/>
26498 <param name="no_ids" value="false"/>
26499 <section name="feature">
26500 <param name="minimal" value="false"/>
26501 <param name="add_metavalues" value="-1"/>
26502 </section>
26503 <section name="id">
26504 <param name="proteins_only" value="false"/>
26505 <param name="peptides_only" value="true"/>
26506 <param name="protein_groups" value="false"/>
26507 <param name="first_dim_rt" value="true"/>
26508 <param name="add_metavalues" value="-1"/>
26509 <param name="add_hit_metavalues" value="-1"/>
26510 <param name="add_protein_hit_metavalues" value="-1"/>
26511 </section>
26512 <section name="consensus">
26513 <param name="sorting_method" value="none"/>
26514 <param name="sort_by_maps" value="false"/>
26515 <param name="sort_by_size" value="false"/>
26516 </section>
26517 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26518 <output name="ctd_out" ftype="xml">
26519 <assert_contents>
26520 <is_valid_xml/>
26521 </assert_contents>
26522 </output>
26523 </test>
26524 <test expect_num_outputs="2">
26525 <conditional name="adv_opts_cond">
26526 <param name="adv_opts_selector" value="advanced"/>
26527 <param name="force" value="false"/>
26528 <param name="test" value="true"/>
26529 </conditional>
26530 <param name="in" value="TextExporter_6_input.featureXML"/>
26531 <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
26532 <param name="separator" value=""/>
26533 <param name="replacement" value="_"/>
26534 <param name="quoting" value="none"/>
26535 <param name="no_ids" value="true"/>
26536 <section name="feature">
26537 <param name="minimal" value="false"/>
26538 <param name="add_metavalues" value="-1"/>
26539 </section>
26540 <section name="id">
26541 <param name="proteins_only" value="false"/>
26542 <param name="peptides_only" value="false"/>
26543 <param name="protein_groups" value="false"/>
26544 <param name="first_dim_rt" value="false"/>
26545 <param name="add_metavalues" value="-1"/>
26546 <param name="add_hit_metavalues" value="-1"/>
26547 <param name="add_protein_hit_metavalues" value="-1"/>
26548 </section>
26549 <section name="consensus">
26550 <param name="sorting_method" value="none"/>
26551 <param name="sort_by_maps" value="false"/>
26552 <param name="sort_by_size" value="false"/>
26553 </section>
26554 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26555 <output name="ctd_out" ftype="xml">
26556 <assert_contents>
26557 <is_valid_xml/>
26558 </assert_contents>
26559 </output>
26560 </test>
26561 <test expect_num_outputs="2">
26562 <conditional name="adv_opts_cond">
26563 <param name="adv_opts_selector" value="advanced"/>
26564 <param name="force" value="false"/>
26565 <param name="test" value="true"/>
26566 </conditional>
26567 <param name="in" value="TextExporter_7_input.consensusXML"/>
26568 <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
26569 <param name="separator" value=""/>
26570 <param name="replacement" value="_"/>
26571 <param name="quoting" value="none"/>
26572 <param name="no_ids" value="false"/>
26573 <section name="feature">
26574 <param name="minimal" value="false"/>
26575 <param name="add_metavalues" value="-1"/>
26576 </section>
26577 <section name="id">
26578 <param name="proteins_only" value="false"/>
26579 <param name="peptides_only" value="false"/>
26580 <param name="protein_groups" value="false"/>
26581 <param name="first_dim_rt" value="false"/>
26582 <param name="add_metavalues" value="-1"/>
26583 <param name="add_hit_metavalues" value="-1"/>
26584 <param name="add_protein_hit_metavalues" value="-1"/>
26585 </section>
26586 <section name="consensus">
26587 <param name="sorting_method" value="RT_then_MZ"/>
26588 <param name="sort_by_maps" value="true"/>
26589 <param name="sort_by_size" value="true"/>
26590 </section>
26591 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26592 <output name="ctd_out" ftype="xml">
26593 <assert_contents>
26594 <is_valid_xml/>
26595 </assert_contents>
26596 </output>
26597 </test>
26598 <test expect_num_outputs="2">
26599 <conditional name="adv_opts_cond">
26600 <param name="adv_opts_selector" value="advanced"/>
26601 <param name="force" value="false"/>
26602 <param name="test" value="true"/>
26603 </conditional>
26604 <param name="in" value="TextExporter_1_input.featureXML"/>
26605 <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
26606 <param name="separator" value=""/>
26607 <param name="replacement" value="_"/>
26608 <param name="quoting" value="none"/>
26609 <param name="no_ids" value="true"/>
26610 <section name="feature">
26611 <param name="minimal" value="false"/>
26612 <param name="add_metavalues" value="-1"/>
26613 </section>
26614 <section name="id">
26615 <param name="proteins_only" value="false"/>
26616 <param name="peptides_only" value="false"/>
26617 <param name="protein_groups" value="false"/>
26618 <param name="first_dim_rt" value="false"/>
26619 <param name="add_metavalues" value="-1"/>
26620 <param name="add_hit_metavalues" value="-1"/>
26621 <param name="add_protein_hit_metavalues" value="-1"/>
26622 </section>
26623 <section name="consensus">
26624 <param name="sorting_method" value="none"/>
26625 <param name="sort_by_maps" value="false"/>
26626 <param name="sort_by_size" value="false"/>
26627 </section>
26628 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26629 <output name="ctd_out" ftype="xml">
26630 <assert_contents>
26631 <is_valid_xml/>
26632 </assert_contents>
26633 </output>
26634 </test>
26635 <test expect_num_outputs="2">
26636 <conditional name="adv_opts_cond">
26637 <param name="adv_opts_selector" value="advanced"/>
26638 <param name="force" value="false"/>
26639 <param name="test" value="true"/>
26640 </conditional>
26641 <param name="in" value="TextExporter_9_input.idXML"/>
26642 <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
26643 <param name="separator" value=""/>
26644 <param name="replacement" value="_"/>
26645 <param name="quoting" value="none"/>
26646 <param name="no_ids" value="false"/>
26647 <section name="feature">
26648 <param name="minimal" value="false"/>
26649 <param name="add_metavalues" value="-1"/>
26650 </section>
26651 <section name="id">
26652 <param name="proteins_only" value="false"/>
26653 <param name="peptides_only" value="false"/>
26654 <param name="protein_groups" value="false"/>
26655 <param name="first_dim_rt" value="false"/>
26656 <param name="add_metavalues" value="0"/>
26657 <param name="add_hit_metavalues" value="0"/>
26658 <param name="add_protein_hit_metavalues" value="-1"/>
26659 </section>
26660 <section name="consensus">
26661 <param name="sorting_method" value="none"/>
26662 <param name="sort_by_maps" value="false"/>
26663 <param name="sort_by_size" value="false"/>
26664 </section>
26665 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26666 <output name="ctd_out" ftype="xml">
26667 <assert_contents>
26668 <is_valid_xml/>
26669 </assert_contents>
26670 </output>
26671 </test>
26672 </xml>
26673 <xml name="autotest_TICCalculator">
26674 <test expect_num_outputs="1">
26675 <conditional name="adv_opts_cond">
26676 <param name="adv_opts_selector" value="advanced"/>
26677 <param name="force" value="false"/>
26678 <param name="test" value="true"/>
26679 </conditional>
26680 <param name="in" value="MapNormalizer_output.mzML"/>
26681 <param name="read_method" value="regular"/>
26682 <param name="loadData" value="true"/>
26683 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26684 <output name="ctd_out" ftype="xml">
26685 <assert_contents>
26686 <is_valid_xml/>
26687 </assert_contents>
26688 </output>
26689 </test>
26690 <test expect_num_outputs="1">
26691 <conditional name="adv_opts_cond">
26692 <param name="adv_opts_selector" value="advanced"/>
26693 <param name="force" value="false"/>
26694 <param name="test" value="true"/>
26695 </conditional>
26696 <param name="in" value="MapNormalizer_output.mzML"/>
26697 <param name="read_method" value="streaming"/>
26698 <param name="loadData" value="true"/>
26699 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26700 <output name="ctd_out" ftype="xml">
26701 <assert_contents>
26702 <is_valid_xml/>
26703 </assert_contents>
26704 </output>
26705 </test>
26706 <test expect_num_outputs="1">
26707 <conditional name="adv_opts_cond">
26708 <param name="adv_opts_selector" value="advanced"/>
26709 <param name="force" value="false"/>
26710 <param name="test" value="true"/>
26711 </conditional>
26712 <param name="in" value="MapNormalizer_output.mzML"/>
26713 <param name="read_method" value="streaming"/>
26714 <param name="loadData" value="false"/>
26715 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26716 <output name="ctd_out" ftype="xml">
26717 <assert_contents>
26718 <is_valid_xml/>
26719 </assert_contents>
26720 </output>
26721 </test>
26722 <test expect_num_outputs="1">
26723 <conditional name="adv_opts_cond">
26724 <param name="adv_opts_selector" value="advanced"/>
26725 <param name="force" value="false"/>
26726 <param name="test" value="true"/>
26727 </conditional>
26728 <param name="in" value="MapNormalizer_output.mzML"/>
26729 <param name="read_method" value="indexed"/>
26730 <param name="loadData" value="true"/>
26731 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26732 <output name="ctd_out" ftype="xml">
26733 <assert_contents>
26734 <is_valid_xml/>
26735 </assert_contents>
26736 </output>
26737 </test>
26738 <test expect_num_outputs="1">
26739 <conditional name="adv_opts_cond">
26740 <param name="adv_opts_selector" value="advanced"/>
26741 <param name="force" value="false"/>
26742 <param name="test" value="true"/>
26743 </conditional>
26744 <param name="in" value="MapNormalizer_output.mzML"/>
26745 <param name="read_method" value="indexed_parallel"/>
26746 <param name="loadData" value="true"/>
26747 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26748 <output name="ctd_out" ftype="xml">
26749 <assert_contents>
26750 <is_valid_xml/>
26751 </assert_contents>
26752 </output>
26753 </test>
26754 </xml>
26755 <xml name="autotest_TOFCalibration">
26756 <test expect_num_outputs="2">
26757 <conditional name="adv_opts_cond">
26758 <param name="adv_opts_selector" value="advanced"/>
26759 <param name="force" value="false"/>
26760 <param name="test" value="true"/>
26761 </conditional>
26762 <param name="in" value="TOFCalibration_1_input.mzML"/>
26763 <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
26764 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
26765 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
26766 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
26767 <param name="peak_data" value="false"/>
26768 <section name="algorithm">
26769 <section name="PeakPicker">
26770 <param name="signal_to_noise" value="3.0"/>
26771 <param name="centroid_percentage" value="0.6"/>
26772 <param name="peak_width" value="0.15"/>
26773 <param name="estimate_peak_width" value="false"/>
26774 <param name="fwhm_lower_bound_factor" value="0.7"/>
26775 <param name="fwhm_upper_bound_factor" value="20.0"/>
26776 <section name="optimization">
26777 <param name="iterations" value="400"/>
26778 <section name="penalties">
26779 <param name="position" value="0.0"/>
26780 <param name="left_width" value="1.0"/>
26781 <param name="right_width" value="1.0"/>
26782 <param name="height" value="1.0"/>
26783 </section>
26784 <section name="2d">
26785 <param name="tolerance_mz" value="2.2"/>
26786 <param name="max_peak_distance" value="1.2"/>
26787 </section>
26788 </section>
26789 <section name="thresholds">
26790 <param name="peak_bound" value="400.0"/>
26791 <param name="peak_bound_ms2_level" value="10.0"/>
26792 <param name="correlation" value="0.0"/>
26793 <param name="noise_level" value="0.1"/>
26794 <param name="search_radius" value="3"/>
26795 </section>
26796 <section name="wavelet_transform">
26797 <param name="spacing" value="0.001"/>
26798 </section>
26799 <section name="deconvolution">
26800 <param name="deconvolution" value="false"/>
26801 <param name="asym_threshold" value="0.3"/>
26802 <param name="left_width" value="2.0"/>
26803 <param name="right_width" value="2.0"/>
26804 <param name="scaling" value="0.12"/>
26805 <section name="fitting">
26806 <param name="fwhm_threshold" value="0.7"/>
26807 <param name="eps_abs" value="9.999999747378752e-06"/>
26808 <param name="eps_rel" value="9.999999747378752e-06"/>
26809 <param name="max_iteration" value="10"/>
26810 <section name="penalties">
26811 <param name="position" value="0.0"/>
26812 <param name="height" value="1.0"/>
26813 <param name="left_width" value="0.0"/>
26814 <param name="right_width" value="0.0"/>
26815 </section>
26816 </section>
26817 </section>
26818 <section name="SignalToNoiseEstimationParameter">
26819 <param name="max_intensity" value="-1"/>
26820 <param name="auto_max_stdev_factor" value="3.0"/>
26821 <param name="auto_max_percentile" value="95"/>
26822 <param name="auto_mode" value="0"/>
26823 <param name="win_len" value="200.0"/>
26824 <param name="bin_count" value="30"/>
26825 <param name="stdev_mp" value="3.0"/>
26826 <param name="min_required_elements" value="10"/>
26827 <param name="noise_for_empty_window" value="1e+20"/>
26828 </section>
26829 </section>
26830 </section>
26831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26832 <output name="ctd_out" ftype="xml">
26833 <assert_contents>
26834 <is_valid_xml/>
26835 </assert_contents>
26836 </output>
26837 </test>
26838 <test expect_num_outputs="2">
26839 <conditional name="adv_opts_cond">
26840 <param name="adv_opts_selector" value="advanced"/>
26841 <param name="force" value="false"/>
26842 <param name="test" value="true"/>
26843 </conditional>
26844 <param name="in" value="TOFCalibration_2_input.mzML"/>
26845 <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
26846 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
26847 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
26848 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
26849 <param name="peak_data" value="true"/>
26850 <section name="algorithm">
26851 <section name="PeakPicker">
26852 <param name="signal_to_noise" value="3.0"/>
26853 <param name="centroid_percentage" value="0.6"/>
26854 <param name="peak_width" value="0.15"/>
26855 <param name="estimate_peak_width" value="false"/>
26856 <param name="fwhm_lower_bound_factor" value="0.7"/>
26857 <param name="fwhm_upper_bound_factor" value="20.0"/>
26858 <section name="optimization">
26859 <param name="iterations" value="400"/>
26860 <section name="penalties">
26861 <param name="position" value="0.0"/>
26862 <param name="left_width" value="1.0"/>
26863 <param name="right_width" value="1.0"/>
26864 <param name="height" value="1.0"/>
26865 </section>
26866 <section name="2d">
26867 <param name="tolerance_mz" value="2.2"/>
26868 <param name="max_peak_distance" value="1.2"/>
26869 </section>
26870 </section>
26871 <section name="thresholds">
26872 <param name="peak_bound" value="400.0"/>
26873 <param name="peak_bound_ms2_level" value="10.0"/>
26874 <param name="correlation" value="0.0"/>
26875 <param name="noise_level" value="0.1"/>
26876 <param name="search_radius" value="3"/>
26877 </section>
26878 <section name="wavelet_transform">
26879 <param name="spacing" value="0.001"/>
26880 </section>
26881 <section name="deconvolution">
26882 <param name="deconvolution" value="false"/>
26883 <param name="asym_threshold" value="0.3"/>
26884 <param name="left_width" value="2.0"/>
26885 <param name="right_width" value="2.0"/>
26886 <param name="scaling" value="0.12"/>
26887 <section name="fitting">
26888 <param name="fwhm_threshold" value="0.7"/>
26889 <param name="eps_abs" value="9.999999747378752e-06"/>
26890 <param name="eps_rel" value="9.999999747378752e-06"/>
26891 <param name="max_iteration" value="10"/>
26892 <section name="penalties">
26893 <param name="position" value="0.0"/>
26894 <param name="height" value="1.0"/>
26895 <param name="left_width" value="0.0"/>
26896 <param name="right_width" value="0.0"/>
26897 </section>
26898 </section>
26899 </section>
26900 <section name="SignalToNoiseEstimationParameter">
26901 <param name="max_intensity" value="-1"/>
26902 <param name="auto_max_stdev_factor" value="3.0"/>
26903 <param name="auto_max_percentile" value="95"/>
26904 <param name="auto_mode" value="0"/>
26905 <param name="win_len" value="200.0"/>
26906 <param name="bin_count" value="30"/>
26907 <param name="stdev_mp" value="3.0"/>
26908 <param name="min_required_elements" value="10"/>
26909 <param name="noise_for_empty_window" value="1e+20"/>
26910 </section>
26911 </section>
26912 </section>
26913 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26914 <output name="ctd_out" ftype="xml">
26915 <assert_contents>
26916 <is_valid_xml/>
26917 </assert_contents>
26918 </output>
26919 </test>
26920 </xml>
26921 <xml name="autotest_TransformationEvaluation">
26922 </xml>
26923 <xml name="autotest_XFDR">
26924 <test expect_num_outputs="4">
26925 <conditional name="adv_opts_cond">
26926 <param name="adv_opts_selector" value="advanced"/>
26927 <param name="force" value="false"/>
26928 <param name="test" value="true"/>
26929 </conditional>
26930 <param name="in" value="XFDR_test_in1.idXML"/>
26931 <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26932 <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26933 <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26934 <param name="decoy_string" value="DECOY_"/>
26935 <param name="minborder" value="-50.0"/>
26936 <param name="maxborder" value="50.0"/>
26937 <param name="mindeltas" value="0.0"/>
26938 <param name="minionsmatched" value="0"/>
26939 <param name="uniquexl" value="false"/>
26940 <param name="no_qvalues" value="false"/>
26941 <param name="minscore" value="-10.0"/>
26942 <param name="binsize" value="0.1"/>
26943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26944 <output name="ctd_out" ftype="xml">
26945 <assert_contents>
26946 <is_valid_xml/>
26947 </assert_contents>
26948 </output>
26949 </test>
26950 <test expect_num_outputs="4">
26951 <conditional name="adv_opts_cond">
26952 <param name="adv_opts_selector" value="advanced"/>
26953 <param name="force" value="false"/>
26954 <param name="test" value="true"/>
26955 </conditional>
26956 <param name="in" value="XFDR_test_in1.idXML"/>
26957 <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26958 <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26959 <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26960 <param name="decoy_string" value="DECOY_"/>
26961 <param name="minborder" value="-50.0"/>
26962 <param name="maxborder" value="50.0"/>
26963 <param name="mindeltas" value="0.0"/>
26964 <param name="minionsmatched" value="0"/>
26965 <param name="uniquexl" value="true"/>
26966 <param name="no_qvalues" value="true"/>
26967 <param name="minscore" value="-10.0"/>
26968 <param name="binsize" value="0.1"/>
26969 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26970 <output name="ctd_out" ftype="xml">
26971 <assert_contents>
26972 <is_valid_xml/>
26973 </assert_contents>
26974 </output>
26975 </test>
26976 <test expect_num_outputs="4">
26977 <conditional name="adv_opts_cond">
26978 <param name="adv_opts_selector" value="advanced"/>
26979 <param name="force" value="false"/>
26980 <param name="test" value="true"/>
26981 </conditional>
26982 <param name="in" value="XFDR_test_in2.xquest.xml"/>
26983 <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26984 <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26985 <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26986 <param name="decoy_string" value="DECOY_"/>
26987 <param name="minborder" value="-50.0"/>
26988 <param name="maxborder" value="50.0"/>
26989 <param name="mindeltas" value="0.0"/>
26990 <param name="minionsmatched" value="0"/>
26991 <param name="uniquexl" value="false"/>
26992 <param name="no_qvalues" value="false"/>
26993 <param name="minscore" value="0.0"/>
26994 <param name="binsize" value="0.1"/>
26995 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26996 <output name="ctd_out" ftype="xml">
26997 <assert_contents>
26998 <is_valid_xml/>
26999 </assert_contents>
27000 </output>
27001 </test>
27002 <test expect_num_outputs="4">
27003 <conditional name="adv_opts_cond">
27004 <param name="adv_opts_selector" value="advanced"/>
27005 <param name="force" value="false"/>
27006 <param name="test" value="true"/>
27007 </conditional>
27008 <param name="in" value="XFDR_test_in2.xquest.xml"/>
27009 <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27010 <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
27011 <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
27012 <param name="decoy_string" value="DECOY_"/>
27013 <param name="minborder" value="-3.0"/>
27014 <param name="maxborder" value="3.0"/>
27015 <param name="mindeltas" value="0.0"/>
27016 <param name="minionsmatched" value="0"/>
27017 <param name="uniquexl" value="false"/>
27018 <param name="no_qvalues" value="false"/>
27019 <param name="minscore" value="-10.0"/>
27020 <param name="binsize" value="0.1"/>
27021 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
27022 <output name="ctd_out" ftype="xml">
27023 <assert_contents>
27024 <is_valid_xml/>
27025 </assert_contents>
27026 </output>
27027 </test>
27028 <test expect_num_outputs="4">
27029 <conditional name="adv_opts_cond">
27030 <param name="adv_opts_selector" value="advanced"/>
27031 <param name="force" value="false"/>
27032 <param name="test" value="true"/>
27033 </conditional>
27034 <param name="in" value="XFDR_test_in3.xquest.xml"/>
27035 <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27036 <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
27037 <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
27038 <param name="decoy_string" value="DECOY_"/>
27039 <param name="minborder" value="-3.0"/>
27040 <param name="maxborder" value="3.0"/>
27041 <param name="mindeltas" value="0.0"/>
27042 <param name="minionsmatched" value="0"/>
27043 <param name="uniquexl" value="false"/>
27044 <param name="no_qvalues" value="false"/>
27045 <param name="minscore" value="-10.0"/>
27046 <param name="binsize" value="0.1"/>
27047 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
27048 <output name="ctd_out" ftype="xml">
27049 <assert_contents>
27050 <is_valid_xml/>
27051 </assert_contents>
27052 </output>
27053 </test>
27054 <test expect_num_outputs="2">
27055 <conditional name="adv_opts_cond">
27056 <param name="adv_opts_selector" value="advanced"/>
27057 <param name="force" value="false"/>
27058 <param name="test" value="true"/>
27059 </conditional>
27060 <param name="in" value="XFDR_test_in4.idXML"/>
27061 <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27062 <param name="decoy_string" value="DECOY_"/>
27063 <param name="minborder" value="-50.0"/>
27064 <param name="maxborder" value="50.0"/>
27065 <param name="mindeltas" value="0.0"/>
27066 <param name="minionsmatched" value="0"/>
27067 <param name="uniquexl" value="false"/>
27068 <param name="no_qvalues" value="false"/>
27069 <param name="minscore" value="-10.0"/>
27070 <param name="binsize" value="0.1"/>
27071 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
27072 <output name="ctd_out" ftype="xml">
27073 <assert_contents>
27074 <is_valid_xml/>
27075 </assert_contents>
27076 </output>
27077 </test>
27078 <test expect_num_outputs="4">
27079 <conditional name="adv_opts_cond">
27080 <param name="adv_opts_selector" value="advanced"/>
27081 <param name="force" value="false"/>
27082 <param name="test" value="true"/>
27083 </conditional>
27084 <param name="in" value="XFDR_test_in2.xquest.xml"/>
27085 <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27086 <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
27087 <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
27088 <param name="decoy_string" value="DECOY_"/>
27089 <param name="minborder" value="-50.0"/>
27090 <param name="maxborder" value="50.0"/>
27091 <param name="mindeltas" value="0.0"/>
27092 <param name="minionsmatched" value="0"/>
27093 <param name="uniquexl" value="true"/>
27094 <param name="no_qvalues" value="false"/>
27095 <param name="minscore" value="0.0"/>
27096 <param name="binsize" value="0.1"/>
27097 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
27098 <output name="ctd_out" ftype="xml">
27099 <assert_contents>
27100 <is_valid_xml/>
27101 </assert_contents>
27102 </output>
27103 </test>
27104 </xml>
27105 <xml name="autotest_XMLValidator">
27106 </xml>
27107 <xml name="autotest_XTandemAdapter">
27108 <test expect_num_outputs="2">
27109 <conditional name="adv_opts_cond">
27110 <param name="adv_opts_selector" value="advanced"/>
27111 <param name="force" value="false"/>
27112 <param name="test" value="true"/>
27113 </conditional>
27114 <param name="in" value="spectra.mzML"/>
27115 <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27116 <param name="database" value="proteins.fasta"/>
27117 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
27118 <param name="ignore_adapter_param" value="false"/>
27119 <param name="precursor_mass_tolerance" value="5.0"/>
27120 <param name="fragment_mass_tolerance" value="0.3"/>
27121 <param name="precursor_error_units" value="ppm"/>
27122 <param name="fragment_error_units" value="Da"/>
27123 <param name="max_precursor_charge" value="0"/>
27124 <param name="no_isotope_error" value="false"/>
27125 <param name="fixed_modifications" value=""/>
27126 <param name="variable_modifications" value="Oxidation (M)"/>
27127 <param name="minimum_fragment_mz" value="150.0"/>
27128 <param name="enzyme" value="Trypsin"/>
27129 <param name="missed_cleavages" value="1"/>
27130 <param name="semi_cleavage" value="false"/>
27131 <param name="output_results" value="all"/>
27132 <param name="max_valid_expect" value="0.1"/>
27133 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
27134 <output name="ctd_out" ftype="xml">
27135 <assert_contents>
27136 <is_valid_xml/>
27137 </assert_contents>
27138 </output>
27139 </test>
27140 <test expect_num_outputs="2">
27141 <conditional name="adv_opts_cond">
27142 <param name="adv_opts_selector" value="advanced"/>
27143 <param name="force" value="false"/>
27144 <param name="test" value="true"/>
27145 </conditional>
27146 <param name="in" value="spectra.mzML"/>
27147 <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27148 <param name="database" value="proteins.fasta"/>
27149 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
27150 <param name="ignore_adapter_param" value="false"/>
27151 <param name="precursor_mass_tolerance" value="5.0"/>
27152 <param name="fragment_mass_tolerance" value="0.3"/>
27153 <param name="precursor_error_units" value="ppm"/>
27154 <param name="fragment_error_units" value="Da"/>
27155 <param name="max_precursor_charge" value="0"/>
27156 <param name="no_isotope_error" value="false"/>
27157 <param name="fixed_modifications" value=""/>
27158 <param name="variable_modifications" value="Oxidation (M)"/>
27159 <param name="minimum_fragment_mz" value="150.0"/>
27160 <param name="enzyme" value="Trypsin"/>
27161 <param name="missed_cleavages" value="1"/>
27162 <param name="semi_cleavage" value="false"/>
27163 <param name="output_results" value="valid"/>
27164 <param name="max_valid_expect" value="1e-14"/>
27165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
27166 <output name="ctd_out" ftype="xml">
27167 <assert_contents>
27168 <is_valid_xml/>
27169 </assert_contents>
27170 </output>
27171 </test>
27172 <test expect_num_outputs="2">
27173 <conditional name="adv_opts_cond">
27174 <param name="adv_opts_selector" value="advanced"/>
27175 <param name="force" value="false"/>
27176 <param name="test" value="true"/>
27177 </conditional>
27178 <param name="in" value="spectra.mzML"/>
27179 <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27180 <param name="database" value="proteinslong.fasta"/>
27181 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
27182 <param name="ignore_adapter_param" value="false"/>
27183 <param name="precursor_mass_tolerance" value="5.0"/>
27184 <param name="fragment_mass_tolerance" value="0.3"/>
27185 <param name="precursor_error_units" value="ppm"/>
27186 <param name="fragment_error_units" value="Da"/>
27187 <param name="max_precursor_charge" value="0"/>
27188 <param name="no_isotope_error" value="false"/>
27189 <param name="fixed_modifications" value=""/>
27190 <param name="variable_modifications" value="Oxidation (M)"/>
27191 <param name="minimum_fragment_mz" value="150.0"/>
27192 <param name="enzyme" value="Trypsin"/>
27193 <param name="missed_cleavages" value="1"/>
27194 <param name="semi_cleavage" value="false"/>
27195 <param name="output_results" value="all"/>
27196 <param name="max_valid_expect" value="0.1"/>
27197 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
27198 <output name="ctd_out" ftype="xml">
27199 <assert_contents>
27200 <is_valid_xml/>
27201 </assert_contents>
27202 </output>
27203 </test>
27204 </xml>
27205 <xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>