Mercurial > repos > galaxyp > openms_openswathconfidencescoring

comparison macros_discarded_auto.xml @ 9:401b29d0f88c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:49:07 -0400
parents
children e8f64a7dc470
comparison
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8:3d24698daa6e 9:401b29d0f88c
1
2 <xml name="manutest_OpenSwathFileSplitter">
3 <test expect_num_outputs="2">
4 <conditional name="adv_opts_cond">
5 <param name="adv_opts_selector" value="advanced"/>
6 <param name="force" value="false"/>
7 <param name="test" value="true"/>
8 </conditional>
9 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
10 <output_collection name="adv_opts_cond.outputDirectory" count=""/>
11 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
12 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/>
13 <output name="ctd_out" ftype="xml">
14 <assert_contents>
15 <is_valid_xml/>
16 </assert_contents>
17 </output>
18 </test></xml>
19 <xml name="manutest_IDRipper">
20 <test expect_num_outputs="1">
21 <conditional name="adv_opts_cond">
22 <param name="adv_opts_selector" value="advanced"/>
23 <param name="force" value="false"/>
24 <param name="test" value="true"/>
25 </conditional>
26 <param name="in" value="IDRipper_1_input.idXML"/>
27 <output_collection name="out_path" count=""/>
28 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
29 <output name="ctd_out" ftype="xml">
30 <assert_contents>
31 <is_valid_xml/>
32 </assert_contents>
33 </output>
34 </test><test expect_num_outputs="1">
35 <conditional name="adv_opts_cond">
36 <param name="adv_opts_selector" value="advanced"/>
37 <param name="force" value="false"/>
38 <param name="test" value="true"/>
39 </conditional>
40 <param name="in" value="IDRipper_2_input.idXML"/>
41 <output_collection name="out_path" count=""/>
42 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
43 <output name="ctd_out" ftype="xml">
44 <assert_contents>
45 <is_valid_xml/>
46 </assert_contents>
47 </output>
48 </test><test expect_num_outputs="1">
49 <conditional name="adv_opts_cond">
50 <param name="adv_opts_selector" value="advanced"/>
51 <param name="force" value="false"/>
52 <param name="test" value="true"/>
53 </conditional>
54 <param name="in" value="IDRipper_3_output.idXML"/>
55 <output_collection name="out_path" count=""/>
56 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
57 <output name="ctd_out" ftype="xml">
58 <assert_contents>
59 <is_valid_xml/>
60 </assert_contents>
61 </output>
62 </test></xml>
63 <xml name="manutest_MzMLSplitter">
64 <test expect_num_outputs="1">
65 <conditional name="adv_opts_cond">
66 <param name="adv_opts_selector" value="advanced"/>
67 <param name="force" value="false"/>
68 <param name="test" value="true"/>
69 </conditional>
70 <param name="in" value="FileFilter_1_input.mzML"/>
71 <output_collection name="out" count=""/>
72 <param name="parts" value="2"/>
73 <param name="size" value="0"/>
74 <param name="unit" value="MB"/>
75 <param name="no_chrom" value="false"/>
76 <param name="no_spec" value="false"/>
77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
78 <output name="ctd_out" ftype="xml">
79 <assert_contents>
80 <is_valid_xml/>
81 </assert_contents>
82 </output>
83 </test><test expect_num_outputs="1">
84 <conditional name="adv_opts_cond">
85 <param name="adv_opts_selector" value="advanced"/>
86 <param name="force" value="false"/>
87 <param name="test" value="true"/>
88 </conditional>
89 <param name="in" value="FileFilter_1_input.mzML"/>
90 <output_collection name="out" count=""/>
91 <param name="parts" value="1"/>
92 <param name="size" value="40"/>
93 <param name="unit" value="KB"/>
94 <param name="no_chrom" value="false"/>
95 <param name="no_spec" value="false"/>
96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
97 <output name="ctd_out" ftype="xml">
98 <assert_contents>
99 <is_valid_xml/>
100 </assert_contents>
101 </output>
102 </test></xml>
103 <xml name="manutest_MSFraggerAdapter">
104 <test expect_num_outputs="3">
105 <conditional name="adv_opts_cond">
106 <param name="adv_opts_selector" value="advanced"/>
107 <param name="force" value="false"/>
108 <param name="test" value="true"/>
109 </conditional>
110 <param name="java_heapmemory" value="2600"/>
111 <param name="in" value="spectra.mzML"/>
112 <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
113 <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
114 <param name="database" value="proteins.fasta"/>
115 <section name="tolerance">
116 <param name="precursor_mass_tolerance" value="20.0"/>
117 <param name="precursor_mass_unit" value="ppm"/>
118 <param name="precursor_true_tolerance" value="0.0"/>
119 <param name="precursor_true_unit" value="ppm"/>
120 <param name="fragment_mass_tolerance" value="20.0"/>
121 <param name="fragment_mass_unit" value="ppm"/>
122 <param name="isotope_error" value="0"/>
123 </section>
124 <section name="digest">
125 <param name="search_enzyme_name" value="Trypsin"/>
126 <param name="search_enzyme_cutafter" value="KR"/>
127 <param name="search_enzyme_nocutbefore" value="P"/>
128 <param name="num_enzyme_termini" value="semi"/>
129 <param name="allowed_missed_cleavage" value="2"/>
130 <param name="min_length" value="7"/>
131 <param name="max_length" value="64"/>
132 <param name="mass_range_min" value="500.0"/>
133 <param name="mass_range_max" value="5000.0"/>
134 </section>
135 <section name="varmod">
136 <param name="clip_nterm_m" value="false"/>
137 <param name="masses" value=""/>
138 <param name="syntaxes" value=""/>
139 <param name="enable_common" value="true"/>
140 <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
141 <param name="max_variable_mods_per_mod" value="2"/>
142 <param name="max_variable_mods_combinations" value="5000"/>
143 </section>
144 <section name="spectrum">
145 <param name="minimum_peaks" value="10"/>
146 <param name="use_topn_peaks" value="50"/>
147 <param name="minimum_ratio" value="0.0"/>
148 <param name="clear_mz_range_min" value="0.0"/>
149 <param name="clear_mz_range_max" value="0.0"/>
150 <param name="max_fragment_charge" value="2"/>
151 <param name="override_charge" value="false"/>
152 <param name="precursor_charge_min" value="1"/>
153 <param name="precursor_charge_max" value="4"/>
154 </section>
155 <section name="search">
156 <param name="track_zero_topn" value="0"/>
157 <param name="zero_bin_accept_expect" value="0.0"/>
158 <param name="zero_bin_mult_expect" value="1.0"/>
159 <param name="add_topn_complementary" value="0"/>
160 <param name="min_fragments_modeling" value="3"/>
161 <param name="min_matched_fragments" value="4"/>
162 <param name="output_report_topn" value="1"/>
163 <param name="output_max_expect" value="50.0"/>
164 </section>
165 <section name="statmod">
166 <param name="add_cterm_peptide" value="0.0"/>
167 <param name="add_nterm_peptide" value="0.0"/>
168 <param name="add_cterm_protein" value="0.0"/>
169 <param name="add_nterm_protein" value="0.0"/>
170 <param name="add_G_glycine" value="0.0"/>
171 <param name="add_A_alanine" value="0.0"/>
172 <param name="add_S_serine" value="0.0"/>
173 <param name="add_P_proline" value="0.0"/>
174 <param name="add_V_valine" value="0.0"/>
175 <param name="add_T_threonine" value="0.0"/>
176 <param name="add_C_cysteine" value="57.021464"/>
177 <param name="add_L_leucine" value="0.0"/>
178 <param name="add_I_isoleucine" value="0.0"/>
179 <param name="add_N_asparagine" value="0.0"/>
180 <param name="add_D_aspartic_acid" value="0.0"/>
181 <param name="add_Q_glutamine" value="0.0"/>
182 <param name="add_K_lysine" value="0.0"/>
183 <param name="add_E_glutamic_acid" value="0.0"/>
184 <param name="add_M_methionine" value="0.0"/>
185 <param name="add_H_histidine" value="0.0"/>
186 <param name="add_F_phenylalanine" value="0.0"/>
187 <param name="add_R_arginine" value="0.0"/>
188 <param name="add_Y_tyrosine" value="0.0"/>
189 <param name="add_W_tryptophan" value="0.0"/>
190 </section>
191 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/>
192 <output name="ctd_out" ftype="xml">
193 <assert_contents>
194 <is_valid_xml/>
195 </assert_contents>
196 </output>
197 </test><test expect_num_outputs="2">
198 <conditional name="adv_opts_cond">
199 <param name="adv_opts_selector" value="advanced"/>
200 <param name="force" value="false"/>
201 <param name="test" value="true"/>
202 </conditional>
203 <param name="java_heapmemory" value="2600"/>
204 <param name="in" value="spectra_comet.mzML"/>
205 <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
206 <param name="database" value="proteins.fasta"/>
207 <section name="tolerance">
208 <param name="precursor_mass_tolerance" value="20.0"/>
209 <param name="precursor_mass_unit" value="ppm"/>
210 <param name="precursor_true_tolerance" value="0.0"/>
211 <param name="precursor_true_unit" value="ppm"/>
212 <param name="fragment_mass_tolerance" value="20.0"/>
213 <param name="fragment_mass_unit" value="ppm"/>
214 <param name="isotope_error" value="0"/>
215 </section>
216 <section name="digest">
217 <param name="search_enzyme_name" value="Trypsin"/>
218 <param name="search_enzyme_cutafter" value="KR"/>
219 <param name="search_enzyme_nocutbefore" value="P"/>
220 <param name="num_enzyme_termini" value="semi"/>
221 <param name="allowed_missed_cleavage" value="2"/>
222 <param name="min_length" value="7"/>
223 <param name="max_length" value="64"/>
224 <param name="mass_range_min" value="500.0"/>
225 <param name="mass_range_max" value="5000.0"/>
226 </section>
227 <section name="varmod">
228 <param name="clip_nterm_m" value="false"/>
229 <param name="masses" value=""/>
230 <param name="syntaxes" value=""/>
231 <param name="enable_common" value="true"/>
232 <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
233 <param name="max_variable_mods_per_mod" value="2"/>
234 <param name="max_variable_mods_combinations" value="5000"/>
235 </section>
236 <section name="spectrum">
237 <param name="minimum_peaks" value="10"/>
238 <param name="use_topn_peaks" value="50"/>
239 <param name="minimum_ratio" value="0.0"/>
240 <param name="clear_mz_range_min" value="0.0"/>
241 <param name="clear_mz_range_max" value="0.0"/>
242 <param name="max_fragment_charge" value="2"/>
243 <param name="override_charge" value="false"/>
244 <param name="precursor_charge_min" value="1"/>
245 <param name="precursor_charge_max" value="4"/>
246 </section>
247 <section name="search">
248 <param name="track_zero_topn" value="0"/>
249 <param name="zero_bin_accept_expect" value="0.0"/>
250 <param name="zero_bin_mult_expect" value="1.0"/>
251 <param name="add_topn_complementary" value="0"/>
252 <param name="min_fragments_modeling" value="3"/>
253 <param name="min_matched_fragments" value="4"/>
254 <param name="output_report_topn" value="1"/>
255 <param name="output_max_expect" value="50.0"/>
256 </section>
257 <section name="statmod">
258 <param name="add_cterm_peptide" value="0.0"/>
259 <param name="add_nterm_peptide" value="0.0"/>
260 <param name="add_cterm_protein" value="0.0"/>
261 <param name="add_nterm_protein" value="0.0"/>
262 <param name="add_G_glycine" value="0.0"/>
263 <param name="add_A_alanine" value="0.0"/>
264 <param name="add_S_serine" value="0.0"/>
265 <param name="add_P_proline" value="0.0"/>
266 <param name="add_V_valine" value="0.0"/>
267 <param name="add_T_threonine" value="0.0"/>
268 <param name="add_C_cysteine" value="57.021464"/>
269 <param name="add_L_leucine" value="0.0"/>
270 <param name="add_I_isoleucine" value="0.0"/>
271 <param name="add_N_asparagine" value="0.0"/>
272 <param name="add_D_aspartic_acid" value="0.0"/>
273 <param name="add_Q_glutamine" value="0.0"/>
274 <param name="add_K_lysine" value="0.0"/>
275 <param name="add_E_glutamic_acid" value="0.0"/>
276 <param name="add_M_methionine" value="0.0"/>
277 <param name="add_H_histidine" value="0.0"/>
278 <param name="add_F_phenylalanine" value="0.0"/>
279 <param name="add_R_arginine" value="0.0"/>
280 <param name="add_Y_tyrosine" value="0.0"/>
281 <param name="add_W_tryptophan" value="0.0"/>
282 </section>
283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
284 <output name="ctd_out" ftype="xml">
285 <assert_contents>
286 <is_valid_xml/>
287 </assert_contents>
288 </output>
289 </test></xml>
290 <xml name="manutest_MaRaClusterAdapter">
291 <test expect_num_outputs="2">
292 <conditional name="adv_opts_cond">
293 <param name="adv_opts_selector" value="advanced"/>
294 <param name="verbose" value="2"/>
295 <param name="precursor_tolerance" value="20.0"/>
296 <param name="precursor_tolerance_units" value="ppm"/>
297 <param name="force" value="false"/>
298 <param name="test" value="true"/>
299 </conditional>
300 <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/>
301 <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/>
302 <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
303 <param name="pcut" value="-10.0"/>
304 <param name="min_cluster_size" value="1"/>
305 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
306 <output name="ctd_out" ftype="xml">
307 <assert_contents>
308 <is_valid_xml/>
309 </assert_contents>
310 </output>
311 </test></xml>
312 <xml name="manutest_NovorAdapter">
313 <test expect_num_outputs="2">
314 <conditional name="adv_opts_cond">
315 <param name="adv_opts_selector" value="advanced"/>
316 <param name="force" value="false"/>
317 <param name="test" value="true"/>
318 </conditional>
319 <param name="in" value="NovorAdapter_in.mzML"/>
320 <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
321 <param name="enzyme" value="Trypsin"/>
322 <param name="fragmentation" value="CID"/>
323 <param name="massAnalyzer" value="Trap"/>
324 <param name="fragment_mass_tolerance" value="0.5"/>
325 <param name="precursor_mass_tolerance" value="15.0"/>
326 <param name="precursor_error_units" value="ppm"/>
327 <param name="variable_modifications" value="Acetyl (K)"/>
328 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
329 <param name="forbiddenResidues" value="I"/>
330 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
331 <output name="ctd_out" ftype="xml">
332 <assert_contents>
333 <is_valid_xml/>
334 </assert_contents>
335 </output>
336 </test></xml>
337 <xml name="manutest_SpectraSTSearchAdapter">
338 <test expect_num_outputs="2">
339 <conditional name="adv_opts_cond">
340 <param name="adv_opts_selector" value="advanced"/>
341 <param name="use_isotopically_averaged_mass" value="false"/>
342 <param name="use_all_charge_states" value="false"/>
343 <param name="force" value="false"/>
344 <param name="test" value="true"/>
345 </conditional>
346 <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
347 <param name="output_files_type" value="pep.xml"/>
348 <output_collection name="output_files" count="1"/>
349 <param name="library_file" value="testLib.splib" ftype="splib"/>
350 <param name="sequence_database_type" value="AA"/>
351 <param name="precursor_mz_tolerance" value="3.0"/>
352 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
353 <output name="ctd_out" ftype="xml">
354 <assert_contents>
355 <is_valid_xml/>
356 </assert_contents>
357 </output>
358 </test><test expect_num_outputs="2">
359 <conditional name="adv_opts_cond">
360 <param name="adv_opts_selector" value="advanced"/>
361 <param name="use_isotopically_averaged_mass" value="false"/>
362 <param name="use_all_charge_states" value="false"/>
363 <param name="force" value="false"/>
364 <param name="test" value="true"/>
365 </conditional>
366 <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
367 <param name="output_files_type" value="tsv"/>
368 <output_collection name="output_files" count="1"/>
369 <param name="library_file" value="testLib.splib" ftype="splib"/>
370 <param name="sequence_database_type" value="AA"/>
371 <param name="precursor_mz_tolerance" value="3.0"/>
372 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
373 <output name="ctd_out" ftype="xml">
374 <assert_contents>
375 <is_valid_xml/>
376 </assert_contents>
377 </output>
378 </test></xml>