Mercurial > repos > galaxyp > openms_rnadigestor
comparison macros_test.xml @ 0:3e7d3f64392b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 03 Sep 2020 16:14:58 +0000 |
parents | |
children | f7bc536b3bf3 |
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-1:000000000000 | 0:3e7d3f64392b |
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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <macros> | |
3 | |
4 <!-- a copy of a FileConverter test without the advanced options used | |
5 in order to check if this works (all other tests enable advanced) --> | |
6 <xml name="manutest_FileConverter"> | |
7 <test expect_num_outputs="1"> | |
8 <param name="in" value="FileConverter_1_input.mzData"/> | |
9 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> | |
10 <param name="out_type" value="mzML"/> | |
11 </test> | |
12 </xml> | |
13 <!-- tests contributed by the galaxyproteomics community --> | |
14 <xml name="manutest_ClusterMassTracesByPrecursor"> | |
15 <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> | |
16 <param name="adv_opts_selector" value="advanced"/> | |
17 <param name="adv_opts_cond|test" value="true"/> | |
18 <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> | |
19 <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> | |
20 <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/> | |
21 </test> | |
22 </xml> | |
23 <xml name="manutest_ClusterMassTraces"> | |
24 <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> | |
25 <param name="adv_opts_selector" value="advanced"/> | |
26 <param name="adv_opts_cond|test" value="true"/> | |
27 <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> | |
28 <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/> | |
29 </test> | |
30 </xml> | |
31 <xml name="manutest_CVInspector"> | |
32 <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 --> | |
33 <test expect_num_outputs="1"> | |
34 <param name="adv_opts_selector" value="advanced"/> | |
35 <param name="adv_opts_cond|test" value="true"/> | |
36 <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> | |
37 <param name="cv_names" value="XLMOD"/> | |
38 <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> | |
39 <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> | |
40 <output name="html" ftype="html" value="CVInspector.html"/> | |
41 </test> | |
42 </xml> | |
43 <xml name="manutest_DeMeanderize"> | |
44 <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below --> | |
45 <param name="adv_opts_selector" value="advanced"/> | |
46 <param name="adv_opts_cond|test" value="true"/> | |
47 <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/> | |
48 <output name="out" ftype="mzml" value="DeMeanderize.mzml"/> | |
49 </test> | |
50 </xml> | |
51 <xml name="manutest_Digestor"> | |
52 <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option --> | |
53 <param name="adv_opts_selector" value="advanced"/> | |
54 <param name="adv_opts_cond|test" value="true"/> | |
55 <param name="in" ftype="fasta" value="random.fa"/> | |
56 <output name="out" ftype="fasta" value="Digestor.fasta"/> | |
57 <param name="out_type" value="fasta"/> | |
58 </test> | |
59 </xml> | |
60 <xml name="manutest_EICExtractor"> | |
61 <test expect_num_outputs="1"><!-- just using some random test data --> | |
62 <param name="adv_opts_selector" value="advanced"/> | |
63 <param name="adv_opts_cond|test" value="true"/> | |
64 <param name="in" value="spectra.mzML"/> | |
65 <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/> | |
66 <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/> | |
67 </test> | |
68 </xml> | |
69 <xml name="manutest_ERPairFinder"> | |
70 <!-- TODO --> | |
71 </xml> | |
72 <xml name="manutest_FeatureFinderIsotopeWavelet"> | |
73 <test expect_num_outputs="1"><!--just use the input of another FeatureFinder --> | |
74 <param name="adv_opts_selector" value="advanced"/> | |
75 <param name="adv_opts_cond|test" value="true"/> | |
76 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> | |
77 <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/> | |
78 </test> | |
79 </xml> | |
80 <xml name="manutest_FFEval"> | |
81 <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself --> | |
82 <param name="adv_opts_selector" value="advanced"/> | |
83 <param name="adv_opts_cond|test" value="true"/> | |
84 <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/> | |
85 <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/> | |
86 <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/> | |
87 <output name="out" value="FFEval.featureXML" compare="sim_size"/> | |
88 <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/> | |
89 </test> | |
90 </xml> | |
91 <xml name="manutest_IDExtractor"> | |
92 <test expect_num_outputs="1"><!-- --> | |
93 <param name="adv_opts_selector" value="advanced"/> | |
94 <param name="adv_opts_cond|test" value="true"/> | |
95 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> | |
96 <param name="best_hits" value="true"/> | |
97 <param name="number_of_peptides" value="1"/> | |
98 <output name="out" value="IDExtractor.idXML" compare="sim_size"/> | |
99 </test> | |
100 </xml> | |
101 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> | |
102 <xml name="manutest_IDRipper"> | |
103 <test expect_num_outputs="2"> | |
104 <conditional name="adv_opts_cond"> | |
105 <param name="adv_opts_selector" value="advanced"/> | |
106 <param name="force" value="false"/> | |
107 <param name="test" value="true"/> | |
108 </conditional> | |
109 <param name="in" value="IDRipper_1_input.idXML"/> | |
110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
111 <output_collection name="out_path" count="2"> | |
112 <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/> | |
113 <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/> | |
114 </output_collection> | |
115 <output name="ctd_out" ftype="xml"> | |
116 <assert_contents> | |
117 <is_valid_xml/> | |
118 </assert_contents> | |
119 </output> | |
120 </test> | |
121 <test expect_num_outputs="2"> | |
122 <conditional name="adv_opts_cond"> | |
123 <param name="adv_opts_selector" value="advanced"/> | |
124 <param name="force" value="false"/> | |
125 <param name="test" value="true"/> | |
126 </conditional> | |
127 <param name="in" value="IDRipper_2_input.idXML"/> | |
128 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
129 <output_collection name="out_path" count="2"> | |
130 <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/> | |
131 <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/> | |
132 </output_collection> | |
133 <output name="ctd_out" ftype="xml"> | |
134 <assert_contents> | |
135 <is_valid_xml/> | |
136 </assert_contents> | |
137 </output> | |
138 </test> | |
139 <test expect_num_outputs="2"> | |
140 <conditional name="adv_opts_cond"> | |
141 <param name="adv_opts_selector" value="advanced"/> | |
142 <param name="force" value="false"/> | |
143 <param name="test" value="true"/> | |
144 </conditional> | |
145 <param name="in" value="IDRipper_3_output.idXML"/> | |
146 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
147 <output_collection name="out_path" count="2"> | |
148 <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/> | |
149 <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/> | |
150 </output_collection> | |
151 <output name="ctd_out" ftype="xml"> | |
152 <assert_contents> | |
153 <is_valid_xml/> | |
154 </assert_contents> | |
155 </output> | |
156 </test> | |
157 </xml> | |
158 <xml name="manutest_LabeledEval"> | |
159 <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML --> | |
160 <param name="adv_opts_selector" value="advanced"/> | |
161 <param name="adv_opts_cond|test" value="true"/> | |
162 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> | |
163 <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/> | |
164 <output name="stdout" value="LabeledEval.txt" compare="sim_size"/> | |
165 </test> | |
166 </xml> | |
167 <xml name="manutest_MapStatistics"> | |
168 <test expect_num_outputs="1"><!-- test with a featureXML input --> | |
169 <param name="adv_opts_selector" value="advanced"/> | |
170 <param name="adv_opts_cond|test" value="true"/> | |
171 <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/> | |
172 <output name="out" ftype="txt" value="MapStatistics.txt"/> | |
173 </test> | |
174 <test expect_num_outputs="1"><!-- test with a consensusxml input --> | |
175 <param name="adv_opts_cond|test" value="true"/> | |
176 <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/> | |
177 <output name="out" ftype="txt" value="MapStatistics2.txt"/> | |
178 </test> | |
179 </xml> | |
180 <xml name="manutest_MetaboliteAdductDecharger"> | |
181 <test expect_num_outputs="3"><!-- same input as used by Decharger --> | |
182 <param name="adv_opts_selector" value="advanced"/> | |
183 <param name="adv_opts_cond|test" value="true"/> | |
184 <param name="in" ftype="featurexml" value="Decharger_input.featureXML"/> | |
185 <output name="out_cm" ftype="consensusxml" value="MetaboliteAdductDecharger_cm.consensusXML" compare="sim_size"/> | |
186 <param name="OPTIONAL_OUTPUTS" value="out_fm_FLAG,outpairs_FLAG"/> | |
187 <output name="out_fm" ftype="featurexml" value="MetaboliteAdductDecharger_fm.featureXML" compare="sim_size"/> | |
188 <output name="outpairs" ftype="consensusxml" value="MetaboliteAdductDecharger_pairs.consensusXML" compare="sim_size"/> | |
189 </test> | |
190 </xml> | |
191 <xml name="manutest_MetaboliteSpectralMatcher"> | |
192 <!-- https://github.com/OpenMS/OpenMS/issues/2078 | |
193 https://github.com/OpenMS/OpenMS/pull/4468--> | |
194 <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML --> | |
195 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database --> | |
196 <param name="adv_opts_selector" value="advanced"/> | |
197 <param name="adv_opts_cond|test" value="true"/> | |
198 <param name="in" ftype="mzml" value="spectra.mzML"/> | |
199 <param name="database" value="MetaboliteSpectralDB.mzML"/> | |
200 <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/> | |
201 </test> | |
202 </xml> | |
203 <xml name="manutest_MRMPairFinder"> | |
204 <!-- TODO no idea about a useful input for pair_in --> | |
205 </xml> | |
206 <xml name="manutest_MSSimulator"> | |
207 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> | |
208 <param name="adv_opts_selector" value="advanced"/> | |
209 <param name="adv_opts_cond|test" value="true"/> | |
210 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> | |
211 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> | |
212 <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> | |
213 <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> | |
214 <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> | |
215 </test> | |
216 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize --> | |
217 <param name="adv_opts_selector" value="advanced"/> | |
218 <param name="adv_opts_cond|test" value="true"/> | |
219 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> | |
220 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> | |
221 <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> | |
222 <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> | |
223 <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> | |
224 <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/> | |
225 </test> | |
226 </xml> | |
227 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> | |
228 <xml name="manutest_MzMLSplitter"> | |
229 <test expect_num_outputs="2"> | |
230 <conditional name="adv_opts_cond"> | |
231 <param name="adv_opts_selector" value="advanced"/> | |
232 <param name="force" value="false"/> | |
233 <param name="test" value="true"/> | |
234 </conditional> | |
235 <param name="in" value="FileFilter_1_input.mzML"/> | |
236 <param name="parts" value="2"/> | |
237 <param name="size" value="0"/> | |
238 <param name="unit" value="MB"/> | |
239 <param name="no_chrom" value="false"/> | |
240 <param name="no_spec" value="false"/> | |
241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
242 <output name="ctd_out" ftype="xml"> | |
243 <assert_contents> | |
244 <is_valid_xml/> | |
245 </assert_contents> | |
246 </output> | |
247 <output_collection name="out" type="list" count="2"> | |
248 <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/> | |
249 <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/> | |
250 </output_collection> | |
251 </test> | |
252 <test expect_num_outputs="2"> | |
253 <conditional name="adv_opts_cond"> | |
254 <param name="adv_opts_selector" value="advanced"/> | |
255 <param name="force" value="false"/> | |
256 <param name="test" value="true"/> | |
257 </conditional> | |
258 <param name="in" value="FileFilter_1_input.mzML"/> | |
259 <param name="parts" value="1"/> | |
260 <param name="size" value="40"/> | |
261 <param name="unit" value="KB"/> | |
262 <param name="no_chrom" value="false"/> | |
263 <param name="no_spec" value="false"/> | |
264 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
265 <output name="ctd_out" ftype="xml"> | |
266 <assert_contents> | |
267 <is_valid_xml/> | |
268 </assert_contents> | |
269 </output> | |
270 <output_collection name="out" type="list" count="2"> | |
271 <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/> | |
272 <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/> | |
273 </output_collection> | |
274 </test> | |
275 </xml> | |
276 <xml name="manutest_OpenSwathDIAPreScoring"> | |
277 <!-- TODO data from a test that included all the needed test files | |
278 currently unusable https://github.com/OpenMS/OpenMS/pull/4443 --> | |
279 <!-- data from a test that included all the needed test files --> | |
280 <!-- <test>--> | |
281 <!-- <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>--> | |
282 <!-- <param name="swath_files" value="OpenSwathWorkflow_10.chrom.mzML.tmp"/> or OpenSwathAnalyzer_2_swathfile.mzML--> | |
283 <!-- <output name="out" ftype="tabular" value="OpenSwathDIAPreScoring_2.tmp"/>--> | |
284 <!-- </test>--> | |
285 </xml> | |
286 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> | |
287 <xml name="manutest_OpenSwathFileSplitter"> | |
288 <test expect_num_outputs="3"> | |
289 <conditional name="adv_opts_cond"> | |
290 <param name="adv_opts_selector" value="advanced"/> | |
291 <param name="force" value="false"/> | |
292 <param name="test" value="true"/> | |
293 </conditional> | |
294 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
295 <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/> | |
296 <output_collection name="adv_opts_cond.outputDirectory" count="6"> | |
297 <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/> | |
298 <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/> | |
299 </output_collection> | |
300 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> | |
301 <output name="ctd_out" ftype="xml"> | |
302 <assert_contents> | |
303 <is_valid_xml/> | |
304 </assert_contents> | |
305 </output> | |
306 </test> | |
307 </xml> | |
308 <xml name="manutest_OpenSwathRewriteToFeatureXML"> | |
309 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> | |
310 <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> | |
311 <param name="adv_opts_cond|test" value="true"/> | |
312 <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> | |
313 </test> | |
314 </xml> | |
315 <xml name="manutest_PepNovoAdapter"> | |
316 <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection | |
317 unclear https://github.com/OpenMS/OpenMS/issues/4719)--> | |
318 <param name="adv_opts_selector" value="advanced"/> | |
319 <param name="adv_opts_cond|test" value="true"/> | |
320 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> | |
321 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> | |
322 <param name="model" value="LTQ_COMP"/> | |
323 </test> | |
324 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> | |
325 <param name="adv_opts_selector" value="advanced"/> | |
326 <param name="adv_opts_cond|test" value="true"/> | |
327 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> | |
328 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> | |
329 <param name="model" value="LTQ_COMP"/> | |
330 </test> | |
331 </xml> | |
332 <xml name="manutest_PhosphoScoring"> | |
333 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> | |
334 <param name="adv_opts_selector" value="advanced"/> | |
335 <param name="adv_opts_cond|test" value="true"/> | |
336 <param name="in" ftype="mzml" value="spectra.mzML"/> | |
337 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/> | |
338 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> | |
339 </test> | |
340 </xml> | |
341 <xml name="manutest_PSMFeatureExtractor"> | |
342 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> | |
343 <param name="adv_opts_cond|test" value="true"/> | |
344 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> | |
345 <param name="multiple_search_engines" value="true"/> | |
346 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> | |
347 <param name="adv_opts_cond|skip_db_check" value="true"/> | |
348 <param name="out_type" value="idxml"/> | |
349 <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="100"/> | |
350 </test> | |
351 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> | |
352 <param name="adv_opts_cond|test" value="true"/> | |
353 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> | |
354 <param name="multiple_search_engines" value="true"/> | |
355 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> | |
356 <param name="adv_opts_cond|skip_db_check" value="true"/> | |
357 <param name="out_type" value="mzid"/> | |
358 <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="100" lines_diff="4"/> | |
359 </test> | |
360 </xml> | |
361 <xml name="manutest_QCCalculator"> | |
362 <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> | |
363 <param name="adv_opts_selector" value="advanced"/> | |
364 <param name="adv_opts_cond|test" value="true"/> | |
365 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> | |
366 <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/> | |
367 </test> | |
368 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input --> | |
369 <param name="adv_opts_selector" value="advanced"/> | |
370 <param name="adv_opts_cond|test" value="true"/> | |
371 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> | |
372 <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/> | |
373 <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/> | |
374 <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/> | |
375 </test> | |
376 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input --> | |
377 <param name="adv_opts_selector" value="advanced"/> | |
378 <param name="adv_opts_cond|test" value="true"/> | |
379 <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/> | |
380 <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/> | |
381 <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/> | |
382 <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/> | |
383 </test> | |
384 </xml> | |
385 <xml name="manutest_QCEmbedder"> | |
386 <!--TODO--> | |
387 </xml> | |
388 <xml name="manutest_QCExporter"> | |
389 <!--TODO--> | |
390 </xml> | |
391 <xml name="manutest_QCExtractor"> | |
392 <!--TODO--> | |
393 </xml> | |
394 <xml name="manutest_QCImporter"> | |
395 <!--TODO--> | |
396 </xml> | |
397 <xml name="manutest_QCMerger"> | |
398 <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) --> | |
399 <param name="adv_opts_selector" value="advanced"/> | |
400 <param name="adv_opts_cond|test" value="true"/> | |
401 <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/> | |
402 <output name="out" ftype="qcml" value="QCMerger.qcML"/> | |
403 </test> | |
404 </xml> | |
405 <xml name="manutest_QCShrinker"> | |
406 <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input --> | |
407 <param name="adv_opts_selector" value="advanced"/> | |
408 <param name="adv_opts_cond|test" value="true"/> | |
409 <param name="in" ftype="qcml" value="QCCalculator1.qcML"/> | |
410 <output name="out" ftype="qcml" value="QCShrinker.qcML"/> | |
411 </test> | |
412 </xml> | |
413 <xml name="manutest_RNADigestor"> | |
414 <test expect_num_outputs="1"><!--random RNAsequence input --> | |
415 <param name="adv_opts_selector" value="advanced"/> | |
416 <param name="adv_opts_cond|test" value="true"/> | |
417 <param name="in" ftype="fasta" value="random_RNA.fa"/> | |
418 <output name="out" ftype="fasta" value="RNADigestor.fasta"/> | |
419 </test> | |
420 </xml> | |
421 <xml name="manutest_RNPxlXICFilter"> | |
422 <test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output--> | |
423 <param name="adv_opts_selector" value="advanced"/> | |
424 <param name="adv_opts_cond|test" value="true"/> | |
425 <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/> | |
426 <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/> | |
427 <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/> | |
428 </test> | |
429 </xml> | |
430 <xml name="manutest_RTEvaluation"> | |
431 <!-- just chosen an arbitrary input and autgenerated output--> | |
432 <!-- https://github.com/OpenMS/OpenMS/pull/4429 --> | |
433 <test expect_num_outputs="1"> | |
434 <param name="adv_opts_selector" value="advanced"/> | |
435 <param name="adv_opts_cond|test" value="true"/> | |
436 <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/> | |
437 <output name="out" ftype="csv" value="RTEvaluation.tsv"/> | |
438 </test> | |
439 </xml> | |
440 <xml name="manutest_SemanticValidator"> | |
441 <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> | |
442 <param name="adv_opts_selector" value="advanced"/> | |
443 <param name="adv_opts_cond|test" value="true"/> | |
444 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> | |
445 <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> | |
446 <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> | |
447 <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> | |
448 </output> | |
449 </test> | |
450 </xml> | |
451 <xml name="manutest_SequenceCoverageCalculator"> | |
452 <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input --> | |
453 <param name="adv_opts_selector" value="advanced"/> | |
454 <param name="adv_opts_cond|test" value="true"/> | |
455 <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/> | |
456 <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/> | |
457 <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/> | |
458 </test> | |
459 </xml> | |
460 <xml name="manutest_SpecLibCreator"> | |
461 <!--TODO could not find test data --> | |
462 </xml> | |
463 <xml name="manutest_SpectraFilterBernNorm"> | |
464 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | |
465 <param name="adv_opts_selector" value="advanced"/> | |
466 <param name="adv_opts_cond|test" value="true"/> | |
467 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
468 <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/> | |
469 </test> | |
470 </xml> | |
471 <xml name="manutest_SpectraFilterMarkerMower"> | |
472 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | |
473 <param name="adv_opts_selector" value="advanced"/> | |
474 <param name="adv_opts_cond|test" value="true"/> | |
475 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
476 <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/> | |
477 </test> | |
478 </xml> | |
479 <xml name="manutest_SpectraFilterNLargest"> | |
480 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | |
481 <param name="adv_opts_selector" value="advanced"/> | |
482 <param name="adv_opts_cond|test" value="true"/> | |
483 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
484 <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/> | |
485 </test> | |
486 </xml> | |
487 <xml name="manutest_SpectraFilterNormalizer"> | |
488 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | |
489 <param name="adv_opts_selector" value="advanced"/> | |
490 <param name="adv_opts_cond|test" value="true"/> | |
491 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
492 <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> | |
493 </test> | |
494 </xml> | |
495 <xml name="manutest_SpectraFilterParentPeakMower"> | |
496 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | |
497 <param name="adv_opts_selector" value="advanced"/> | |
498 <param name="adv_opts_cond|test" value="true"/> | |
499 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
500 <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/> | |
501 </test> | |
502 </xml> | |
503 <xml name="manutest_SpectraFilterScaler"> | |
504 <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | |
505 <param name="adv_opts_selector" value="advanced"/> | |
506 <param name="adv_opts_cond|test" value="true"/> | |
507 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
508 <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/> | |
509 </test> | |
510 </xml> | |
511 <xml name="manutest_SpectraFilterThresholdMower"> | |
512 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | |
513 <param name="adv_opts_selector" value="advanced"/> | |
514 <param name="adv_opts_cond|test" value="true"/> | |
515 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | |
516 <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/> | |
517 </test> | |
518 </xml> | |
519 <xml name="manutest_SpectraMerger"> | |
520 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> | |
521 <param name="adv_opts_selector" value="advanced"/> | |
522 <param name="adv_opts_cond|test" value="true"/> | |
523 <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> | |
524 <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> | |
525 </test> | |
526 </xml> | |
527 <xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer"> | |
528 <!-- -TODO model_output_file creates multiple files--> | |
529 </xml> | |
530 <xml name="manutest_TransformationEvaluation"> | |
531 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> | |
532 <param name="adv_opts_selector" value="advanced"/> | |
533 <param name="adv_opts_cond|test" value="true"/> | |
534 <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/> | |
535 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> | |
536 <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/> | |
537 </test> | |
538 </xml> | |
539 <xml name="manutest_XMLValidator"> | |
540 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> | |
541 <param name="adv_opts_selector" value="advanced"/> | |
542 <param name="adv_opts_cond|test" value="true"/> | |
543 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> | |
544 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> | |
545 <assert_contents><has_text text="Success: the file is valid!"/></assert_contents> | |
546 </output> | |
547 </test> | |
548 </xml> | |
549 <xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/></macros> |