Mercurial > repos > galaxyp > openms_msfraggeradapter

comparison macros_test.xml @ 0:52a0856534d9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:48:23 +0000
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children 5a9c3e827da5
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-1:000000000000 0:52a0856534d9
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>