Mercurial > repos > galaxyp > openms_databasesuitability

comparison macros_test.xml @ 0:3f555d385d45 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 18:22:43 +0000
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-1:000000000000 0:3f555d385d45
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_MetaboliteSpectralMatcher">
181 <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
182 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
183 <param name="adv_opts_selector" value="advanced"/>
184 <param name="adv_opts_cond|test" value="true"/>
185 <param name="in" ftype="mzml" value="spectra.mzML"/>
186 <param name="database" value="MetaboliteSpectralDB.mzML"/>
187 <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
188 </test>
189 </xml>
190 <xml name="manutest_MRMPairFinder">
191 <!-- TODO no idea about a useful input for pair_in -->
192 </xml>
193 <xml name="manutest_MSSimulator">
194 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
195 <param name="adv_opts_selector" value="advanced"/>
196 <param name="adv_opts_cond|test" value="true"/>
197 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
198 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
199 <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
200 <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
201 <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
202 </test>
203 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize -->
204 <param name="adv_opts_selector" value="advanced"/>
205 <param name="adv_opts_cond|test" value="true"/>
206 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
207 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
208 <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
209 <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
210 <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
211 <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/>
212 </test>
213 </xml>
214 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
215 <xml name="manutest_MzMLSplitter">
216 <test expect_num_outputs="2">
217 <conditional name="adv_opts_cond">
218 <param name="adv_opts_selector" value="advanced"/>
219 <param name="force" value="false"/>
220 <param name="test" value="true"/>
221 </conditional>
222 <param name="in" value="FileFilter_1_input.mzML"/>
223 <param name="parts" value="2"/>
224 <param name="size" value="0"/>
225 <param name="unit" value="MB"/>
226 <param name="no_chrom" value="false"/>
227 <param name="no_spec" value="false"/>
228 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
229 <output name="ctd_out" ftype="xml">
230 <assert_contents>
231 <is_valid_xml/>
232 </assert_contents>
233 </output>
234 <output_collection name="out" type="list" count="2">
235 <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
236 <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
237 </output_collection>
238 </test>
239 <test expect_num_outputs="2">
240 <conditional name="adv_opts_cond">
241 <param name="adv_opts_selector" value="advanced"/>
242 <param name="force" value="false"/>
243 <param name="test" value="true"/>
244 </conditional>
245 <param name="in" value="FileFilter_1_input.mzML"/>
246 <param name="parts" value="1"/>
247 <param name="size" value="40"/>
248 <param name="unit" value="KB"/>
249 <param name="no_chrom" value="false"/>
250 <param name="no_spec" value="false"/>
251 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
252 <output name="ctd_out" ftype="xml">
253 <assert_contents>
254 <is_valid_xml/>
255 </assert_contents>
256 </output>
257 <output_collection name="out" type="list" count="2">
258 <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
259 <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
260 </output_collection>
261 </test>
262 </xml>
263 <xml name="manutest_OpenSwathDIAPreScoring">
264 <!-- data from a test that included all the needed test files -->
265 <test>
266 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
267 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
268 <output_collection name="output_files" count="1">
269 <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
270 </output_collection>
271 </test>
272
273 <!-- test with two inputs (actually the same file .. symlinked) -->
274 <test>
275 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
276 <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
277 <output_collection name="output_files" count="2">
278 <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
279 <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
280 </output_collection>
281 </test>
282 </xml>
283 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
284 <xml name="manutest_OpenSwathFileSplitter">
285 <test expect_num_outputs="3">
286 <conditional name="adv_opts_cond">
287 <param name="adv_opts_selector" value="advanced"/>
288 <param name="force" value="false"/>
289 <param name="test" value="true"/>
290 </conditional>
291 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
292 <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
293 <output_collection name="outputDirectory" count="6">
294 <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
295 <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
296 </output_collection>
297 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
298 <output name="ctd_out" ftype="xml">
299 <assert_contents>
300 <is_valid_xml/>
301 </assert_contents>
302 </output>
303 </test>
304 </xml>
305 <xml name="manutest_OpenSwathRewriteToFeatureXML">
306 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
307 <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
308 <param name="adv_opts_cond|test" value="true"/>
309 <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
310 </test>
311 </xml>
312 <xml name="manutest_PepNovoAdapter">
313 <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection
314 unclear https://github.com/OpenMS/OpenMS/issues/4719)-->
315 <param name="adv_opts_selector" value="advanced"/>
316 <param name="adv_opts_cond|test" value="true"/>
317 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
318 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
319 <param name="model" value="LTQ_COMP"/>
320 </test>
321 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
322 <param name="adv_opts_selector" value="advanced"/>
323 <param name="adv_opts_cond|test" value="true"/>
324 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
325 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
326 <param name="model" value="LTQ_COMP"/>
327 </test>
328 </xml>
329 <xml name="manutest_PhosphoScoring">
330 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
331 <param name="adv_opts_selector" value="advanced"/>
332 <param name="adv_opts_cond|test" value="true"/>
333 <param name="in" ftype="mzml" value="spectra.mzML"/>
334 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
335 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
336 </test>
337 </xml>
338 <xml name="manutest_PSMFeatureExtractor">
339 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
340 <param name="adv_opts_cond|test" value="true"/>
341 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
342 <param name="multiple_search_engines" value="true"/>
343 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
344 <param name="adv_opts_cond|skip_db_check" value="true"/>
345 <param name="out_type" value="idxml"/>
346 <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
347 </test>
348 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
349 <param name="adv_opts_cond|test" value="true"/>
350 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
351 <param name="multiple_search_engines" value="true"/>
352 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
353 <param name="adv_opts_cond|skip_db_check" value="true"/>
354 <param name="out_type" value="mzid"/>
355 <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
356 </test>
357 </xml>
358 <xml name="manutest_QCCalculator">
359 <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
360 <param name="adv_opts_selector" value="advanced"/>
361 <param name="adv_opts_cond|test" value="true"/>
362 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
363 <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
364 </test>
365 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input -->
366 <param name="adv_opts_selector" value="advanced"/>
367 <param name="adv_opts_cond|test" value="true"/>
368 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
369 <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
370 <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
371 <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
372 </test>
373 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input -->
374 <param name="adv_opts_selector" value="advanced"/>
375 <param name="adv_opts_cond|test" value="true"/>
376 <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
377 <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
378 <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
379 <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
380 </test>
381 </xml>
382 <xml name="manutest_QCEmbedder">
383 <!--TODO-->
384 </xml>
385 <xml name="manutest_QCExporter">
386 <!--TODO-->
387 </xml>
388 <xml name="manutest_QCExtractor">
389 <!--TODO-->
390 </xml>
391 <xml name="manutest_QCImporter">
392 <!--TODO-->
393 </xml>
394 <xml name="manutest_QCMerger">
395 <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
396 <param name="adv_opts_selector" value="advanced"/>
397 <param name="adv_opts_cond|test" value="true"/>
398 <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
399 <output name="out" ftype="qcml" value="QCMerger.qcML"/>
400 </test>
401 </xml>
402 <xml name="manutest_QCShrinker">
403 <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input -->
404 <param name="adv_opts_selector" value="advanced"/>
405 <param name="adv_opts_cond|test" value="true"/>
406 <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
407 <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
408 </test>
409 </xml>
410 <xml name="manutest_RNADigestor">
411 <test expect_num_outputs="1"><!--random RNAsequence input -->
412 <param name="adv_opts_selector" value="advanced"/>
413 <param name="adv_opts_cond|test" value="true"/>
414 <param name="in" ftype="fasta" value="random_RNA.fa"/>
415 <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
416 </test>
417 </xml>
418 <xml name="manutest_RNPxlXICFilter">
419 <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-->
420 <param name="adv_opts_selector" value="advanced"/>
421 <param name="adv_opts_cond|test" value="true"/>
422 <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
423 <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
424 <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
425 </test>
426 </xml>
427 <xml name="manutest_RTEvaluation">
428 <!-- just chosen an arbitrary input and autgenerated output-->
429 <test expect_num_outputs="1">
430 <param name="adv_opts_selector" value="advanced"/>
431 <param name="adv_opts_cond|test" value="true"/>
432 <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
433 <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
434 </test>
435 </xml>
436 <xml name="manutest_SemanticValidator">
437 <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
438 <param name="adv_opts_selector" value="advanced"/>
439 <param name="adv_opts_cond|test" value="true"/>
440 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
441 <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
442 <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
443 <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents>
444 </output>
445 </test>
446 </xml>
447 <xml name="manutest_SequenceCoverageCalculator">
448 <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input -->
449 <param name="adv_opts_selector" value="advanced"/>
450 <param name="adv_opts_cond|test" value="true"/>
451 <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
452 <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
453 <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
454 </test>
455 </xml>
456 <xml name="manutest_SpecLibCreator">
457 <!--TODO could not find test data -->
458 </xml>
459 <xml name="manutest_SpectraFilterBernNorm">
460 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
461 <param name="adv_opts_selector" value="advanced"/>
462 <param name="adv_opts_cond|test" value="true"/>
463 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
464 <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/>
465 </test>
466 </xml>
467 <xml name="manutest_SpectraFilterMarkerMower">
468 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
469 <param name="adv_opts_selector" value="advanced"/>
470 <param name="adv_opts_cond|test" value="true"/>
471 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
472 <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/>
473 </test>
474 </xml>
475 <xml name="manutest_SpectraFilterNLargest">
476 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
477 <param name="adv_opts_selector" value="advanced"/>
478 <param name="adv_opts_cond|test" value="true"/>
479 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
480 <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/>
481 </test>
482 </xml>
483 <xml name="manutest_SpectraFilterNormalizer">
484 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
485 <param name="adv_opts_selector" value="advanced"/>
486 <param name="adv_opts_cond|test" value="true"/>
487 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
488 <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
489 </test>
490 </xml>
491 <xml name="manutest_SpectraFilterParentPeakMower">
492 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
493 <param name="adv_opts_selector" value="advanced"/>
494 <param name="adv_opts_cond|test" value="true"/>
495 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
496 <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
497 </test>
498 </xml>
499 <xml name="manutest_SpectraFilterScaler">
500 <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
501 <param name="adv_opts_selector" value="advanced"/>
502 <param name="adv_opts_cond|test" value="true"/>
503 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
504 <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/>
505 </test>
506 </xml>
507 <xml name="manutest_SpectraFilterThresholdMower">
508 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
509 <param name="adv_opts_selector" value="advanced"/>
510 <param name="adv_opts_cond|test" value="true"/>
511 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
512 <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/>
513 </test>
514 </xml>
515 <xml name="manutest_SpectraMerger">
516 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
517 <param name="adv_opts_selector" value="advanced"/>
518 <param name="adv_opts_cond|test" value="true"/>
519 <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
520 <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
521 </test>
522 </xml>
523 <xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer">
524 <!-- -TODO model_output_file creates multiple files-->
525 </xml>
526 <xml name="manutest_TransformationEvaluation">
527 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
528 <param name="adv_opts_selector" value="advanced"/>
529 <param name="adv_opts_cond|test" value="true"/>
530 <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/>
531 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
532 <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/>
533 </test>
534 </xml>
535 <xml name="manutest_XMLValidator">
536 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
537 <param name="adv_opts_selector" value="advanced"/>
538 <param name="adv_opts_cond|test" value="true"/>
539 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
540 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
541 <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
542 </output>
543 </test>
544 </xml>
545 <xml name="manutest_MetaboliteAdductDecharger"/><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"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>