Mercurial > repos > galaxyp > openms_consensusid

comparison macros_test.xml @ 17:abffdfee3021 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 22 Feb 2021 10:46:10 +0000
parents feebe2054e40
children
comparison
equal deleted inserted replaced
16:01dbaf6a57e0 17:abffdfee3021
125 <param name="test" value="true"/> 125 <param name="test" value="true"/>
126 </conditional> 126 </conditional>
127 <param name="in" value="IDRipper_2_input.idXML"/> 127 <param name="in" value="IDRipper_2_input.idXML"/>
128 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 128 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
129 <output_collection name="out_path" count="2"> 129 <output_collection name="out_path" count="2">
130 <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/> 130 <element name="IDRipper_2_output_1" file="IDRipper_2_output1.idXML" ftype="idxml"/>
131 <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/> 131 <element name="IDRipper_2_output_2" file="IDRipper_2_output2.idXML" ftype="idxml"/>
132 </output_collection> 132 </output_collection>
133 <output name="ctd_out" ftype="xml"> 133 <output name="ctd_out" ftype="xml">
134 <assert_contents> 134 <assert_contents>
135 <is_valid_xml/> 135 <is_valid_xml/>
136 </assert_contents> 136 </assert_contents>
264 <!-- data from a test that included all the needed test files --> 264 <!-- data from a test that included all the needed test files -->
265 <test> 265 <test>
266 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 266 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
267 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> 267 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
268 <output_collection name="output_files" count="1"> 268 <output_collection name="output_files" count="1">
269 <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> 269 <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
270 </output_collection> 270 </output_collection>
271 </test> 271 </test>
272
273 <!-- test with two inputs (actually the same file .. symlinked) --> 272 <!-- test with two inputs (actually the same file .. symlinked) -->
274 <test> 273 <test>
275 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 274 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
276 <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> 275 <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
277 <output_collection name="output_files" count="2"> 276 <output_collection name="output_files" count="2">
278 <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> 277 <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
279 <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> 278 <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
280 </output_collection> 279 </output_collection>
281 </test> 280 </test>
282 </xml> 281 </xml>
283 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> 282 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
284 <xml name="manutest_OpenSwathFileSplitter"> 283 <xml name="manutest_OpenSwathFileSplitter">
333 <param name="in" ftype="mzml" value="spectra.mzML"/> 332 <param name="in" ftype="mzml" value="spectra.mzML"/>
334 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/> 333 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
335 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> 334 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
336 </test> 335 </test>
337 </xml> 336 </xml>
337 <!-- TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 -->
338 <xml name="manutest_PSMFeatureExtractor"> 338 <xml name="manutest_PSMFeatureExtractor">
339 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> 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"/> 340 <param name="adv_opts_cond|test" value="true"/>
341 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> 341 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
342 <param name="multiple_search_engines" value="true"/> 342 <param name="multiple_search_engines" value="true"/>
352 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> 352 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
353 <param name="adv_opts_cond|skip_db_check" value="true"/> 353 <param name="adv_opts_cond|skip_db_check" value="true"/>
354 <param name="out_type" value="mzid"/> 354 <param name="out_type" value="mzid"/>
355 <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> 355 <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
356 </test> 356 </test>
357 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
358 <param name="adv_opts_cond|test" value="true"/>
359 <param name="in_single" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
360 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
361 <param name="out_type" value="idxml"/>
362 <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
363 </test>
357 </xml> 364 </xml>
358 <xml name="manutest_QCCalculator"> 365 <xml name="manutest_QCCalculator">
359 <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> 366 <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
360 <param name="adv_opts_selector" value="advanced"/> 367 <param name="adv_opts_selector" value="advanced"/>
361 <param name="adv_opts_cond|test" value="true"/> 368 <param name="adv_opts_cond|test" value="true"/>