Mercurial > repos > galaxyp > openms_qcshrinker

annotate macros_test.xml @ 10:ea3197d16843 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
author galaxyp
date Wed, 23 Sep 2020 15:04:23 +0000
parents ccfc3e189087
children 910f1fdf039a
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ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <macros>
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3
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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4 <!-- a copy of a FileConverter test without the advanced options used
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5 in order to check if this works (all other tests enable advanced) -->
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6 <xml name="manutest_FileConverter">
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7 <test expect_num_outputs="1">
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8 <param name="in" value="FileConverter_1_input.mzData"/>
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9 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
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10 <param name="out_type" value="mzML"/>
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11 </test>
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12 </xml>
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13 <!-- tests contributed by the galaxyproteomics community -->
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14 <xml name="manutest_ClusterMassTracesByPrecursor">
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15 <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
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16 <param name="adv_opts_selector" value="advanced"/>
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17 <param name="adv_opts_cond|test" value="true"/>
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18 <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
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19 <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
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20 <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
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21 </test>
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22 </xml>
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23 <xml name="manutest_ClusterMassTraces">
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24 <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
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25 <param name="adv_opts_selector" value="advanced"/>
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26 <param name="adv_opts_cond|test" value="true"/>
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27 <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
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28 <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
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29 </test>
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30 </xml>
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31 <xml name="manutest_CVInspector">
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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 -->
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33 <test expect_num_outputs="1">
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34 <param name="adv_opts_selector" value="advanced"/>
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35 <param name="adv_opts_cond|test" value="true"/>
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36 <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
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37 <param name="cv_names" value="XLMOD"/>
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38 <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
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39 <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
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40 <output name="html" ftype="html" value="CVInspector.html"/>
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41 </test>
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42 </xml>
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43 <xml name="manutest_DeMeanderize">
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44 <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->
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45 <param name="adv_opts_selector" value="advanced"/>
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46 <param name="adv_opts_cond|test" value="true"/>
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47 <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
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48 <output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
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49 </test>
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50 </xml>
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51 <xml name="manutest_Digestor">
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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 -->
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53 <param name="adv_opts_selector" value="advanced"/>
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54 <param name="adv_opts_cond|test" value="true"/>
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55 <param name="in" ftype="fasta" value="random.fa"/>
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56 <output name="out" ftype="fasta" value="Digestor.fasta"/>
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57 <param name="out_type" value="fasta"/>
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58 </test>
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59 </xml>
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60 <xml name="manutest_EICExtractor">
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61 <test expect_num_outputs="1"><!-- just using some random test data -->
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62 <param name="adv_opts_selector" value="advanced"/>
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63 <param name="adv_opts_cond|test" value="true"/>
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64 <param name="in" value="spectra.mzML"/>
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65 <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
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66 <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
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67 </test>
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68 </xml>
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69 <xml name="manutest_ERPairFinder">
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70 <!-- TODO -->
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71 </xml>
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72 <xml name="manutest_FeatureFinderIsotopeWavelet">
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73 <test expect_num_outputs="1"><!--just use the input of another FeatureFinder -->
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74 <param name="adv_opts_selector" value="advanced"/>
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75 <param name="adv_opts_cond|test" value="true"/>
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76 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
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77 <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
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78 </test>
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79 </xml>
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80 <xml name="manutest_FFEval">
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81 <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
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82 <param name="adv_opts_selector" value="advanced"/>
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83 <param name="adv_opts_cond|test" value="true"/>
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diff changeset
84 <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
85 <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
86 <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
87 <output name="out" value="FFEval.featureXML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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88 <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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89 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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90 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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91 <xml name="manutest_IDExtractor">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
92 <test expect_num_outputs="1"><!-- -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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93 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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94 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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95 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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96 <param name="best_hits" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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97 <param name="number_of_peptides" value="1"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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98 <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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99 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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100 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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101 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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102 <xml name="manutest_IDRipper">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
103 <test expect_num_outputs="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
104 <conditional name="adv_opts_cond">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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105 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
106 <param name="force" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
107 <param name="test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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108 </conditional>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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109 <param name="in" value="IDRipper_1_input.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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111 <output_collection name="out_path" count="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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112 <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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113 <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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114 </output_collection>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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115 <output name="ctd_out" ftype="xml">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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116 <assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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117 <is_valid_xml/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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118 </assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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119 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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120 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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121 <test expect_num_outputs="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
122 <conditional name="adv_opts_cond">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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123 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
124 <param name="force" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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125 <param name="test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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126 </conditional>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
127 <param name="in" value="IDRipper_2_input.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
128 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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129 <output_collection name="out_path" count="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
130 <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
131 <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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132 </output_collection>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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133 <output name="ctd_out" ftype="xml">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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134 <assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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135 <is_valid_xml/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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136 </assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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137 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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138 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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139 <test expect_num_outputs="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
140 <conditional name="adv_opts_cond">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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141 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
142 <param name="force" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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143 <param name="test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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144 </conditional>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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145 <param name="in" value="IDRipper_3_output.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
146 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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147 <output_collection name="out_path" count="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
148 <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
149 <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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150 </output_collection>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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151 <output name="ctd_out" ftype="xml">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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152 <assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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153 <is_valid_xml/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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154 </assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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155 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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156 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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157 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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158 <xml name="manutest_LabeledEval">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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159 <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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160 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
161 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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162 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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163 <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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164 <output name="stdout" value="LabeledEval.txt" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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165 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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166 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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167 <xml name="manutest_MapStatistics">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
168 <test expect_num_outputs="1"><!-- test with a featureXML input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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169 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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170 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
171 <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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172 <output name="out" ftype="txt" value="MapStatistics.txt"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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173 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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174 <test expect_num_outputs="1"><!-- test with a consensusxml input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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175 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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176 <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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177 <output name="out" ftype="txt" value="MapStatistics2.txt"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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178 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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179 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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180 <xml name="manutest_MetaboliteAdductDecharger">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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181 <test expect_num_outputs="3"><!-- same input as used by Decharger -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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182 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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183 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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184 <param name="in" ftype="featurexml" value="Decharger_input.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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185 <output name="out_cm" ftype="consensusxml" value="MetaboliteAdductDecharger_cm.consensusXML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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186 <param name="OPTIONAL_OUTPUTS" value="out_fm_FLAG,outpairs_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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187 <output name="out_fm" ftype="featurexml" value="MetaboliteAdductDecharger_fm.featureXML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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188 <output name="outpairs" ftype="consensusxml" value="MetaboliteAdductDecharger_pairs.consensusXML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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189 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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190 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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191 <xml name="manutest_MetaboliteSpectralMatcher">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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192 <!-- https://github.com/OpenMS/OpenMS/issues/2078
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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193 https://github.com/OpenMS/OpenMS/pull/4468-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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194 <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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195 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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196 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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197 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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198 <param name="in" ftype="mzml" value="spectra.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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199 <param name="database" value="MetaboliteSpectralDB.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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200 <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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201 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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202 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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203 <xml name="manutest_MRMPairFinder">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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204 <!-- TODO no idea about a useful input for pair_in -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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205 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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206 <xml name="manutest_MSSimulator">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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207 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
208 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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209 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
210 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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211 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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diff changeset
212 <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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213 <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
214 <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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215 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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216 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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217 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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218 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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219 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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220 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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221 <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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222 <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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223 <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
224 <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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225 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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226 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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227 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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228 <xml name="manutest_MzMLSplitter">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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229 <test expect_num_outputs="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
230 <conditional name="adv_opts_cond">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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231 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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232 <param name="force" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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233 <param name="test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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234 </conditional>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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235 <param name="in" value="FileFilter_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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diff changeset
236 <param name="parts" value="2"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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237 <param name="size" value="0"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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238 <param name="unit" value="MB"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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239 <param name="no_chrom" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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240 <param name="no_spec" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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242 <output name="ctd_out" ftype="xml">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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243 <assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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244 <is_valid_xml/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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245 </assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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246 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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247 <output_collection name="out" type="list" count="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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248 <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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249 <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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250 </output_collection>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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251 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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252 <test expect_num_outputs="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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253 <conditional name="adv_opts_cond">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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254 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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255 <param name="force" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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256 <param name="test" value="true"/>
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257 </conditional>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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258 <param name="in" value="FileFilter_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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259 <param name="parts" value="1"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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260 <param name="size" value="40"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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261 <param name="unit" value="KB"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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262 <param name="no_chrom" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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263 <param name="no_spec" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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264 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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265 <output name="ctd_out" ftype="xml">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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266 <assert_contents>
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267 <is_valid_xml/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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268 </assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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269 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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270 <output_collection name="out" type="list" count="2">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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271 <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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272 <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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273 </output_collection>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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274 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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275 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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276 <xml name="manutest_OpenSwathDIAPreScoring">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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277 <!-- TODO data from a test that included all the needed test files
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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278 currently unusable https://github.com/OpenMS/OpenMS/pull/4443 -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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279 <!-- data from a test that included all the needed test files -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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280 <!-- <test>-->
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281 <!-- <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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282 <!-- <param name="swath_files" value="OpenSwathWorkflow_10.chrom.mzML.tmp"/> or OpenSwathAnalyzer_2_swathfile.mzML-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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283 <!-- <output name="out" ftype="tabular" value="OpenSwathDIAPreScoring_2.tmp"/>-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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284 <!-- </test>-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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285 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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286 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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287 <xml name="manutest_OpenSwathFileSplitter">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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288 <test expect_num_outputs="3">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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289 <conditional name="adv_opts_cond">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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290 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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291 <param name="force" value="false"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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292 <param name="test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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293 </conditional>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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294 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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295 <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
10
ea3197d16843 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
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296 <output_collection name="outputDirectory" count="6">
9
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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297 <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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298 <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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299 </output_collection>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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300 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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301 <output name="ctd_out" ftype="xml">
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302 <assert_contents>
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303 <is_valid_xml/>
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304 </assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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305 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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306 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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307 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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308 <xml name="manutest_OpenSwathRewriteToFeatureXML">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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309 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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310 <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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311 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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312 <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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313 </test>
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314 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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315 <xml name="manutest_PepNovoAdapter">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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316 <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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317 unclear https://github.com/OpenMS/OpenMS/issues/4719)-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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318 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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319 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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320 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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321 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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322 <param name="model" value="LTQ_COMP"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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323 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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324 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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325 <param name="adv_opts_selector" value="advanced"/>
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326 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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327 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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328 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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329 <param name="model" value="LTQ_COMP"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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330 </test>
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331 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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332 <xml name="manutest_PhosphoScoring">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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333 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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334 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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335 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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336 <param name="in" ftype="mzml" value="spectra.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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337 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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338 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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339 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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340 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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341 <xml name="manutest_PSMFeatureExtractor">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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parents:
diff changeset
342 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
343 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
344 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
345 <param name="multiple_search_engines" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
346 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
347 <param name="adv_opts_cond|skip_db_check" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
348 <param name="out_type" value="idxml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
349 <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="100"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
350 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
351 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
352 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
353 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
354 <param name="multiple_search_engines" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
355 <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
356 <param name="adv_opts_cond|skip_db_check" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
357 <param name="out_type" value="mzid"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
358 <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="100" lines_diff="4"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
359 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
360 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
361 <xml name="manutest_QCCalculator">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
362 <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
363 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
364 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
365 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
366 <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
367 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
368 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
369 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
370 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
371 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
372 <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
373 <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
374 <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
375 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
376 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
377 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
378 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
379 <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
380 <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
381 <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
382 <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
383 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
384 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
385 <xml name="manutest_QCEmbedder">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
386 <!--TODO-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
387 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
388 <xml name="manutest_QCExporter">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
389 <!--TODO-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
390 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
391 <xml name="manutest_QCExtractor">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
392 <!--TODO-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
393 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
394 <xml name="manutest_QCImporter">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
395 <!--TODO-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
396 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
397 <xml name="manutest_QCMerger">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
398 <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
399 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
400 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
401 <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
402 <output name="out" ftype="qcml" value="QCMerger.qcML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
403 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
404 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
405 <xml name="manutest_QCShrinker">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
406 <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
407 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
408 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
409 <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
410 <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
411 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
412 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
413 <xml name="manutest_RNADigestor">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
414 <test expect_num_outputs="1"><!--random RNAsequence input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
415 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
416 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
417 <param name="in" ftype="fasta" value="random_RNA.fa"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
418 <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
419 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
420 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
421 <xml name="manutest_RNPxlXICFilter">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
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-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
423 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
424 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
425 <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
426 <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
427 <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
428 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
429 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
430 <xml name="manutest_RTEvaluation">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
431 <!-- just chosen an arbitrary input and autgenerated output-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
432 <!-- https://github.com/OpenMS/OpenMS/pull/4429 -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
433 <test expect_num_outputs="1">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
434 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
435 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
436 <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
437 <output name="out" ftype="csv" value="RTEvaluation.tsv"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
438 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
439 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
440 <xml name="manutest_SemanticValidator">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
441 <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
442 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
443 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
444 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
445 <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
446 <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
447 <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
448 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
449 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
450 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
451 <xml name="manutest_SequenceCoverageCalculator">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
452 <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
453 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
454 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
455 <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
456 <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
457 <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
458 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
459 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
460 <xml name="manutest_SpecLibCreator">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
461 <!--TODO could not find test data -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
462 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
463 <xml name="manutest_SpectraFilterBernNorm">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
464 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
465 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
466 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
467 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
468 <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
469 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
470 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
471 <xml name="manutest_SpectraFilterMarkerMower">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
472 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
473 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
474 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
475 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
476 <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
477 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
478 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
479 <xml name="manutest_SpectraFilterNLargest">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
480 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
481 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
482 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
483 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
484 <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
485 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
486 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
487 <xml name="manutest_SpectraFilterNormalizer">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
488 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
489 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
490 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
491 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
492 <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
493 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
494 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
495 <xml name="manutest_SpectraFilterParentPeakMower">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
496 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
497 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
498 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
499 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
500 <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
501 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
502 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
503 <xml name="manutest_SpectraFilterScaler">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
504 <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
505 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
506 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
507 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
508 <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
509 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
510 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
511 <xml name="manutest_SpectraFilterThresholdMower">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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512 <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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513 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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514 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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515 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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516 <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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517 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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518 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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519 <xml name="manutest_SpectraMerger">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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520 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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521 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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522 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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523 <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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524 <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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525 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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526 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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527 <xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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528 <!-- -TODO model_output_file creates multiple files-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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529 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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530 <xml name="manutest_TransformationEvaluation">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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531 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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532 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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533 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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534 <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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535 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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536 <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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537 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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538 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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539 <xml name="manutest_XMLValidator">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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540 <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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541 <param name="adv_opts_selector" value="advanced"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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542 <param name="adv_opts_cond|test" value="true"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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543 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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544 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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545 <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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546 </output>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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547 </test>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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548 </xml>
ccfc3e189087 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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>