| Previous changeset 8:59736982ab7b (2020-12-14) Next changeset 10:63fea23042c4 (2022-12-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 173ee0ef8aa320d2f17433d6560fff05093d127e-dirty" |
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modified:
PSMFeatureExtractor.xml |
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added:
macros_discarded_auto.xml |
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removed:
test-data/spectrast.log |
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| diff -r 59736982ab7b -r 047020d9012f PSMFeatureExtractor.xml --- a/PSMFeatureExtractor.xml Mon Dec 14 16:54:21 2020 +0000 +++ b/PSMFeatureExtractor.xml Sat Jan 30 11:38:47 2021 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Utilities]--> -<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy1" profile="20.05"> +<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy2" profile="20.05"> <description>Computes extra features for each input PSM.</description> <macros> <token name="@EXECUTABLE@">PSMFeatureExtractor</token> @@ -34,7 +34,7 @@ #if $in ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} #else if $in_single -'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && +'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' #end if -out 'out/output.${out_type}' |
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| diff -r 59736982ab7b -r 047020d9012f macros_discarded_auto.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_discarded_auto.xml Sat Jan 30 11:38:47 2021 +0000 |
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| b'@@ -0,0 +1,378 @@\n+\n+<xml name="manutest_OpenSwathFileSplitter">\n+<test expect_num_outputs="2">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>\n+ <output_collection name="outputDirectory" count=""/>\n+ <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+</test></xml>\n+<xml name="manutest_IDRipper">\n+<test expect_num_outputs="1">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="IDRipper_1_input.idXML"/>\n+ <output_collection name="out_path" count=""/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test><test expect_num_outputs="1">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="IDRipper_2_input.idXML"/>\n+ <output_collection name="out_path" count=""/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test><test expect_num_outputs="1">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="IDRipper_3_output.idXML"/>\n+ <output_collection name="out_path" count=""/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test></xml>\n+<xml name="manutest_MzMLSplitter">\n+<test expect_num_outputs="1">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="FileFilter_1_input.mzML"/>\n+ <output_collection name="out" count=""/>\n+ <param name="parts" value="2"/>\n+ <param name="size" value="0"/>\n+ <param name="unit" value="MB"/>\n+ <param name="no_chrom" value="false"/>\n+ <param name="no_spec" value="false"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test><test expect_num_outputs="1">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="FileFilter_1_input.mzML"/>\n+ <output_collection name="out" count=""/>\n+ <param name="parts" value="1"/>\n+ <param name="size" value="40"/>\n+ <param name="unit" value="KB"/>\n+ <param name="no_chrom" value="false"/>\n+ <param name="no_spec" value="false"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert'..b'" value="2"/>\n+ <param name="precursor_tolerance" value="20.0"/>\n+ <param name="precursor_tolerance_units" value="ppm"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/>\n+ <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/>\n+ <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>\n+ <param name="pcut" value="-10.0"/>\n+ <param name="min_cluster_size" value="1"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test></xml>\n+<xml name="manutest_NovorAdapter">\n+<test expect_num_outputs="2">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="NovorAdapter_in.mzML"/>\n+ <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>\n+ <param name="enzyme" value="Trypsin"/>\n+ <param name="fragmentation" value="CID"/>\n+ <param name="massAnalyzer" value="Trap"/>\n+ <param name="fragment_mass_tolerance" value="0.5"/>\n+ <param name="precursor_mass_tolerance" value="15.0"/>\n+ <param name="precursor_error_units" value="ppm"/>\n+ <param name="variable_modifications" value="Acetyl (K)"/>\n+ <param name="fixed_modifications" value="Carbamidomethyl (C)"/>\n+ <param name="forbiddenResidues" value="I"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test></xml>\n+<xml name="manutest_SpectraSTSearchAdapter">\n+<test expect_num_outputs="2">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="use_isotopically_averaged_mass" value="false"/>\n+ <param name="use_all_charge_states" value="false"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>\n+ <param name="output_files_type" value="pep.xml"/>\n+ <output_collection name="output_files" count="1"/>\n+ <param name="library_file" value="testLib.splib" ftype="splib"/>\n+ <param name="sequence_database_type" value="AA"/>\n+ <param name="precursor_mz_tolerance" value="3.0"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test><test expect_num_outputs="2">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="use_isotopically_averaged_mass" value="false"/>\n+ <param name="use_all_charge_states" value="false"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>\n+ <param name="output_files_type" value="tsv"/>\n+ <output_collection name="output_files" count="1"/>\n+ <param name="library_file" value="testLib.splib" ftype="splib"/>\n+ <param name="sequence_database_type" value="AA"/>\n+ <param name="precursor_mz_tolerance" value="3.0"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test></xml>\n' |
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| diff -r 59736982ab7b -r 047020d9012f test-data/spectrast.log --- a/test-data/spectrast.log Mon Dec 14 16:54:21 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML -GENERAL: File offset size is 8 bytes. Big library supported. -GENERAL: Pointer size is 8 bytes. -MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z -MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; -PERFORMANCE: Total Run Time = 0 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0 seconds.. - -END: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML -========== -START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML -GENERAL: File offset size is 8 bytes. Big library supported. -GENERAL: Pointer size is 8 bytes. -MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z -MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; -PERFORMANCE: Total Run Time = 1 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0.333333 seconds.. - -END: (Sun Dec 13 17:22:44 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML -========== |