| Previous changeset 1:797c755b9e74 (2016-02-21) Next changeset 3:b4ccaf21855d (2017-01-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6 |
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modified:
msgfplus.xml |
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added:
test-data/201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid |
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removed:
test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid test-data/201208-378803-msgf-50ppm-semitryptic-no_mods.mzid |
| b |
| diff -r 797c755b9e74 -r 058a2ab1d462 msgfplus.xml --- a/msgfplus.xml Sun Feb 21 11:27:00 2016 -0500 +++ b/msgfplus.xml Wed Dec 07 16:43:17 2016 -0500 |
| [ |
| @@ -3,7 +3,7 @@ Identifies peptides in tandem mass spectra using the MS-GF+ search engine. </description> <requirements> - <requirement type="package" version="v10089">msgfplus</requirement> + <requirement type="package" version="2016.10.26">msgf_plus</requirement> <environment_variable name="LC_ALL" action="set_to">C</environment_variable> </requirements> <stdio> @@ -12,12 +12,20 @@ <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> </stdio> <command> + <![CDATA[ - #set $db_name = $d.display_name.replace(".fasta", "") + ".fasta" - #set $input_name = $s.display_name + #if $msgf_input.intype_selector == "single" + #set $db_name = $msgf_input.d.display_name.replace(".fasta", "") + ".fasta" + #set $input_name = $msgf_input.s.display_name + ln -s '$msgf_input.s' '${input_name}' && + ln -s '$msgf_input.d' '${db_name}' && + #else if $msgf_input.intype_selector == "fractions" + #set $db_name = $msgf_input.db_spectra.reverse.display_name.replace(".fasta", "") + ".fasta" + #set $input_name = $msgf_input.db_spectra.forward.display_name + ln -s '$msgf_input.db_spectra.forward' '${input_name}' && + ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && + #end if #set $output_name = $input_name.replace(".mzML", "") + ".mzid" - ln -s '$s' '${input_name}' && - ln -s '$d' '${db_name}' && echo \\#Mods > Mods.txt && #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) @@ -29,10 +37,7 @@ echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt && #end for - msgfjar=\$(which MSGFPlus.jar) && - ( [ -f "\$msgfjar" ] || (echo MSGFPlus.jar not found && exit 1)) && - - java -jar \$msgfjar + msgf_plus -s '$input_name' -d '$db_name' -thread \${GALAXY_SLOTS:-1} @@ -56,8 +61,20 @@ ]]> </command> <inputs> - <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> - <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> + <conditional name="msgf_input"> + <param name="intype_selector" type="select" label="Type of MSGF+ analysis"> + <option value="single">Single database</option> + <option value="fractions">Prefractionated database</option> + </param> + <when value="single"> + <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> + <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> + </when> + <when value="fractions"> + <param name="db_spectra" type="data_collection" collection_type="paired" + label="Collection: Pairs of FASTA database (forward) and spectra (reverse)"/> + </when> + </conditional> <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" /> <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments"> @@ -203,8 +220,21 @@ </outputs> <tests> <test> - <param name="s" value="input/201208-378803.mzML" /> - <param name="d" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="msgf_input.intype_selector" value="single" /> + <param name="msgf_input.s" value="input/201208-378803.mzML" /> + <param name="msgf_input.d" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="tda" value="1" /> + <param name="ntt" value="1" /> + <param name="t" value="50" /> + <param name="precursor_ion_tol_units" value="ppm" /> + <param name="common_fixed_modifications" value="" /> + <param name="common_variable_modifications" value="" /> + <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> + </test> + <test> + <param name="msgf_input.intype_selector" value="fractions" /> + <param name="msgf_input.db_spectra.forward" value="input/201208-378803.mzML" /> + <param name="msgf_input.db_spectra.reverse" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="tda" value="1" /> <param name="ntt" value="1" /> <param name="t" value="50" /> @@ -214,8 +244,9 @@ <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" /> </test> <test> - <param name="s" value="input/201208-378803.mzML" /> - <param name="d" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="msgf_input.intype_selector" value="single" /> + <param name="msgf_input.s" value="input/201208-378803.mzML" /> + <param name="msgf_input.d" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="tda" value="1" /> <param name="t" value="0.02" /> <param name="precursor_ion_tol_units" value="Da" /> @@ -242,12 +273,12 @@ <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" /> <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" /> - <param name="custom_mods_1|aa_specificity" value="CS" /> + <param name="custom_mods_1|aa_specificity" value="C,S" /> <param name="custom_mods_1|fix_or_opt" value="opt" /> <param name="custom_mods_1|position_specificity" value="any" /> <param name="custom_mods_1|mod_name" value="cGMP" /> - <output name="output" file="201208-378803-msgf-2mmu-tryptic-many_mods.mzid" lines_diff="6" /> + <output name="output" file="201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid" lines_diff="6" /> </test> </tests> <help> |
| b |
| diff -r 797c755b9e74 -r 058a2ab1d462 test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid --- a/test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid Sun Feb 21 11:27:00 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3039 +0,0 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-11-09T22:47:09" >\n-<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n- <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>\n- <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>\n- <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>\n-</cvList>\n-<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n- <AnalysisSoftware version="Beta (v10089)" name="MS-GF+" id="ID_software">\n- <SoftwareName>\n- <cvParam 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searchDatabase_ref="SearchDB_1" length="811" id="DBSeq28473">\n- <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528968106|ref|XP_005212568.1| PREDICTED: exocyst complex component 6B isoform X2 [Bos taurus]" name="protein description"/>\n- </DBSequence>\n- <DBSequence accession="gi|528968108|ref|XP_005212569.1|" searchDatabase_ref="SearchDB_1" length="766" id="DBSeq29285">\n- <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528968108|ref|XP_005212569.1| PREDICTED: exocyst complex component 6B isoform X3 [Bos taurus]" name="protein description"/>\n- </DBSequence>\n- <DBSequence accession="gi|115497338|ref|NP_001069884.1|" searchDatabase_ref="SearchDB_1" length="626" id="DBSeq37511">\n- <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|115497338|ref|NP_001069884.1| exocyst complex component 6B [Bos taurus]" name="protein description"/>\n- </DBSequence>\n- <DBSequence accession="XXX_gi|358418103|ref|XP_600387.4|" searchDatabase_ref="SearchDB_1" length="854" 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name="NTermIonCurrentRatio"/>\n- <userParam value="0.0" name="CTermIonCurrentRatio"/>\n- <userParam value="1027.0" name="MS2IonCurrent"/>\n- <userParam value="1" name="NumMatchedMainIons"/>\n- <userParam value="1.8923733" name="MeanErrorAll"/>\n- <userParam value="0.0" name="StdevErrorAll"/>\n- <userParam value="1.8923733" name="MeanErrorTop7"/>\n- <userParam value="0.0" name="StdevErrorTop7"/>\n- <userParam value="-1.8923733" name="MeanRelErrorAll"/>\n- <userParam value="0.0" name="StdevRelErrorAll"/>\n- <userParam value="-1.8923733" name="MeanRelErrorTop7"/>\n- <userParam value="0.0" name="StdevRelErrorTop7"/>\n- </SpectrumIdentificationItem>\n- </SpectrumIdentificationResult>\n- <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="sample=1 period=1 cycle=1428 experiment=2" id="SIR_105">\n- <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep71" calculatedMassToCharge="585.5540161132812" experimentalMassToCharge="585.301513671875" chargeState="4" id="SII_105_1">\n- <PeptideEvidenceRef peptideEvidence_ref="PepEv_10335_71_831"/>\n- <PeptideEvidenceRef peptideEvidence_ref="PepEv_17946_71_831"/>\n- <PeptideEvidenceRef peptideEvidence_ref="PepEv_39268_71_755"/>\n- <cvParam accession="MS:1002049" cvRef="PSI-MS" value="-47" name="MS-GF:RawScore"/>\n- <cvParam accession="MS:1002050" cvRef="PSI-MS" value="93" name="MS-GF:DeNovoScore"/>\n- <cvParam accession="MS:1002052" cvRef="PSI-MS" value="0.02323054" name="MS-GF:SpecEValue"/>\n- <cvParam accession="MS:1002053" cvRef="PSI-MS" value="947.295" name="MS-GF:EValue"/>\n- <cvParam accession="MS:1002054" cvRef="PSI-MS" value="1.0" name="MS-GF:QValue"/>\n- <cvParam accession="MS:1002055" cvRef="PSI-MS" value="1.0" name="MS-GF:PepQValue"/>\n- <userParam value="-1" name="IsotopeError"/>\n- <userParam value="HCD" name="AssumedDissociationMethod"/>\n- <userParam value="0.0" name="ExplainedIonCurrentRatio"/>\n- <userParam value="0.0" name="NTermIonCurrentRatio"/>\n- <userParam value="0.0" name="CTermIonCurrentRatio"/>\n- <userParam value="330.0" name="MS2IonCurrent"/>\n- </SpectrumIdentificationItem>\n- </SpectrumIdentificationResult>\n- </SpectrumIdentificationList>\n- </AnalysisData>\n-</DataCollection>\n-</MzIdentML>\n' |
| b |
| diff -r 797c755b9e74 -r 058a2ab1d462 test-data/201208-378803-msgf-50ppm-semitryptic-no_mods.mzid --- a/test-data/201208-378803-msgf-50ppm-semitryptic-no_mods.mzid Sun Feb 21 11:27:00 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,2619 +0,0 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-11-09T22:46:41" >\n-<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n- <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>\n- <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>\n- <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>\n-</cvList>\n-<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n- <AnalysisSoftware version="Beta (v10089)" name="MS-GF+" id="ID_software">\n- <SoftwareName>\n- <cvParam 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| b |
| diff -r 797c755b9e74 -r 058a2ab1d462 test-data/201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid Wed Dec 07 16:43:17 2016 -0500 |
| [ |
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| b |
| diff -r 797c755b9e74 -r 058a2ab1d462 test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid Wed Dec 07 16:43:17 2016 -0500 |
| [ |
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