Mercurial > repos > galaxyp > bibliospec
diff test-data/msgf-test.mzid @ 0:5a4801b7d106 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
author | galaxyp |
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date | Tue, 08 May 2018 14:16:45 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/msgf-test.mzid Tue May 08 14:16:45 2018 -0400 @@ -0,0 +1,195 @@ +<?xml version="1.0" encoding="UTF-8"?> +<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="2014-01-17T14:17:27" > +<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> + <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"/> + <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/> + <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/> +</cvList> +<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> + <AnalysisSoftware version="Beta (v9881)" name="MS-GF+" id="ID_software"> + <SoftwareName> + <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/> + </SoftwareName> + </AnalysisSoftware> +</AnalysisSoftwareList> +<SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> + <DBSequence accession="gi|24373345|ref|NP_717388.1|" searchDatabase_ref="SearchDB_1" length="735" id="DBSeq1"> + <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24373345|ref|NP_717388.1| extracelllular iron oxide respiratory system surface decaheme cytochrome c component OmcA [Shewanella oneidensis MR-1]" name="protein description"/> + </DBSequence> + <DBSequence accession="gi|24371739|ref|NP_715781.1|" searchDatabase_ref="SearchDB_1" length="178" id="DBSeq737"> + <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24371739|ref|NP_715781.1| ferritin Ftn [Shewanella oneidensis MR-1]" name="protein description"/> + </DBSequence> + <DBSequence accession="gi|24371954|ref|NP_715996.1|" searchDatabase_ref="SearchDB_1" length="400" id="DBSeq1994"> + <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24371954|ref|NP_715996.1| ISSod4 transposase TnpA_ISSod4 [Shewanella oneidensis MR-1]" name="protein description"/> + </DBSequence> + <DBSequence accession="gi|24373023|ref|NP_717065.1|" searchDatabase_ref="SearchDB_1" length="188" id="DBSeq1805"> + <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24373023|ref|NP_717065.1| site-specific recombinase phage integrase family [Shewanella oneidensis MR-1]" name="protein description"/> + </DBSequence> + <Peptide id="Pep1"> + <PeptideSequence>FKWNGTDTNSAAEK</PeptideSequence> + </Peptide> + <Peptide id="Pep2"> + <PeptideSequence>GGESIMNAQSQPQA</PeptideSequence> + </Peptide> + <Peptide id="Pep3"> + <PeptideSequence>VIYTTNAVEAVHRQFRKLTK</PeptideSequence> + </Peptide> + <Peptide id="Pep4"> + <PeptideSequence>VMRMLR</PeptideSequence> + </Peptide> + <PeptideEvidence isDecoy="false" post="R" pre="R" end="556" start="543" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_543_1_543"/> + <PeptideEvidence isDecoy="false" post="-" pre="K" end="178" start="165" peptide_ref="Pep2" dBSequence_ref="DBSeq737" id="PepEv_901_2_165"/> + <PeptideEvidence isDecoy="false" post="T" pre="K" end="346" start="327" peptide_ref="Pep3" dBSequence_ref="DBSeq1994" id="PepEv_2320_3_327"/> + <PeptideEvidence isDecoy="false" post="H" pre="R" end="161" start="156" peptide_ref="Pep4" dBSequence_ref="DBSeq1805" id="PepEv_1960_4_156"/> +</SequenceCollection> +<AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> + <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1"> + <InputSpectra spectraData_ref="SID_1"/> + <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/> + </SpectrumIdentification> +</AnalysisCollection> +<AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> + <SpectrumIdentificationProtocol 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<ModificationParams> + <SearchModification residues="C" massDelta="57.021465" fixedMod="true"> + <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/> + </SearchModification> + </ModificationParams> + <Enzymes> + <Enzyme missedCleavages="1000" semiSpecific="true" id="Tryp"> + <EnzymeName> + <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/> + </EnzymeName> + </Enzyme> + </Enzymes> + <ParentTolerance> + <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="20.0" name="search tolerance plus value"/> + <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="20.0" name="search tolerance minus value"/> + </ParentTolerance> + <Threshold> + <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/> + </Threshold> + </SpectrumIdentificationProtocol> +</AnalysisProtocolCollection> +<DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> + <Inputs> + <SearchDatabase numDatabaseSequences="10" location="C:\cygwin\home\kims336\Data\SkylineDemo\Abbreviated.fasta" id="SearchDB_1"> + <FileFormat> + <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/> + </FileFormat> + <DatabaseName> + <userParam name="Abbreviated.fasta"/> + </DatabaseName> + <cvParam accession="MS:1001197" cvRef="PSI-MS" name="DB composition target+decoy"/> + <cvParam accession="MS:1001283" cvRef="PSI-MS" value="^XXX" name="decoy DB accession regexp"/> + <cvParam accession="MS:1001195" cvRef="PSI-MS" name="decoy DB type reverse"/> + </SearchDatabase> + <SpectraData location="msgf-test.mzML" name="msgf-test.mzML" id="SID_1"> + <FileFormat> + <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/> + </FileFormat> + <SpectrumIDFormat> + <cvParam accession="MS:1000768" cvRef="PSI-MS" name="Thermo nativeID format"/> + </SpectrumIDFormat> + </SpectraData> + </Inputs> + <AnalysisData> + 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