| Next changeset 1:797c755b9e74 (2016-02-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit bdb474693831a3375db79755e88641ad32b3b4e6 |
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added:
COPYING msgfplus.xml test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid test-data/201208-378803-msgf-50ppm-semitryptic-no_mods.mzid test-data/input/201208-378803.mzML test-data/input/cow.protein.PRG2012-subset.fasta tool_dependencies.xml |
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| diff -r 000000000000 -r ee56530a559f COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Sun Feb 21 11:04:06 2016 -0500 |
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| @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. 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| diff -r 000000000000 -r ee56530a559f msgfplus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msgfplus.xml Sun Feb 21 11:04:06 2016 -0500 |
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| b'@@ -0,0 +1,265 @@\n+<tool id="msgfplus" name="MS-GF+" version="0.1">\n+ <description>\n+ Identifies peptides in tandem mass spectra using the MS-GF+ search engine.\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="10089">msgfplus</requirement>\n+ <environment_variable name="LC_ALL" action="set_to">C</environment_variable> \n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Job Failed" />\n+ <regex match="java.*Exception" level="fatal" description="Java Exception"/> \n+ <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>\n+ </stdio>\n+ <command>\n+<![CDATA[\n+ #set $db_name = $d.display_name.replace(".fasta", "") + ".fasta"\n+ #set $input_name = $s.display_name\n+ #set $output_name = $input_name.replace(".mzML", "") + ".mzid"\n+ ln -s \'$s\' \'${input_name}\' &&\n+ ln -s \'$d\' \'${db_name}\' &&\n+\n+ echo \\\\#Mods > Mods.txt &&\n+ #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)\n+ #for $mod in $common_mods.split(",")\n+ echo \'$mod.replace("_", ",")\' >> Mods.txt &&\n+ #end for\n+\n+ #for $mod in $custom_mods\n+ echo \'${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}\' >> Mods.txt &&\n+ #end for\n+\n+ msgfjar=\\$(which MSGFPlus.jar) &&\n+ ( [ -f "\\$msgfjar" ] || (echo MSGFPlus.jar not found && exit 1)) &&\n+\n+ java -jar \\$msgfjar\n+ -s \'$input_name\'\n+ -d \'$db_name\'\n+ -thread \\${GALAXY_SLOTS:-1}\n+ -mod Mods.txt\n+ -tda $tda\n+ -t $t$precursor_ion_tol_units\n+ -ti $advanced.isotope_low,$advanced.isotope_high\n+ -m $advanced.m\n+ -inst $inst\n+ -e $e\n+ -protocol $advanced.protocol\n+ -ntt $ntt\n+ -minLength $advanced.minLength\n+ -maxLength $advanced.maxLength\n+ -minCharge $advanced.minCharge\n+ -maxCharge $advanced.maxCharge\n+ -n $advanced.n\n+ -addFeatures $advanced.addFeatures\n+ &&\n+ mv \'$output_name\' output\n+]]>\n+ </command>\n+ <inputs>\n+ <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>\n+ <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>\n+ <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" />\n+ <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>\n+ <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">\n+ <option value="ppm" selected="true">Parts per million (ppm)</option>\n+ <option value="Da">Daltons</option>\n+ </param>\n+ <param argument="-inst" label="Instrument type" type="select" help="The instrument type that generated the MS/MS spectra is used to determine the scoring model">\n+ <option value="0" selected="true">Low-res (LCQ/LTQ)</option>\n+ <option value="1" >High-res (LTQ-Orbitrap)</option>\n+ <option value="2" >Q-TOF</option>\n+ <option value="3" >Q-Exactive</option>\n+ </param>\n+ <param argument="-e" type="select" label="Enzyme" help="Enzyme used to digest proteins in sample preparation; trypsin is the most commonly used enzyme">\n+ <option value="0">Unspecific cleavage</option>\n+ <option value="1" selected="true">Trypsin, no P rule</option>\n+ <option value="2">Chymotryps'..b'tures" label="Calculate additional scoring features?" type="boolean" truevalue="1" falsevalue="0" help="If true, several extra derivative scores are calculated for each match" />\n+ <param name="isotope_low" label="Lower isotope error range" type="integer" value="0" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation (-ti)" />\n+ <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" /> \n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="mzid" from_work_dir="output" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="s" value="input/201208-378803.mzML" />\n+ <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />\n+ <param name="tda" value="1" />\n+ <param name="ntt" value="1" />\n+ <param name="t" value="50" />\n+ <param name="precursor_ion_tol_units" value="ppm" /> \n+ <param name="common_fixed_modifications" value="" />\n+ <param name="common_variable_modifications" value="" />\n+ <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" />\n+ </test>\n+ <test>\n+ <param name="s" value="input/201208-378803.mzML" />\n+ <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />\n+ <param name="tda" value="1" />\n+ <param name="t" value="0.02" />\n+ <param name="precursor_ion_tol_units" value="Da" />\n+ <param name="isotope_low" value="-1" />\n+ <param name="isotope_high" value="0" />\n+ <param name="m" value="3" />\n+ <param name="inst" value="2" />\n+ <param name="e" value="3" />\n+ <param name="protocol" value="2" />\n+ <param name="minLength" value="10" />\n+ <param name="maxLength" value="20" />\n+ <param name="minCharge" value="2" />\n+ <param name="maxCharge" value="6" />\n+ <param name="n" value="2" />\n+ <param name="addFeatures" value="1" />\n+\n+ <param name="common_fixed_modifications" value="C2H3N1O1_C_fix_any_Carbamidomethyl,144.102063_*_fix_N-term_iTRAQ4plex,144.102063_K_fix_any_iTRAQ4plex" />\n+ <param name="common_variable_modifications" value="O1_M_opt_any_Oxidation,H-3N-1_Q_opt_N-term_Gln->pyro-Glu" />\n+\n+ <param name="custom_mods_0|formula_or_mass" value="C-2H-2O-2" />\n+ <param name="custom_mods_0|aa_specificity" value="G" />\n+ <param name="custom_mods_0|fix_or_opt" value="opt" />\n+ <param name="custom_mods_0|position_specificity" value="c-term" />\n+ <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" />\n+\n+ <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" />\n+ <param name="custom_mods_1|aa_specificity" value="CS" />\n+ <param name="custom_mods_1|fix_or_opt" value="opt" />\n+ <param name="custom_mods_1|position_specificity" value="any" />\n+ <param name="custom_mods_1|mod_name" value="cGMP" />\n+\n+ <output name="output" file="201208-378803-msgf-2mmu-tryptic-many_mods.mzid" lines_diff="6" />\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+Performs protein identification via database search using MS-GF+.\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1038/ncomms6277</citation>\n+ <citation type="doi">10.1021/pr8001244</citation>\n+ <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Gruening, B, Chambers, MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n+ year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ee56530a559f test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid Sun Feb 21 11:04:06 2016 -0500 |
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| b'@@ -0,0 +1,3039 @@\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 accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/>\n+ </SoftwareName>\n+ </AnalysisSoftware>\n+</AnalysisSoftwareList>\n+<SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">\n+ <DBSequence accession="gi|30794280|ref|NP_851335.1|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq43937">\n+ <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|30794280|ref|NP_851335.1| serum albumin precursor [Bos taurus]" name="protein description"/>\n+ </DBSequence>\n+ <DBSequence accession="XXX_gi|528944676|ref|XP_005204734.1|" searchDatabase_ref="SearchDB_1" length="7610" id="DBSeq65480"/>\n+ <DBSequence accession="gi|528968104|ref|XP_005212567.1|" searchDatabase_ref="SearchDB_1" length="815" id="DBSeq27657">\n+ <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528968104|ref|XP_005212567.1| PREDICTED: exocyst complex component 6B isoform X1 [Bos taurus]" name="protein description"/>\n+ </DBSequence>\n+ <DBSequence accession="gi|528968106|ref|XP_005212568.1|" 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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peptideEvidence_ref="PepEv_46016_70_368"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_46092_70_444"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_46168_70_520"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_46244_70_596"/>\n+ <cvParam accession="MS:1002049" cvRef="PSI-MS" value="-39" name="MS-GF:RawScore"/>\n+ <cvParam accession="MS:1002050" cvRef="PSI-MS" value="80" name="MS-GF:DeNovoScore"/>\n+ <cvParam accession="MS:1002052" cvRef="PSI-MS" value="0.019098723" name="MS-GF:SpecEValue"/>\n+ <cvParam accession="MS:1002053" cvRef="PSI-MS" value="781.5961" 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="9.7370986E-4" name="ExplainedIonCurrentRatio"/>\n+ <userParam value="9.7370986E-4" 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" 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| diff -r 000000000000 -r ee56530a559f test-data/201208-378803-msgf-50ppm-semitryptic-no_mods.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/201208-378803-msgf-50ppm-semitryptic-no_mods.mzid Sun Feb 21 11:04:06 2016 -0500 |
| [ |
| b'@@ -0,0 +1,2619 @@\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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<PeptideEvidenceRef peptideEvidence_ref="PepEv_79447_112_190"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_79654_112_190"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_79832_112_161"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_101180_112_198"/>\n+ <cvParam accession="MS:1002049" cvRef="PSI-MS" value="-53" name="MS-GF:RawScore"/>\n+ <cvParam accession="MS:1002050" cvRef="PSI-MS" value="65" name="MS-GF:DeNovoScore"/>\n+ <cvParam accession="MS:1002052" cvRef="PSI-MS" value="0.0051770797" name="MS-GF:SpecEValue"/>\n+ <cvParam accession="MS:1002053" cvRef="PSI-MS" value="208.82787" 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="0" name="IsotopeError"/>\n+ <userParam value="HCD" name="AssumedDissociationMethod"/>\n+ </SpectrumIdentificationItem>\n+ </SpectrumIdentificationResult>\n+ <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="sample=1 period=1 cycle=1188 experiment=2" id="SIR_5">\n+ <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep113" calculatedMassToCharge="489.1896667480469" experimentalMassToCharge="489.1662292480469" chargeState="3" id="SII_5_1">\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_9796_113_292"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_17407_113_292"/>\n+ <PeptideEvidenceRef peptideEvidence_ref="PepEv_38729_113_216"/>\n+ <cvParam accession="MS:1002049" cvRef="PSI-MS" value="-61" name="MS-GF:RawScore"/>\n+ <cvParam accession="MS:1002050" cvRef="PSI-MS" value="64" name="MS-GF:DeNovoScore"/>\n+ <cvParam accession="MS:1002052" cvRef="PSI-MS" value="0.0058590886" name="MS-GF:SpecEValue"/>\n+ <cvParam accession="MS:1002053" cvRef="PSI-MS" value="234.54517" 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="0" name="IsotopeError"/>\n+ <userParam value="HCD" name="AssumedDissociationMethod"/>\n+ </SpectrumIdentificationItem>\n+ </SpectrumIdentificationResult>\n+ </SpectrumIdentificationList>\n+ </AnalysisData>\n+</DataCollection>\n+</MzIdentML>\n' |
| b |
| diff -r 000000000000 -r ee56530a559f test-data/input/201208-378803.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/201208-378803.mzML Sun Feb 21 11:04:06 2016 -0500 |
| b |
| b'@@ -0,0 +1,5375 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">\n+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="201208-378803-ABRR-AUG-1" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.65.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" 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| diff -r 000000000000 -r ee56530a559f test-data/input/cow.protein.PRG2012-subset.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/cow.protein.PRG2012-subset.fasta Sun Feb 21 11:04:06 2016 -0500 |
| [ |
| b'@@ -0,0 +1,144 @@\n+>gi|528903801|ref|XP_871686.4| PREDICTED: cationic trypsin isoformX1 [Bos taurus]\n+MKTFIFLALLGAAVAFPVDDDDKIVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN\n+>gi|528908802|ref|XP_005199340.1| PREDICTED: zinc finger protein 169 isoform X1 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908804|ref|XP_005199341.1| PREDICTED: zinc finger protein 169 isoform X2 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908806|ref|XP_005199342.1| PREDICTED: zinc finger protein 169 isoform X3 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908808|ref|XP_005199343.1| PREDICTED: zinc finger protein 169 isoform X4 [Bos taurus]\n+MRRVFSRKSTHQTKNMAPGLLTTRDEALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908810|ref|XP_005199344.1| PREDICTED: zinc finger protein 169 isoform X5 [Bos taurus]\n+MSVLDHALMAFRDVAVAFTQKEWKLLSPAQRTLYRDVMLENYSHMVSLGIAFPKPKLIIQLEQGDEPWREESECLLDLCAAEGRKEFQPCLSCPVTFSSPQILHHYMLCGHALQIFPGSSAESHFLLDAPSCLNEKAKDGEREGSGTVFGRLQLSGTSRAFFSSSQGQPVDQGGSSSGRIDQGMISDEADAVLTETNISESGAVICENYRLGFSRKSSLFSLQKHHVCPECGRNFCQKSDLVKHQRTHSGEKPFSCRECGRGFGRRSSLTVHQRKHSGEKPYVCRECGRHFRYTSSLTNHKRIHSGERPFVCQQCGRGFRQKIALILHQRTHLEEKPFVCPECGRGFCQKASLLQHRSSHSGERPFVCLECGRGFRQQSLLLSHQVTHSGEKPYVCAECGHSFRQKVTLIRHQRTHTGEKPYLCSECGRGFSQKVSLMGHQRTHTGEKPYVCSECGRGFGQKVTLIRHQRTHTGEKPFLCPECGRTFGFKSLLTRHKRIHSGEEADVYRVCEQRLGLKIQLTSDQRTHSGEKPCVCDECGRGFGFKSALIRHQRTHSGEKPYVCRDCGRGFSQKSHLHRHRKTKSGHHLLPQELFS\n+>gi|528908812|ref|XP_609847.5| PREDICTED: zinc finger protein 169 isoform X6 [Bos taurus]\n+MAFRDVAVAFTQKEWKLLS'..b'ily 12 member 1 isoform X3 [Bos taurus]\n+MSLNNSSNVFLDSTPSNTNRFQVNVINESHESSAAMNDNADPPHYEETSFGDEGQNRFRISFRPGNQECYDNFLQTGETAKTDASFHAYDSHTNTYYLQTFGHNTVDAVPKIEYYRNTGSVSGPKVNRPSLLDIHEQLAKNVSVAPGSADVVANGEGTPGDEQAENKGEDQAGAVKFGWVKGVLVRCMLNIWGVMLFIRLSWIVGEAGIGLGVIIIGLSVVVTTLTGISMSAICTNGVVRGGGAYYLISRSLGPEFGGSIGLIFAFANAVAVAMYVVGFAETVVDLLKETDSMMVDPTNDIRIIGSITVVILLGISVAGMEWEAKAQVILLIILLIAIANFFIGTVIPSNNEKRARGFFNYQASIFAENFGPSFTKGEGFFSVFAIFFPAATGILAGANISGDLEDPQDAIPKGTMLAIFITTVAYLGVAICVGACVVRDATGSVNDTIISGMNCNGSAACGLGYDFSRCRHEPCQYGLMNNFQVMSMVSGFGPLITAGIFSATLSSALASLVSAPKVFQALCKDNIYKALQFFAKGYGKNNEPLRGYFLTFVIAMAFILIAELNTIAPIISNFFLASYALINFSCFHASYAKSPGWRPAYGIYNMWVSLFGAVLCCAVMFVINWWAAVITYVIEFFLYIYVTYKKPDVNWGSSTQALSYMSALDNALELTTVEDHVKNFRPQCIVLTGGPMTRPALLDITHAFTKNSGLCICCEVFVGPRKLCVKEMNSGMAKKQAWLIKNKIKAFYAAVAADCFRDGVRSLLQASGLGRMKPNTLVIGYKKNWRKAPLTEIENYVGIIHDAFDFEIGVVIVRISQGFDISQVLQVREELEKLEQERLALEATIKDNESEEGNGGIRGLFKKAGKLNITKPTPKKDSSINTIQSMHVGEFNQKLVEASTQFKKKQGKGTIDVWWLFDDGGLILLIPYILTLRKKWKDCKLRIYVGGKINRIEEEKIAMASLLSKFRIKFADIHVIGDINVKPNKESWKVFEEMIEPYCLHESCKDLTTAEKLKRETPWKITDAELEAVKEKSYRQVRLNELLQEHSRAANLIVLSLPVARKGSISDWLYMAWLEILTKNLPPVLLVRGNHKNVLTFYS\n+>gi|297479727|ref|XP_002690982.1| PREDICTED: solute carrier family 12 member 1 isoform X1 [Bos taurus]\n+MSLNNSSNVFLDSTPSNTNRFQVNVINESHESSAAMNDNADPPHYEETSFGDEGQNRFRISFRPGNQECYDNFLQTGETAKTDASFHAYDSHTNTYYLQTFGHNTVDAVPKIEYYRNTGSVSGPKVNRPSLLDIHEQLAKNVSVAPGSADVVANGEGTPGDEQAENKGEDQAGAVKFGWVKGVLVRCMLNIWGVMLFIRLSWIVGEAGIGLGVLIILLSTMVTSITGLSTSAIATNGFVRGGGAYYLISRSLGPEFGGSIGLIFAFANAVAVAMYVVGFAETVVDLLKETDSMMVDPTNDIRIIGSITVVILLGISVAGMEWEAKAQVILLIILLIAIANFFIGTVIPSNNEKRARGFFNYQASIFAENFGPSFTKGEGFFSVFAIFFPAATGILAGANISGDLEDPQDAIPKGTMLAIFITTVAYLGVAICVGACVVRDATGSVNDTIISGMNCNGSAACGLGYDFSRCRHEPCQYGLMNNFQVMSMVSGFGPLITAGIFSATLSSALASLVSAPKVFQALCKDNIYKALQFFAKGYGKNNEPLRGYFLTFVIAMAFILIAELNTIAPIISNFFLASYALINFSCFHASYAKSPGWRPAYGIYNMWVSLFGAVLCCAVMFVINWWAAVITYVIEFFLYIYVTYKKPDVNWGSSTQALSYMSALDNALELTTVEDHVKNFRPQCIVLTGGPMTRPALLDITHAFTKNSGLCICCEVFVGPRKLCVKEMNSGMAKKQAWLIKNKIKAFYAAVAADCFRDGVRSLLQASGLGRMKPNTLVIGYKKNWRKAPLTEIENYVGIIHDAFDFEIGVVIVRISQGFDISQVLQVREELEKLEQERLALEATIKDNESEEGNGGIRGLFKKAGKLNITKPTPKKDSSINTIQSMHVGEFNQKLVEASTQFKKKQGKGTIDVWWLFDDGGLILLIPYILTLRKKWKDCKLRIYVGGKINRIEEEKIAMASLLSKFRIKFADIHVIGDINVKPNKESWKVFEEMIEPYCLHESCKDLTTAEKLKRETPWKITDAELEAVKEKSYRQVRLNELLQEHSRAANLIVLSLPVARKGSISDWLYMAWLEILTKNLPPVLLVRGNHKNVLTFYS\n+>gi|529012038|ref|XP_005226889.1| PREDICTED: pregnancy-associated glycoprotein 2 isoform X1 [Bos taurus]\n+MKWLVLLGLVALSECIVILPLKKMKTLRETLREKNLLNNFLEEQAYRLSKNDSKITIHPLRNYLDTAYVGNITIGTPPQEFRVVFDTGSANLWVPCITCTSPACYTHKTFNPQNSSSFREVGSPITIFYGSGIIQGFLGSDTVRIGNLVSPEQSFGLSLEEYGFDSLPFDGILGLAFPAMGIEDTIPIFDNLWSHGAFSEPVFAFYLNTISMNGTVTACSCGCEALLDTGTSMIYGPTKLVTNIHKLMNARLENSEYVVSCDAVKTLPPVIFNINGIDYPLRPQAYIIKIQNSCRSVFQGGTENSSLNTWILGDIFLRQYFSVFDRKNRRIGLAPAV\n+>gi|156523214|ref|NP_001096021.1| protein KHNYN [Bos taurus]\n+MPTWGAGSPSPDRFAVSAEAEDKVREQLPRVERIFRVGMSVLPKDCPENPHIWLQLEGPKENASRAKEYLKGLCSPELQNEIHYPPKLHCIFLGAQGFFLDCLTWSTSAHLVPGVPGSLMVSGLTEAFVMVQSRVEELVERLSWDFRLGPSPGASQCAGVLREFSALLQARGDAHTEALLQLPQAVQEELLSLVQEASRGQGPQAFPSWGWGGPGPLGAQQQGVRTPLGDGGVSLDTGPTGWQESRGERHAVEKEGTKQGGAREMDLGWKEWPGEEAWERQVAFRPQSGGGEASGGGEAGQAGPPKGKALGKEGVPQERGRLGVQGQPPSTQGPYQRASQLRGASLLQRLHNGEASPPRVPSPPPAPEPPWHCGDRGDRGDRADKQLVVARGRGSPWKRGTRGGNLVTGTQRFQEALQDPFTLCLANVPGKPDLRHIVIDGSNVAMVHGLQHYFSSRGIAIAVQYFWDRGHRDITVFVPQWRFSKDSKVREGHFLHKLYSLSLLSLTPSRVLDGKRISSYDDRFMVKLAEETDGIIVSNDQFRDLAEESEKWMAIIRERLLPFTFVGNLFMVPDDPLGRNGPTLDEFLKKPVRAPGSSKPQQSARGVTEHSNQQQGRKEEEKGNGGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF\n+>gi|28849951|ref|NP_788787.1| pregnancy-associated glycoprotein 2 precursor [Bos taurus]\n+MKWLVLLGLVALSECIVILPLKKMKTLRETLREKNLLNNFLEEQAYRLSKNDSKITIHPLRNYLDTAYVGNITIGTPPQEFRVVFDTGSANLWVPCITCTSPACYTHKTFNPQNSSSFREVGSPITIFYGSGIIQGFLGSDTVRIGNLVSPEQSFGLSLEEYGFDSLPFDGILGLAFPAMGIEDTIPIFDNLWSHGAFSEPVFAFYLNTNKPEGSVVMFGGVDHRYYKGELNWIPVSQTSHWQISMNNISMNGTVTACSCGCEALLDTGTSMIYGPTKLVTNIHKLMNARLENSEYVVSCDAVKTLPPVIFNINGIDYPLRPQAYIIKIQNSCRSVFQGGTENSSLNTWILGDIFLRQYFSVFDRKNRRIGLAPAV\n' |
| b |
| diff -r 000000000000 -r ee56530a559f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Feb 21 11:04:06 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="msgfplus" version="10089"> + <repository changeset_revision="c1863143aa2a" name="package_msgfplus_v10089" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |