Mercurial > repos > iracooke > msgfplus
changeset 7:9ee2e20c6f1a draft
Uploaded
| author | simonalpha |
|---|---|
| date | Mon, 05 Jan 2015 17:17:32 -0500 |
| parents | 79ed4588f7ae |
| children | dfb2b78b3aff |
| files | README README.md msgfplus_search.xml repository_dependencies.xml test-data/bsa.fasta test-data/bsa.mzML test-data/bsa.mzid tool-data/msgfplus_mods.loc.sample tool-data/pepxml_databases.loc.sample tool_dependencies.xml |
| diffstat | 10 files changed, 0 insertions(+), 527 deletions(-) [+] |
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--- a/README Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -This package is a galaxy wrapper for the MSGF+ search tool. - -Requirements: -This package depends on the galaxy_protk, protk_msgfplus, protk_proteowizard packages -Please see instructions for those packages before installing - -In addition to basic requirements you must also have unzip and java 6 runtime (or greater) installed
--- a/README.md Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -## What is it? -Galaxy tool definition file and wrapper scripts for the [MSGF+ Search Engine](http://proteomics.ucsd.edu/Software/MSGFPlus.html). - -## Installation -Install from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ - -Depends on command-line scripts and databases available in the [protk ruby gem](https://bitbucket.org/iracooke/protk). -
--- a/msgfplus_search.xml Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,188 +0,0 @@ -<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.2"> - <description>Run an MSGF+ Search</description> - <requirements> - <requirement type="package" version="1.2.6">protk</requirement> - <requirement type="package" version="20140210">msgfplus</requirement> - <requirement type="package" version="3_0_4388">proteowizard</requirement> - </requirements> - <command> - msgfplus_search.rb - #if $database.source_select=="built_in": - --galaxy -d $database.dbkey - #else - --galaxy -d $database.fasta_file - #end if - - --var-mods=' - $variable_mods - #for $custom_variable_mod in $custom_variable_mods: - ,${custom_variable_mod.custom_mod} - #end for - ' - - --fix-mods=' - $fixed_mods - #for $custom_fix_mod in $custom_fix_mods: - ,${custom_fix_mod.custom_mod} - #end for - ' - - $input_file - -o $output - -r - --enzyme=$enzyme - --precursor-ion-tol-units=$precursor_tolu - -v $missed_cleavages - $cleavage_semi - -f $fragment_ion_tol - -p $precursor_ion_tol - --instrument=$instrument - --isotope-error-range=$isotope_error_range - --fragment-method=$fragment_method - --protocol=$protocol - --min-pep-len=$min_pep_len - --max-pep-len=$max_pep_len - --max-pep-charge=$max_pep_charge - --min-pep-charge=$min_pep_charge - --num-reported-matches=$num_reported_matches - --java-mem=$java_mem - #unless $pepxml_output_use: - --no-pepxml - #end unless - </command> - - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option value="input_ref">Your Upload File</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> - <options from_file="msgfplus_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - <repeat name="custom_variable_mods" title="Custom Variable Modifications" - help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these"> - <param name="custom_mod" type="text" /> - </repeat> - <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed"> - <options from_file="msgfplus_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these"> - <param name="custom_mod" type="text"> - </param> - </repeat> - <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> - <label>Missed Cleavages Allowed</label> - <option value="0">0</option> - <option value="1">1</option> - <option value="2">2</option> - </param> - - <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" /> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="0">unspecific cleavage</option> - <option value="1">Trypsin</option> - <option value="2">Chymotrypsin</option> - <option value="3">Lys-C</option> - <option value="4">Lys-N</option> - <option value="5">glutamyl endopeptidase</option> - <option value="6">Arg-C</option> - <option value="7">Asp-N</option> - <option value="8">alphaLP</option> - <option value="9">no cleavage</option> - </param> - - <param name="instrument" type="select" format="text"> - <label>Instrument Type</label> - <option value="2">TOF</option> - <option value="0">Low-res LCQ/LTQ</option> - <option value="1">High-res LTQ</option> - </param> - - <param name="fragment_method" type="select" format="text"> - <label>Fragmentation Method</label> - <option value="0">Respect Input File</option> - <option value="1">CID</option> - <option value="2">ETD</option> - <option value="3">HCD</option> - <option value="4">Merge spectra from same precursor</option> - </param> - - <param name="protocol" type="select" format="text"> - <label>Protocol</label> - <option value="0">NoProtocol</option> - <option value="1">Phosphorylation</option> - <option value="2">iTRAQ</option> - <option value="3">iTRAQPhospho</option> - </param> - - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> - - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> - <param name="precursor_tolu" type="select" format="text"> - <label>Precursor Ion Tolerance Units</label> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - - <param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/> - <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/> - <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/> - <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/> - <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> - <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/> - <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/> - <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> - </inputs> - <outputs> - <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"> - <change_format> - <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file" - label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="source_select" value="input_ref"/> - <param name="fasta_file" value="bsa.fasta"/> - <param name="input_file" value="bsa.mzML"/> - <output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> - </test> - </tests> - <help> - -**What it does** - -Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. - ----- - -**References** - -Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm - - </help> -</tool>
--- a/repository_dependencies.xml Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes, MSGF+ and Protk"> - <repository changeset_revision="7101f7e4b00b" name="proteomics_datatypes" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </repositories>
--- a/test-data/bsa.fasta Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ ->sp|ALBU_BOVIN| -MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIA -FSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCK -VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF -KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC -LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE -FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE -CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL -GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL -KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS -RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC -TESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQT -ALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV -STQTALA ->sp|AMYS_HUMAN| -MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPK -GFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTR -CNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWD -FNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNH -LIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVI -DLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWG -FMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGF -TRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCE -HRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWT -FSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAED -PFIAIHAESKL \ No newline at end of file
--- a/test-data/bsa.mzML Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -<?xml version="1.0" encoding="ISO-8859-1"?> -<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/mzML1.1.1_idx.xsd"> - <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="bsa" version="1.1.0"> - <cvList count="2"> - <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.30.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> - <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/> - </cvList> - <fileDescription> - 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<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="sp|ALBU_BOVIN|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq1"> - <cvParam accession="MS:1001088" cvRef="PSI-MS" value="sp|ALBU_BOVIN|" name="protein description"/> - </DBSequence> - <Peptide id="Pep1"> - <PeptideSequence>YICDNQDTISSK</PeptideSequence> - <Modification monoisotopicMassDelta="57.021463735" location="3"> - <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/> - </Modification> - </Peptide> - <PeptideEvidence isDecoy="false" post="L" pre="K" end="297" start="286" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_286_1_286"/> -</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 analysisSoftware_ref="ID_software" id="SearchProtocol_1"> - <SearchType> - <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/> - </SearchType> - <AdditionalSearchParams> - <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/> - <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/> - <userParam value="false" name="TargetDecoyApproach"/> - <userParam value="0" name="MinIsotopeError"/> - <userParam value="1" name="MaxIsotopeError"/> - <userParam value="As written in the spectrum or CID if no info" name="FragmentMethod"/> - <userParam value="LowRes" name="Instrument"/> - <userParam value="NoProtocol" name="Protocol"/> - <userParam value="2" name="NumTolerableTermini"/> - <userParam value="1" name="NumMatchesPerSpec"/> - <userParam value="6" name="MinPepLength"/> - <userParam value="40" name="MaxPepLength"/> - <userParam value="2" name="MinCharge"/> - <userParam value="3" name="MaxCharge"/> - </AdditionalSearchParams> - <ModificationParams> - <SearchModification residues="C" massDelta="57.021465" fixedMod="true"> - <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/> - </SearchModification> - </ModificationParams> - <Enzymes> - <Enzyme missedCleavages="1000" semiSpecific="false" 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="200.0" name="search tolerance plus value"/> - <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="200.0" 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="2" location="/Users/iracooke/Sources/protk-wk/bsa.fasta" id="SearchDB_1"> - <FileFormat> - <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/> - </FileFormat> - <DatabaseName> - <userParam name="bsa.fasta"/> - </DatabaseName> - </SearchDatabase> - <SpectraData location="/Users/iracooke/Sources/protk-wk/bsa.mzML" name="bsa.mzML" id="SID_1"> - <FileFormat> - <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/> - </FileFormat> - <SpectrumIDFormat> - <cvParam accession="MS:1000774" cvRef="PSI-MS" name="multiple peak list nativeID format"/> - </SpectrumIDFormat> - </SpectraData> - </Inputs> - <AnalysisData> - <SpectrumIdentificationList id="SI_LIST_1"> - <FragmentationTable> - <Measure id="Measure_MZ"> - <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/> - </Measure> - </FragmentationTable> - <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="index=0" id="SIR_1"> - <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="722.3251953125" experimentalMassToCharge="722.3522338867188" chargeState="2" id="SII_1_1"> - <PeptideEvidenceRef peptideEvidence_ref="PepEv_286_1_286"/> - <cvParam accession="MS:1002049" cvRef="PSI-MS" value="21" name="MS-GF:RawScore"/> - <cvParam accession="MS:1002050" cvRef="PSI-MS" value="71" name="MS-GF:DeNovoScore"/> - <cvParam accession="MS:1002052" cvRef="PSI-MS" value="2.0246382E-9" name="MS-GF:SpecEValue"/> - <cvParam accession="MS:1002053" cvRef="PSI-MS" value="2.2635456E-6" name="MS-GF:EValue"/> - <userParam value="0" name="IsotopeError"/> - <userParam value="CID" name="AssumedDissociationMethod"/> - <userParam value="0.5818614" name="ExplainedIonCurrentRatio"/> - <userParam value="0.12558742" name="NTermIonCurrentRatio"/> - <userParam value="0.45627397" name="CTermIonCurrentRatio"/> - <userParam value="18513.0" name="MS2IonCurrent"/> - <userParam value="61.02686" name="MeanErrorAll"/> - <userParam value="64.35494" name="StdevErrorAll"/> - <userParam value="88.56576" name="MeanErrorTop7"/> - <userParam value="86.03032" name="StdevErrorTop7"/> - </SpectrumIdentificationItem> - </SpectrumIdentificationResult> - </SpectrumIdentificationList> - </AnalysisData> -</DataCollection> -</MzIdentML>
--- a/tool-data/msgfplus_mods.loc.sample Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -#This file lists the names of inbuilt chemical modifications accepted by msgfplus -#Each entry consists of 4 tab separated fields like this -#<Displayed Name> <DBKey> <Modification String> <DBKey> -# -#Modification strings should conform to the standard MSGFPlus syntax with the following exception -#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods -#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType -#value -# -#Standard MSGFPlus syntax is -# -# To input a modification, use the following command: -# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required). -# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num]) -# - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed. -# - Atom can be omitted. The sequence of atoms must be followed. -# - Negative numbers are allowed. -# - E.g. C2H2O1 (valid), H2C1O1 (invalid) -# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient). -# - E.g. 15.994915 -# Residues: affected amino acids (must be upper letters) -# - Must be uppor letters or * -# - Use * if this modification is applicable to any residue. -# - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) -# - E.g. NQ, * -# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive) -# Position: position in the peptide where the modification can be attached. -# - One of the following five values should be used: -# - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) -# - Case insensitive -# - "-" can be omitted -# - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid -# Name: name of the modification (Unimod PSI-MS name) -# - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name -# - E.g. Phospho, Acetyl -#C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C -# Variable Modifications (default: none) -#O1,M,opt,any,Oxidation # Oxidation M -#15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr) -#H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed. -#C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term -#H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E -#H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q -#C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term -#C2H2O1,K,opt,any,Acetyl # Acetylation K -#CH2,K,opt,any,Methy # Methylation K -#HO3P,STY,opt,any,Phospho # Phosphorylation STY - -Carbamidomethyl C carbamidomethyl_c_ C2H3N1O1,C,opt,any,Carbamidomethyl carbamidomethyl_c_ -Oxidation M oxidation_m_ O1,M,opt,any,Oxidation oxidation_m_ \ No newline at end of file
--- a/tool-data/pepxml_databases.loc.sample Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#This file lists the names of protein databases installed locally in protk. -# These are used by omssa and x!tandem as well as the "mascot to pepxml" tool -# In order to combine search results with Interprophet searches must be run against an identical database -# -# Entries should follow the be structured as follows -# Display_name omssa_tandem_dbname dbkey -# -# -Swissprot spall_ spall spall_ -Combined PlasmboDB (falciparum) and Swissprot Human plasmodb_pfalciparum_sphuman_ plasmodb_pfalciparum_sphuman plasmodb_pfalciparum_sphuman_ -Swissprot Human sphuman_ sphuman sphuman_ -Combined Swissprot/TRembl Human sptrhuman_ sptrhuman sptrhuman_ -Swissprot Mouse spmouse_ spmouse spmouse_
--- a/tool_dependencies.xml Tue Mar 18 19:46:10 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="protk" version="1.2.6"> - <repository changeset_revision="1b21ba7de3e7" name="package_protk_1_2_6" owner="iracooke" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="proteowizard" version="3_0_4388"> - <repository changeset_revision="a2cbef24e9fd" name="package_proteowizard_3_0_4388" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="msgfplus" version="20140210"> - <repository changeset_revision="7d614a857e51" name="package_msgfplus_20140210" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>