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Uploaded
author iracooke
date Mon, 03 Mar 2014 19:05:35 -0500
parents
children d3994c3ec487
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, 524 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,7 @@
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,8 @@
+## 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). 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msgfplus_search.xml	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,185 @@
+<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.1">
+    <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 
+        -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
+        #if $pepxml_output_use
+        #else
+        --no-pepxml
+        #end if
+    </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="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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,4 @@
+<?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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.fasta	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,26 @@
+>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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.mzML	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,96 @@
+<?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>
+      <fileContent>
+        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
+        <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
+      </fileContent>
+      <sourceFileList count="1">
+        <sourceFile id="bsa.mgf" name="bsa.mgf" location="file:///">
+          <cvParam cvRef="MS" accession="MS:1000774" name="multiple peak list nativeID format" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001062" name="Mascot MGF file" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="92c6fa5d4ff59e2124950546a651bb9a85bbfd92"/>
+        </sourceFile>
+      </sourceFileList>
+    </fileDescription>
+    <softwareList count="1">
+      <software id="pwiz_3.0.4140" version="3.0.4140">
+        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard" value=""/>
+      </software>
+    </softwareList>
+    <instrumentConfigurationList count="1">
+      <instrumentConfiguration id="IC">
+        <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" value=""/>
+      </instrumentConfiguration>
+    </instrumentConfigurationList>
+    <dataProcessingList count="1">
+      <dataProcessing id="pwiz_Reader_conversion">
+        <processingMethod order="0" softwareRef="pwiz_3.0.4140">
+          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+        </processingMethod>
+        <processingMethod order="1" softwareRef="pwiz_3.0.4140">
+          <userParam name="most intense count (excluding ties at the threshold)" value="100"/>
+        </processingMethod>
+      </dataProcessing>
+    </dataProcessingList>
+    <run id="bsa" defaultInstrumentConfigurationRef="IC">
+      <spectrumList count="1" defaultDataProcessingRef="pwiz_Reader_conversion">
+        <spectrum index="0" id="index=0" defaultArrayLength="97" dataProcessingRef="pwiz_Reader_conversion">
+          <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
+          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000796" name="spectrum title" value="Cmpd 1, +MSn(722.3522), 33.5 min"/>
+          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="198.13402"/>
+          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1280.62643"/>
+          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="21166.0"/>
+          <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="249.17284"/>
+          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="2164.0"/>
+          <scanList count="1">
+            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
+            <scan>
+            </scan>
+          </scanList>
+          <precursorList count="1">
+            <precursor>
+              <selectedIonList count="1">
+                <selectedIon>
+                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="722.35225" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                </selectedIon>
+              </selectedIonList>
+              <activation>
+              </activation>
+            </precursor>
+          </precursorList>
+          <binaryDataArrayList count="2">
+            <binaryDataArray encodedLength="1036">
+              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <binary>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</binary>
+            </binaryDataArray>
+            <binaryDataArray encodedLength="520">
+              <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
+              <binary>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</binary>
+            </binaryDataArray>
+          </binaryDataArrayList>
+        </spectrum>
+      </spectrumList>
+    </run>
+  </mzML>
+  <indexList count="2">
+    <index name="spectrum">
+      <offset idRef="index=0">2685</offset>
+    </index>
+  </indexList>
+  <indexListOffset>7058</indexListOffset>
+  <fileChecksum>b76171188a63cfad075d3738a172b15f1f9e0c4c</fileChecksum>
+</indexedmzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.mzid	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,123 @@
+<?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="2013-06-05T16:52:19" >
+<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 (v9517)" 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="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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/msgfplus_mods.loc.sample	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,50 @@
+#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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pepxml_databases.loc.sample	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,13 @@
+#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_
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 03 19:05:35 2014 -0500
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="protk" version="1.2.6">
+         <repository changeset_revision="bc16eb3ec159" 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="9b21b161ac97" name="package_msgfplus__20140210" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>