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Uploaded
author iracooke
date Tue, 05 Mar 2013 00:47:39 -0500
parents a5414905da0f
children 16080891c80d
files README repository_dependencies.xml tandem.xml test-data/bsa.fasta test-data/bsa.mzML test-data/bsa.pepXML tool-data/pepxml_databases.loc.sample tool-data/repository_dependencies.xml tool-data/tandem.xml tool-data/tandem_mods.loc.sample tool-data/test-data/bsa.fasta tool-data/test-data/bsa.mzML tool-data/test-data/bsa.pepXML tool-data/tool-data/pepxml_databases.loc.sample tool-data/tool-data/tandem_mods.loc.sample tool-data/tool_dependencies.xml tool_dependencies.xml
diffstat 17 files changed, 0 insertions(+), 905 deletions(-) [+]
line wrap: on
line diff
--- a/README	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-This package installs a wrapper script for the X!Tandem search engine 
-
-Requirements:
-This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages
-Please see instructions for those packages before installing
--- a/repository_dependencies.xml	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<!-- <repositories description="X!Tandem requires Proteomics Datatypes as well the trans proteomic pipeline">
-     <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/>
- </repositories>
- -->
-<repositories description="Proteomics datatypes and the TPP">
- 
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/>
-
-<!-- 	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
- -->
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/>
-
-
- </repositories>
-
--- a/tandem.xml	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,143 +0,0 @@
-<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1">
-
-   <requirements>
-    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
-    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
-   </requirements>
-
-	<description>Run an X!Tandem Search</description>
-
-	<command>
-		#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey 
-		#else #rvm 1.9.3@protk-1.2.0 do tandem_search.rb -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 $allow_multi_isotope_search --keep-params-files
-		
-	</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="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
-
-		<repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<param name="custom_mod" type="text">
-			</param>
-		</repeat>
-		
-		
-		<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
-
-		<repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<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="Trypsin">Trypsin</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="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue="--strict-monoisotopic-mass"/>
-
-	</inputs>
-
-
-	<outputs>
-		<data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
-	</outputs>
-
-	<tests>
-    	<test>
-    		<param name="source_select" value="input_ref"/>
-	      	<param name="fasta_file" value="bsa.fasta"/>
-   		   	<param name="input_file" value="bsa.mzML"/>
-      		<param name="variable_mods" value="15.994915@M"/>
-      		<param name="fixed_mods" value="57.021464@C"/>
-      		<param name="allow_multi_isotope_search" value="false"/>
-      		<output name="output" file="bsa.pepXML" compare="sim_size" delta="100" /> 
-    	</test>
-  	</tests>
-
-
-  <help>
-
-**What it does**
-
-Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
-
-----
-
-**References**
-
-Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
-
-  </help>
-
-</tool>
--- a/test-data/bsa.fasta	Tue Mar 05 00:38:28 2013 -0500
+++ /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 05 00:38:28 2013 -0500
+++ /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>
-      <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	26693" 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>
--- a/test-data/bsa.pepXML	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?>
-<msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2013:02:27:09:50:15" summary_xml="/data/galaxy/galaxy/database/job_working_directory/004/4155//data/galaxy/galaxy/database/files/004/dataset_4786.dat" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">
-   <msms_run_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783.dat" search_engine="X! Tandem (k-score)" raw_data_type="raw" raw_data="mzML">
-      <sample_enzyme name="trypsin">
-<specificity cut="KR" no_cut="P" sense="C"/>
-</sample_enzyme>
-<search_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem" search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
-         <search_database local_path="/data/galaxy/galaxy/database/files/004/dataset_4785.dat" type="AA"/>
-         <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="1"/>
-         <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/>
-         <aminoacid_modification aminoacid="C" massdiff="-17.0265" mass="143.0041" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->
-         <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->
-         <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->
-         
-         <!-- Input parameters -->
-         <parameter name="list path, default parameters" value="/data/galaxy/tools/tpp/default/bin/isb_default_input_kscore.xml"/>
-         <parameter name="list path, taxonomy information" value="/data/galaxy/galaxy/database/files/004/dataset_4783.taxonomy.xml"/>
-         <parameter name="output, histogram column width" value="30"/>
-         <parameter name="output, histograms" value="no"/>
-         <parameter name="output, log path" value=""/>
-         <parameter name="output, maximum valid expectation value" value="0.1"/>
-         <parameter name="output, message" value="1234567890"/>
-         <parameter name="output, one sequence copy" value="no"/>
-         <parameter name="output, parameters" value="yes"/>
-         <parameter name="output, path" value="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem"/>
-         <parameter name="output, path hashing" value="no"/>
-         <parameter name="output, performance" value="yes"/>
-         <parameter name="output, proteins" value="yes"/>
-         <parameter name="output, results" value="all"/>
-         <parameter name="output, sequence path" value=""/>
-         <parameter name="output, sequences" value="no"/>
-         <parameter name="output, sort results by" value="spectrum"/>
-         <parameter name="output, spectra" value="yes"/>
-         <parameter name="output, xsl path" value="tandem-style.xsl"/>
-         <parameter name="protein, C-terminal residue modification mass" value=""/>
-         <parameter name="protein, N-terminal residue modification mass" value=""/>
-         <parameter name="protein, cleavage semi" value="yes"/>
-         <parameter name="protein, cleavage site" value="[RK]|{P}"/>
-         <parameter name="protein, homolog management" value="no"/>
-         <parameter name="protein, modified residue mass file" value=""/>
-         <parameter name="protein, taxon" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/>
-         <parameter name="refine" value="no"/>
-         <parameter name="refine, maximum valid expectation value" value="0.1"/>
-         <parameter name="refine, sequence path" value=""/>
-         <parameter name="refine, spectrum synthesis" value="yes"/>
-         <parameter name="residue, modification mass" value="57.021464@C"/>
-         <parameter name="residue, potential modification mass" value=""/>
-         <parameter name="residue, potential modification motif" value=""/>
-         <parameter name="scoring, a ions" value="no"/>
-         <parameter name="scoring, algorithm" value="k-score"/>
-         <parameter name="scoring, b ions" value="yes"/>
-         <parameter name="scoring, c ions" value="no"/>
-         <parameter name="scoring, cyclic permutation" value="no"/>
-         <parameter name="scoring, include reverse" value="no"/>
-         <parameter name="scoring, maximum missed cleavage sites" value="2"/>
-         <parameter name="scoring, minimum ion count" value="1"/>
-         <parameter name="scoring, x ions" value="no"/>
-         <parameter name="scoring, y ions" value="yes"/>
-         <parameter name="scoring, z ions" value="no"/>
-         <parameter name="spectrum, dynamic range" value="10000.0"/>
-         <parameter name="spectrum, fragment mass type" value="monoisotopic"/>
-         <parameter name="spectrum, fragment monoisotopic mass error" value="0.65"/>
-         <parameter name="spectrum, fragment monoisotopic mass error units" value="Daltons"/>
-         <parameter name="spectrum, maximum parent charge" value="5"/>
-         <parameter name="spectrum, minimum fragment mz" value="125.0"/>
-         <parameter name="spectrum, minimum parent m+h" value="600.0"/>
-         <parameter name="spectrum, minimum peaks" value="10"/>
-         <parameter name="spectrum, parent monoisotopic mass error minus" value="50.0"/>
-         <parameter name="spectrum, parent monoisotopic mass error plus" value="50.0"/>
-         <parameter name="spectrum, parent monoisotopic mass error units" value="ppm"/>
-         <parameter name="spectrum, parent monoisotopic mass isotope error" value="no"/>
-         <parameter name="spectrum, path" value="/data/galaxy/galaxy/database/files/004/dataset_4783.dat"/>
-         <parameter name="spectrum, sequence batch size" value="1000"/>
-         <parameter name="spectrum, threads" value="1"/>
-         <parameter name="spectrum, total peaks" value="400"/>
-         <parameter name="spectrum, use conditioning" value="no"/>
-         <parameter name="spectrum, use noise suppression" value="yes"/>
-         <!-- Unused input parameters -->
-         <parameter name="refine, cleavage semi" value="yes"/>
-         <parameter name="refine, modification mass" value="57.012@C"/>
-         <parameter name="refine, point mutations" value="no"/>
-         <parameter name="refine, potential C-terminus modifications" value=""/>
-         <parameter name="refine, potential N-terminus modifications" value=""/>
-         <parameter name="refine, potential modification mass" value="15.994915@M"/>
-         <parameter name="refine, potential modification motif" value=""/>
-         <parameter name="refine, tic percent" value="10"/>
-         <parameter name="refine, unanticipated cleavage" value="no"/>
-         <parameter name="refine, use potential modifications for full refinement" value="no"/>
-         <parameter name="scoring, pluggable scoring" value="yes"/>
-         <!-- Performance parameters -->
-         <parameter name="list path, sequence source #1" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/>
-         <parameter name="list path, sequence source description #1" value="no description"/>
-         <parameter name="modelling, spectrum noise suppression ratio" value="0.00"/>
-         <parameter name="modelling, total peptides used" value="1"/>
-         <parameter name="modelling, total proteins used" value="2"/>
-         <parameter name="modelling, total spectra used" value="1"/>
-         <parameter name="process, start time" value="2013:02:27:09:50:15"/>
-         <parameter name="process, version" value="x! tandem 2010.10.01.1 (LabKey, Insilicos and ISB)"/>
-         <parameter name="quality values" value="0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/>
-         <parameter name="refining, # input models" value="0"/>
-         <parameter name="refining, # input spectra" value="0"/>
-         <parameter name="refining, # partial cleavage" value="0"/>
-         <parameter name="refining, # point mutations" value="0"/>
-         <parameter name="refining, # potential C-terminii" value="0"/>
-         <parameter name="refining, # potential N-terminii" value="0"/>
-         <parameter name="refining, # unanticipated cleavage" value="0"/>
-         <parameter name="timing, initial modelling total (sec)" value="0.00"/>
-         <parameter name="timing, initial modelling/spectrum (sec)" value="0.000"/>
-         <parameter name="timing, load sequence models (sec)" value="0.00"/>
-         <parameter name="timing, refinement/spectrum (sec)" value="0.000"/>
-      </search_summary>
-      
-      <spectrum_query spectrum="dataset_4783.dat.00000.00000.2" start_scan="0" end_scan="0" precursor_neutral_mass="1442.6899" assumed_charge="2" index="1">
-      <search_result>
-         <search_hit hit_rank="1" peptide="YICDNQDTISSK" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|ALBU_BOVIN|" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="22" calc_neutral_pep_mass="1442.6347" massdiff="0.055" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
-            <modification_info>
-               <mod_aminoacid_mass position="3" mass="160.0306"/>
-            </modification_info>
-            <search_score name="hyperscore" value="491"/>
-            <search_score name="nextscore" value="287"/>
-            <search_score name="bscore" value="0"/>
-            <search_score name="yscore" value="2"/>
-            <search_score name="cscore" value="0"/>
-            <search_score name="zscore" value="0"/>
-            <search_score name="ascore" value="0"/>
-            <search_score name="xscore" value="0"/>
-            <search_score name="expect" value="0.12"/>
-         </search_hit>
-      </search_result>
-      </spectrum_query>
-   </msms_run_summary>
-</msms_pipeline_analysis>
--- a/tool-data/pepxml_databases.loc.sample	Tue Mar 05 00:38:28 2013 -0500
+++ /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-data/repository_dependencies.xml	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<!-- <repositories description="X!Tandem requires Proteomics Datatypes as well the trans proteomic pipeline">
-     <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/>
- </repositories>
- -->
-<repositories description="X!Tandem requires Proteomics Datatypes as well the trans proteomic pipeline">
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="c10a62c886b8"/>
- </repositories>
\ No newline at end of file
--- a/tool-data/tandem.xml	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,143 +0,0 @@
-<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0">
-
-   <requirements>
-    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
-    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
-   </requirements>
-
-	<description>Run an X!Tandem Search</description>
-
-	<command>
-		#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey 
-		#else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -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 $allow_multi_isotope_search --keep-params-files
-		
-	</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="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
-
-		<repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<param name="custom_mod" type="text">
-			</param>
-		</repeat>
-		
-		
-		<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
-
-		<repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<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="Trypsin">Trypsin</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="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue="--strict-monoisotopic-mass"/>
-
-	</inputs>
-
-
-	<outputs>
-		<data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
-	</outputs>
-
-	<tests>
-    	<test>
-    		<param name="source_select" value="input_ref"/>
-	      	<param name="fasta_file" value="bsa.fasta"/>
-   		   	<param name="input_file" value="bsa.mzML"/>
-      		<param name="variable_mods" value="15.994915@M"/>
-      		<param name="fixed_mods" value="57.021464@C"/>
-      		<param name="allow_multi_isotope_search" value="false"/>
-      		<output name="output" file="bsa.pepXML" compare="sim_size" delta="100" /> 
-    	</test>
-  	</tests>
-
-
-  <help>
-
-**What it does**
-
-Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
-
-----
-
-**References**
-
-Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
-
-  </help>
-
-</tool>
--- a/tool-data/tandem_mods.loc.sample	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-#This file lists the names of inbuilt chemical modifications accepted by X!Tandem
-#
-#
-Carbamidomethyl C	carbamidomethyl_c_	57.021464@C	carbamidomethyl_c_
-Glycocapture-N	glycocapture_n_	0.998@N!{P}[ST]	glycocapture_n_
-Oxidation M	oxidation_m_	15.994915@M	oxidation_m_
\ No newline at end of file
--- a/tool-data/test-data/bsa.fasta	Tue Mar 05 00:38:28 2013 -0500
+++ /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/tool-data/test-data/bsa.mzML	Tue Mar 05 00:38:28 2013 -0500
+++ /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>
-      <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	26693" 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"/>
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-            </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>
--- a/tool-data/test-data/bsa.pepXML	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?>
-<msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2013:02:27:09:50:15" summary_xml="/data/galaxy/galaxy/database/job_working_directory/004/4155//data/galaxy/galaxy/database/files/004/dataset_4786.dat" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">
-   <msms_run_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783.dat" search_engine="X! Tandem (k-score)" raw_data_type="raw" raw_data="mzML">
-      <sample_enzyme name="trypsin">
-<specificity cut="KR" no_cut="P" sense="C"/>
-</sample_enzyme>
-<search_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem" search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
-         <search_database local_path="/data/galaxy/galaxy/database/files/004/dataset_4785.dat" type="AA"/>
-         <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="1"/>
-         <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/>
-         <aminoacid_modification aminoacid="C" massdiff="-17.0265" mass="143.0041" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->
-         <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->
-         <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->
-         
-         <!-- Input parameters -->
-         <parameter name="list path, default parameters" value="/data/galaxy/tools/tpp/default/bin/isb_default_input_kscore.xml"/>
-         <parameter name="list path, taxonomy information" value="/data/galaxy/galaxy/database/files/004/dataset_4783.taxonomy.xml"/>
-         <parameter name="output, histogram column width" value="30"/>
-         <parameter name="output, histograms" value="no"/>
-         <parameter name="output, log path" value=""/>
-         <parameter name="output, maximum valid expectation value" value="0.1"/>
-         <parameter name="output, message" value="1234567890"/>
-         <parameter name="output, one sequence copy" value="no"/>
-         <parameter name="output, parameters" value="yes"/>
-         <parameter name="output, path" value="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem"/>
-         <parameter name="output, path hashing" value="no"/>
-         <parameter name="output, performance" value="yes"/>
-         <parameter name="output, proteins" value="yes"/>
-         <parameter name="output, results" value="all"/>
-         <parameter name="output, sequence path" value=""/>
-         <parameter name="output, sequences" value="no"/>
-         <parameter name="output, sort results by" value="spectrum"/>
-         <parameter name="output, spectra" value="yes"/>
-         <parameter name="output, xsl path" value="tandem-style.xsl"/>
-         <parameter name="protein, C-terminal residue modification mass" value=""/>
-         <parameter name="protein, N-terminal residue modification mass" value=""/>
-         <parameter name="protein, cleavage semi" value="yes"/>
-         <parameter name="protein, cleavage site" value="[RK]|{P}"/>
-         <parameter name="protein, homolog management" value="no"/>
-         <parameter name="protein, modified residue mass file" value=""/>
-         <parameter name="protein, taxon" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/>
-         <parameter name="refine" value="no"/>
-         <parameter name="refine, maximum valid expectation value" value="0.1"/>
-         <parameter name="refine, sequence path" value=""/>
-         <parameter name="refine, spectrum synthesis" value="yes"/>
-         <parameter name="residue, modification mass" value="57.021464@C"/>
-         <parameter name="residue, potential modification mass" value=""/>
-         <parameter name="residue, potential modification motif" value=""/>
-         <parameter name="scoring, a ions" value="no"/>
-         <parameter name="scoring, algorithm" value="k-score"/>
-         <parameter name="scoring, b ions" value="yes"/>
-         <parameter name="scoring, c ions" value="no"/>
-         <parameter name="scoring, cyclic permutation" value="no"/>
-         <parameter name="scoring, include reverse" value="no"/>
-         <parameter name="scoring, maximum missed cleavage sites" value="2"/>
-         <parameter name="scoring, minimum ion count" value="1"/>
-         <parameter name="scoring, x ions" value="no"/>
-         <parameter name="scoring, y ions" value="yes"/>
-         <parameter name="scoring, z ions" value="no"/>
-         <parameter name="spectrum, dynamic range" value="10000.0"/>
-         <parameter name="spectrum, fragment mass type" value="monoisotopic"/>
-         <parameter name="spectrum, fragment monoisotopic mass error" value="0.65"/>
-         <parameter name="spectrum, fragment monoisotopic mass error units" value="Daltons"/>
-         <parameter name="spectrum, maximum parent charge" value="5"/>
-         <parameter name="spectrum, minimum fragment mz" value="125.0"/>
-         <parameter name="spectrum, minimum parent m+h" value="600.0"/>
-         <parameter name="spectrum, minimum peaks" value="10"/>
-         <parameter name="spectrum, parent monoisotopic mass error minus" value="50.0"/>
-         <parameter name="spectrum, parent monoisotopic mass error plus" value="50.0"/>
-         <parameter name="spectrum, parent monoisotopic mass error units" value="ppm"/>
-         <parameter name="spectrum, parent monoisotopic mass isotope error" value="no"/>
-         <parameter name="spectrum, path" value="/data/galaxy/galaxy/database/files/004/dataset_4783.dat"/>
-         <parameter name="spectrum, sequence batch size" value="1000"/>
-         <parameter name="spectrum, threads" value="1"/>
-         <parameter name="spectrum, total peaks" value="400"/>
-         <parameter name="spectrum, use conditioning" value="no"/>
-         <parameter name="spectrum, use noise suppression" value="yes"/>
-         <!-- Unused input parameters -->
-         <parameter name="refine, cleavage semi" value="yes"/>
-         <parameter name="refine, modification mass" value="57.012@C"/>
-         <parameter name="refine, point mutations" value="no"/>
-         <parameter name="refine, potential C-terminus modifications" value=""/>
-         <parameter name="refine, potential N-terminus modifications" value=""/>
-         <parameter name="refine, potential modification mass" value="15.994915@M"/>
-         <parameter name="refine, potential modification motif" value=""/>
-         <parameter name="refine, tic percent" value="10"/>
-         <parameter name="refine, unanticipated cleavage" value="no"/>
-         <parameter name="refine, use potential modifications for full refinement" value="no"/>
-         <parameter name="scoring, pluggable scoring" value="yes"/>
-         <!-- Performance parameters -->
-         <parameter name="list path, sequence source #1" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/>
-         <parameter name="list path, sequence source description #1" value="no description"/>
-         <parameter name="modelling, spectrum noise suppression ratio" value="0.00"/>
-         <parameter name="modelling, total peptides used" value="1"/>
-         <parameter name="modelling, total proteins used" value="2"/>
-         <parameter name="modelling, total spectra used" value="1"/>
-         <parameter name="process, start time" value="2013:02:27:09:50:15"/>
-         <parameter name="process, version" value="x! tandem 2010.10.01.1 (LabKey, Insilicos and ISB)"/>
-         <parameter name="quality values" value="0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/>
-         <parameter name="refining, # input models" value="0"/>
-         <parameter name="refining, # input spectra" value="0"/>
-         <parameter name="refining, # partial cleavage" value="0"/>
-         <parameter name="refining, # point mutations" value="0"/>
-         <parameter name="refining, # potential C-terminii" value="0"/>
-         <parameter name="refining, # potential N-terminii" value="0"/>
-         <parameter name="refining, # unanticipated cleavage" value="0"/>
-         <parameter name="timing, initial modelling total (sec)" value="0.00"/>
-         <parameter name="timing, initial modelling/spectrum (sec)" value="0.000"/>
-         <parameter name="timing, load sequence models (sec)" value="0.00"/>
-         <parameter name="timing, refinement/spectrum (sec)" value="0.000"/>
-      </search_summary>
-      
-      <spectrum_query spectrum="dataset_4783.dat.00000.00000.2" start_scan="0" end_scan="0" precursor_neutral_mass="1442.6899" assumed_charge="2" index="1">
-      <search_result>
-         <search_hit hit_rank="1" peptide="YICDNQDTISSK" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|ALBU_BOVIN|" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="22" calc_neutral_pep_mass="1442.6347" massdiff="0.055" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
-            <modification_info>
-               <mod_aminoacid_mass position="3" mass="160.0306"/>
-            </modification_info>
-            <search_score name="hyperscore" value="491"/>
-            <search_score name="nextscore" value="287"/>
-            <search_score name="bscore" value="0"/>
-            <search_score name="yscore" value="2"/>
-            <search_score name="cscore" value="0"/>
-            <search_score name="zscore" value="0"/>
-            <search_score name="ascore" value="0"/>
-            <search_score name="xscore" value="0"/>
-            <search_score name="expect" value="0.12"/>
-         </search_hit>
-      </search_result>
-      </spectrum_query>
-   </msms_run_summary>
-</msms_pipeline_analysis>
--- a/tool-data/tool-data/pepxml_databases.loc.sample	Tue Mar 05 00:38:28 2013 -0500
+++ /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-data/tool-data/tandem_mods.loc.sample	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-#This file lists the names of inbuilt chemical modifications accepted by X!Tandem
-#
-#
-Carbamidomethyl C	carbamidomethyl_c_	57.021464@C	carbamidomethyl_c_
-Glycocapture-N	glycocapture_n_	0.998@N!{P}[ST]	glycocapture_n_
-Oxidation M	oxidation_m_	15.994915@M	oxidation_m_
\ No newline at end of file
--- a/tool-data/tool_dependencies.xml	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-<!--     <package name="galaxy_protk" version="1.1.9">
-	     <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/>
-    </package>
-
-    <package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://10.211.55.28:9009" name="protk_tpp" owner="iracooke" changeset_revision="e44f0d3bb9dd" />
-    </package>
- -->
-    <package name="galaxy_protk" version="1.1.9">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
-    </package>
-
-    <package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297" />
-    </package>
-
-
-
-</tool_dependency>
\ No newline at end of file
--- a/tool_dependencies.xml	Tue Mar 05 00:38:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-<!--     <package name="galaxy_protk" version="1.2.0">
-	     <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/>
-    </package>
-
-    <package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://10.211.55.28:9009" name="protk_tpp" owner="iracooke" changeset_revision="e44f0d3bb9dd" />
-    </package>
- -->
-    <package name="galaxy_protk" version="1.2.0">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
-    </package>
-
-    <package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" />
-    </package>
-
-
-
-</tool_dependency>
\ No newline at end of file