# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1391769718 -3600
# Node ID c317e0f939df7570bd2691252de4461c84a6af68
# Parent  153e9eb5f2ff2da726e6bea2449a2ce326e55ab3
Made converter more robust and added support for mzXML in xtandem interface

diff -r 153e9eb5f2ff -r c317e0f939df MassComb.jar
Binary file MassComb.jar has changed
diff -r 153e9eb5f2ff -r c317e0f939df masscomb_dbsearch_converter.xml
--- a/masscomb_dbsearch_converter.xml	Fri Jan 31 12:06:57 2014 +0100
+++ b/masscomb_dbsearch_converter.xml	Fri Feb 07 11:41:58 2014 +0100
@@ -14,6 +14,7 @@
 	    	-isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero
         #end if
 	   -inputFile $fileType.inputFormatType.inputFile 
+	   -outputMsMsFragmentationData $outputMsMsFragmentationData
 	   -outputFile $outputFile 
 	</command>
 	<inputs>
@@ -27,6 +28,7 @@
 	      	<param name="inputFormat" type="select" label="inputFormat">
 		    		<option value="xtandem">X!Tandem</option>
 		    		<option value="omssa">OMSSA</option>
+		    		<option value="proteomediscoverer_pepxml">Proteome Discoverer (pepxml) [beta]</option>
 			</param>
 			<when value="xtandem">
 	      		<param name="inputFile" type="data" format="bioml,xml" label="MS/MS search results" help="Note: the spectra index values in the resulting file will only be reliable for when X!Tandem has executed on MzML data"/>
@@ -38,6 +40,9 @@
 	      	<when value="omssa">
 	      		<param name="inputFile" type="data" format="omx" label="MS/MS search results"/>
 	      	</when>
+	      	<when value="proteomediscoverer_pepxml">
+	      		<param name="inputFile" type="data" format="pepxml" label="MS/MS search results (pepxml)"/>
+	      	</when>
 	      </conditional>
 	    </when>
 	    <when value="fileSet">
@@ -59,6 +64,10 @@
 		      </conditional>
 	    </when>
 	  </conditional>
+	  <param name="outputMsMsFragmentationData" type="boolean" checked="false" 
+	  label="Output MS/MS fragmentation data" 
+	  help="NB: this will add to the output also the fragment ions related to each peptide identification"/>
+     	
 	</inputs>
 	<outputs>
 	  <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} ">
@@ -73,7 +82,7 @@
   
 .. class:: infomark
   
-This tool translates X!Tandem and OMSSA results to mzIdentML format.
+This tool translates X!Tandem, OMSSA or Proteome Discoverer peptide identification results to mzIdentML format.
 It uses the library at http://code.google.com/p/mzidentml-parsers/ 
 -----
 
diff -r 153e9eb5f2ff -r c317e0f939df masscomb_dbsearch_xtandem.xml
--- a/masscomb_dbsearch_xtandem.xml	Fri Jan 31 12:06:57 2014 +0100
+++ b/masscomb_dbsearch_xtandem.xml	Fri Feb 07 11:41:58 2014 +0100
@@ -26,7 +26,7 @@
       <option value="fileSet">fileSet</option>
     </param>
     <when value="single">
-   		<param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/>
+   		<param name="inputFile" type="data" format="mzml,mzxml" label="MS/MS input file (mzml or mzxml)"/>
     </when>
     <when value="fileSet">
       <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/>
@@ -214,6 +214,7 @@
 	&lt;Files/&gt;
 	&lt;Parameters&gt;  
 		  &lt;Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/bin" type="Unknown" description=""/&gt;
+		  &lt;Attribute attributeName="xtandemLocation_dev" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-13-09-01-1/bin/" type="Unknown" description=""/&gt;
 		  &lt;Attribute attributeName="database" value="${database}" type="Unknown" description=""/&gt;
 		  &lt;Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/&gt;
 		  &lt;Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/&gt;