Mercurial > repos > pieterlukasse > prims_masscomb

diff masscomb_dbsearch_xtandem.xml @ 9:c317e0f939df

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Made converter more robust and added support for mzXML in xtandem interface
author pieter.lukasse@wur.nl
date Fri, 07 Feb 2014 11:41:58 +0100
parents 153e9eb5f2ff
children
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--- 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;