Mercurial > repos > pieterlukasse > prims_masscomb

diff masscomb_dbsearch_xtandem.xml @ 4:b34fb7461546

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Putting back old fix
author pieter.lukasse@wur.nl
date Fri, 10 Jan 2014 17:35:38 +0100
parents d6001e8d7441
children 153e9eb5f2ff
line wrap: on
line diff
--- a/masscomb_dbsearch_xtandem.xml	Fri Jan 10 17:03:50 2014 +0100
+++ b/masscomb_dbsearch_xtandem.xml	Fri Jan 10 17:35:38 2014 +0100
@@ -1,5 +1,9 @@
 <tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0">
 	<description>MS/MS DB search</description>
+	<requirements>
+		<requirement type="set_environment">XTANDEM_12_10_01_PATH</requirement>
+		<requirement type="package" version="12.10011">xtandem</requirement>
+	</requirements>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
 	       java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 
@@ -72,7 +76,7 @@
 		<option value="45.987721@C,224.152478@K,224.152478@[">Methylthio + TMT (C,K,nt)</option>
 		<option value="45.987721@C,225.155833@K,225.155833@[">Methylthio + TMT2plex (C,K,nt)</option>
 		<option value="45.987721@C,229.1629328@K,229.1629328@[">Methylthio + TMT6plex (C,K,nt)</option>
-		<option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option>
+		<option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option>
    </param>
       <param name="potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications" help="">
       	<option value="15.994915@M">Oxidation (M)</option>
@@ -206,7 +210,7 @@
 &lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"&gt;
 	&lt;Files/&gt;
 	&lt;Parameters&gt;  
-		  &lt;Attribute attributeName="xtandemLocation" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-12-10-01-1/bin/" type="Unknown" description=""/&gt;
+		  &lt;Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/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;