Mercurial > repos > pieterlukasse > prims_masscomb

comparison 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
comparison
equal deleted inserted replaced
3:88495b2a6957 4:b34fb7461546
1 <tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0"> 1 <tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0">
2 <description>MS/MS DB search</description> 2 <description>MS/MS DB search</description>
3 <requirements>
4 <requirement type="set_environment">XTANDEM_12_10_01_PATH</requirement>
5 <requirement type="package" version="12.10011">xtandem</requirement>
6 </requirements>
3 <!-- 7 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter: 8 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 9 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 --> 10 -->
7 <command interpreter="java -jar"> 11 <command interpreter="java -jar">
204 <configfiles> 208 <configfiles>
205 <configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt; 209 <configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
206 &lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"&gt; 210 &lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"&gt;
207 &lt;Files/&gt; 211 &lt;Files/&gt;
208 &lt;Parameters&gt; 212 &lt;Parameters&gt;
209 &lt;Attribute attributeName="xtandemLocation" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-12-10-01-1/bin/" type="Unknown" description=""/&gt; 213 &lt;Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/bin" type="Unknown" description=""/&gt;
210 &lt;Attribute attributeName="database" value="${database}" type="Unknown" description=""/&gt; 214 &lt;Attribute attributeName="database" value="${database}" type="Unknown" description=""/&gt;
211 &lt;Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/&gt; 215 &lt;Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/&gt;
212 &lt;Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/&gt; 216 &lt;Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/&gt;
213 &lt;Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/&gt; 217 &lt;Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/&gt;
214 &lt;Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/&gt; 218 &lt;Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/&gt;