Mercurial > repos > pieterlukasse > prims_masscomb

comparison 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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8:153e9eb5f2ff 9:c317e0f939df
24 <param name="type" type="select" label="select MS/MS input type"> 24 <param name="type" type="select" label="select MS/MS input type">
25 <option value="single" selected="true">single-File</option> 25 <option value="single" selected="true">single-File</option>
26 <option value="fileSet">fileSet</option> 26 <option value="fileSet">fileSet</option>
27 </param> 27 </param>
28 <when value="single"> 28 <when value="single">
29 <param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/> 29 <param name="inputFile" type="data" format="mzml,mzxml" label="MS/MS input file (mzml or mzxml)"/>
30 </when> 30 </when>
31 <when value="fileSet"> 31 <when value="fileSet">
32 <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/> 32 <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/>
33 </when> 33 </when>
34 </conditional> 34 </conditional>
212 <configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt; 212 <configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
213 &lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"&gt; 213 &lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"&gt;
214 &lt;Files/&gt; 214 &lt;Files/&gt;
215 &lt;Parameters&gt; 215 &lt;Parameters&gt;
216 &lt;Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/bin" type="Unknown" description=""/&gt; 216 &lt;Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/bin" type="Unknown" description=""/&gt;
217 &lt;Attribute attributeName="xtandemLocation_dev" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-13-09-01-1/bin/" type="Unknown" description=""/&gt;
217 &lt;Attribute attributeName="database" value="${database}" type="Unknown" description=""/&gt; 218 &lt;Attribute attributeName="database" value="${database}" type="Unknown" description=""/&gt;
218 &lt;Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/&gt; 219 &lt;Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/&gt;
219 &lt;Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/&gt; 220 &lt;Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/&gt;
220 &lt;Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/&gt; 221 &lt;Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/&gt;
221 &lt;Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/&gt; 222 &lt;Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/&gt;