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comparison OpenSwathRewriteToFeatureXML.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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-1:000000000000 0:3d84209d3178
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="1.12.0">
3 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
4 <macros>
5 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>OpenSwathRewriteToFeatureXML
11
12 -csv ${param_csv}
13 -featureXML ${param_featureXML}
14 -out ${param_out}
15 -FDR_cutoff ${param_FDR_cutoff}
16 -threads \${GALAXY_SLOTS:-24}
17 </command>
18 <inputs>
19 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv)"/>
20 <param name="param_featureXML" type="data" format="featureXML" optional="False" label="input featureXML file" help="(-featureXML)"/>
21 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" help="(-FDR_cutoff)"/>
22 </inputs>
23 <outputs>
24 <data name="param_out" label="output featureXML file" format="featureXML"/>
25 </outputs>
26 <help>**What it does**
27
28 Combines featureXML and mProphet tsv to FDR filtered featureXML.
29
30
31 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html
32
33 @REFERENCES@
34 </help>
35 </tool>