|
0
|
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: "all_peakgroups.xls"" 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>
|
