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comparison OpenSwathRewriteToFeatureXML.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.0.0">
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 #if $param_csv:
13 -csv $param_csv
14 #end if
15 #if $param_featureXML:
16 -featureXML $param_featureXML
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_FDR_cutoff:
22 -FDR_cutoff $param_FDR_cutoff
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
25 #if $adv_opts.adv_opts_selector=='advanced':
26 #if $adv_opts.param_force:
27 -force
28 #end if
29 #end if
30 </command>
31 <inputs>
32 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv) "/>
33 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/>
34 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
35 <expand macro="advanced_options">
36 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
37 </expand>
38 </inputs>
39 <outputs>
40 <data name="param_out" format="featurexml"/>
41 </outputs>
42 <help>**What it does**
43
44 Combines featureXML and mProphet tsv to FDR filtered featureXML.
45
46
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html</help>
48 <expand macro="references"/>
49 </tool>