Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml

comparison OpenSwathRewriteToFeatureXML.xml @ 0:1e14ca98808b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:57:11 -0500
parents
children 62cc5897c340
comparison
equal deleted inserted replaced
-1:000000000000 0:1e14ca98808b
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.1.0">
5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathRewriteToFeatureXML
14
15 #if $param_csv:
16 -csv $param_csv
17 #end if
18 #if $param_featureXML:
19 -featureXML $param_featureXML
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_FDR_cutoff:
25 -FDR_cutoff $param_FDR_cutoff
26 #end if
27 #if $adv_opts.adv_opts_selector=='advanced':
28 #if $adv_opts.param_force:
29 -force
30 #end if
31 #end if
32 </command>
33 <inputs>
34 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv) "/>
35 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/>
36 <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)"/>
37 <expand macro="advanced_options">
38 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
39 </expand>
40 </inputs>
41 <outputs>
42 <data name="param_out" format="featurexml"/>
43 </outputs>
44 <help>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/doxygen/parameters/output/TOPP_OpenSwathRewriteToFeatureXML.html</help>
48 </tool>