Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml

annotate OpenSwathRewriteToFeatureXML.xml @ 0:1e14ca98808b draft

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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
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1e14ca98808b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.1.0">
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5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>OpenSwathRewriteToFeatureXML
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14
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15 #if $param_csv:
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16 -csv $param_csv
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17 #end if
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18 #if $param_featureXML:
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19 -featureXML $param_featureXML
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_FDR_cutoff:
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25 -FDR_cutoff $param_FDR_cutoff
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26 #end if
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27 #if $adv_opts.adv_opts_selector=='advanced':
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28 #if $adv_opts.param_force:
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29 -force
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30 #end if
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31 #end if
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32 </command>
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33 <inputs>
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34 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv) "/>
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35 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/>
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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)"/>
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37 <expand macro="advanced_options">
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38 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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39 </expand>
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40 </inputs>
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41 <outputs>
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42 <data name="param_out" format="featurexml"/>
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43 </outputs>
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44 <help>Combines featureXML and mProphet tsv to FDR filtered featureXML.
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45
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46
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47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/TOPP_OpenSwathRewriteToFeatureXML.html</help>
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48 </tool>