view OpenSwathRewriteToFeatureXML.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?xml version="1.0" encoding="UTF-8"?>
  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
  <!--Proposed Tool Section: [Targeted Experiments]-->
  <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.0.0">
    <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
    <macros>
      <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>OpenSwathRewriteToFeatureXML

#if $param_csv:
  -csv $param_csv
#end if
#if $param_featureXML:
  -featureXML $param_featureXML
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_FDR_cutoff:
  -FDR_cutoff $param_FDR_cutoff
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="tabular" help="(-csv) " label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" name="param_csv" optional="True" type="data"/>
      <param format="xml" help="(-featureXML) " label="input featureXML file" name="param_featureXML" optional="False" type="data"/>
      <param help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" label="FDR cutoff (" name="param_FDR_cutoff" type="float" value="-1.0"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
    </outputs>
    <help>Combines featureXML and mProphet tsv to FDR filtered featureXML.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html</help>
  </tool>