annotate OpenSwathMzMLFileCacher.xml @ 2:fea041417ce2 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

<?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="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="2.2.0">
  <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathMzMLFileCacher

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_type:
  -out_type
  #if " " in str($param_out_type):
    "$param_out_type"
  #else
    $param_out_type
  #end if
#end if
#if $param_convert_back:
  -convert_back
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml,sqMass" optional="False" label="Input mzML file" help="(-in) "/>
    <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
      <option value="mzML">mzML</option>
      <option value="sqMass">sqMass</option>
    </param>
    <param name="param_convert_back" display="radio" type="boolean" truevalue="-convert_back" falsevalue="" checked="false" optional="True" label="Convert back to mzML" help="(-convert_back) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="mzml"/>
  </outputs>
  <help>This tool caches the spectra and chromatogram data of an mzML to disk.


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