annotate SeedListGenerator.xml @ 0:c82757bc39d7 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Quantitation]-->
<tool id="SeedListGenerator" name="SeedListGenerator" version="2.3.0">
  <description>Generates seed lists for feature detection.</description>
  <macros>
    <token name="@EXECUTABLE@">SeedListGenerator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SeedListGenerator

#if $param_in:
  -in $param_in
#end if

#if $rep_param_out:
-out
  #for token in $rep_param_out:
    #if " " in str(token):
      "$token.param_out"
    #else
      $token.param_out
    #end if
  #end for
#end if
#if $param_use_peptide_mass:
  -use_peptide_mass
#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,idxml,featurexml,consensusxml" optional="False" label="Input file (see below for details)" help="(-in) "/>
    <param name="param_use_peptide_mass" display="radio" type="boolean" truevalue="-use_peptide_mass" falsevalue="" checked="false" optional="True" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help="(-use_peptide_mass) "/>
    <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="featurexml"/>
  </outputs>
  <help>Generates seed lists for feature detection.


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