view SeedListGenerator.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: [Quantitation]-->
  <tool id="SeedListGenerator" name="SeedListGenerator" version="2.0.0">
    <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 $rep_param_out:
    #if &quot; &quot; in str(token):
      &quot;$token.param_out&quot;
    #else
      $token.param_out
    #end if
  #end for
#end if
#if $param_use_peptide_mass:
  -use_peptide_mass
#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="xml,consensusxml,mzml" help="(-in) " label="Input file (see below for details)" name="param_in" optional="False" type="data"/>
      <param checked="false" falsevalue="" help="(-use_peptide_mass) " label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" name="param_use_peptide_mass" optional="True" truevalue="-use_peptide_mass" type="boolean"/>
      <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>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>