annotate IDExtractor.xml @ 9:1b6ca25c12c3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

<?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: [Utilities]-->
<tool id="IDExtractor" name="IDExtractor" version="2.3.0">
  <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
  <macros>
    <token name="@EXECUTABLE@">IDExtractor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[IDExtractor

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_number_of_peptides:
  -number_of_peptides $param_number_of_peptides
#end if
#if $param_number_of_rand_invokations:
  -number_of_rand_invokations $param_number_of_rand_invokations
#end if
#if $param_best_hits:
  -best_hits
#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="idxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_number_of_peptides" type="integer" min="1" optional="True" value="10" label="Number of randomly chosen peptides" help="(-number_of_peptides) "/>
    <param name="param_number_of_rand_invokations" type="integer" min="0" optional="True" value="0" label="Number of rand invocations before random draw" help="(-number_of_rand_invokations) "/>
    <param name="param_best_hits" display="radio" type="boolean" truevalue="-best_hits" falsevalue="" checked="false" optional="True" label="If this flag is set the best n peptides are chosen" help="(-best_hits) "/>
    <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="idxml"/>
  </outputs>
  <help>Extracts 'n' peptides randomly or best 'n' from idXML files.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDExtractor.html</help>
</tool>