annotate IDScoreSwitcher.xml @ 4:476b5e296979 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab

<?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: [Utilities]-->
<tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="2.2.0">
  <description>Switches between different scores of peptide or protein hits in identification data</description>
  <macros>
    <token name="@EXECUTABLE@">IDScoreSwitcher</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDScoreSwitcher

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_new_score:
  -new_score     "$param_new_score"
#end if
#if $param_new_score_orientation:
  -new_score_orientation
  #if " " in str($param_new_score_orientation):
    "$param_new_score_orientation"
  #else
    $param_new_score_orientation
  #end if
#end if
#if $param_new_score_type:
  -new_score_type     "$param_new_score_type"
#end if
#if $param_old_score:
  -old_score     "$param_old_score"
#end if
#if $param_proteins:
  -proteins
#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_new_score" type="text" size="30" label="Name of the meta value to use as the new score" help="(-new_score) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_new_score_orientation" display="radio" type="select" optional="False" label="Orientation of the new score (are higher or lower values better?)" help="(-new_score_orientation) ">
      <option value="lower_better">lower_better</option>
      <option value="higher_better">higher_better</option>
    </param>
    <param name="param_new_score_type" type="text" size="30" label="Name to use as the type of the new score (default: same as 'new_score')" help="(-new_score_type) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_old_score" type="text" size="30" label="Name to use for the meta value storing the old score (default: old score type)" help="(-old_score) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_proteins" display="radio" type="boolean" truevalue="-proteins" falsevalue="" checked="false" optional="True" label="Apply to protein scores instead of PSM scores" help="(-proteins) "/>
    <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>Switches between different scores of peptide or protein hits in identification data


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