view IDMerger.xml @ 12:2d2fc029cea7 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: [File Handling]-->
<tool id="IDMerger" name="IDMerger" version="2.3.0">
  <description>Merges several protein/peptide identification files into one file.</description>
  <macros>
    <token name="@EXECUTABLE@">IDMerger</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[IDMerger

-in
#if $merge.select_merge == 'single':
    #for $token in $merge.param_in:
      $token
    #end for
#else:
    #for $token in $merge.inputs:
      $token.param_in
    #end for
#end if

#if $param_out:
  -out $param_out
#end if
#if $param_add_to:
  -add_to $param_add_to
#end if
#if $param_annotate_file_origin:
  -annotate_file_origin
#end if
#if $param_pepxml_protxml:
  -pepxml_protxml
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
      -force
    #end if
#end if
]]></command>
  <inputs>

    <conditional name="merge">
        <param help="" label="Reduce collections" name="select_merge" type="select">
            <option selected="True" value="single">Reduce collections into one file</option>
            <option value="repeat">Reduce collections, by aggregating single files of multiple collections</option>
        </param>
        <when value="single">
            <param name="param_in" type="data" multiple="True" format="idxml" label="Input files separated by blanks" help="(-in) "/>
        </when>
        <when value="repeat">
           <repeat name="inputs" min="2" title="Input idxml files">
               <param name="param_in" type="data" format="idxml" label="Input file" help="(-in) "/>
           </repeat>
        </when>
    </conditional>
    
    <param name="param_add_to" type="data" format="idxml" optional="True" label="Optional input file" help="(-add_to) IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)"/>
    <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help="(-annotate_file_origin) "/>
    <param name="param_pepxml_protxml" display="radio" type="boolean" truevalue="-pepxml_protxml" falsevalue="" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
    <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>Merges several protein/peptide identification files into one file.


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