annotate QCExporter.xml @ 3:c7b430a151c4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d4b74e94ddabaccec6b1c5f9540d074c39207600

<?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="QCExporter" name="QCExporter" version="2.2.0">
  <description>Will extract several qp from several run/sets in a tabular format.</description>
  <macros>
    <token name="@EXECUTABLE@">QCExporter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>QCExporter

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

#if $rep_param_names:
-names
  #for token in $rep_param_names:
    #if " " in str(token):
      "$token.param_names"
    #else
      $token.param_names
    #end if
  #end for
#end if
#if $param_mapping:
  -mapping $param_mapping
#end if
#if $param_out_csv:
  -out_csv $param_out_csv
#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="qcml" optional="False" label="Input qcml file" help="(-in) "/>
    <repeat name="rep_param_names" min="0" max="1" title="param_names">
      <param name="param_names" type="text" size="30" label="The name of the target runs or sets to be exported from" help="(-names) If empty, from all will be exported">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_mapping" type="data" format="tabular" optional="False" label="The mapping of the exported table's headers to the according qp cvs" help="(-mapping) The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported"/>
    <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_csv" format="tabular"/>
  </outputs>
  <help>Will extract several qp from several run/sets in a tabular format.


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