view QCShrinker.xml @ 0:2092c98a7c43 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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="QCShrinker" name="QCShrinker" version="2.1.0">
  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
  <macros>
    <token name="@EXECUTABLE@">QCShrinker</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>QCShrinker

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

#if $rep_param_qp_accessions:
-qp_accessions
  #for token in $rep_param_qp_accessions:
    #if " " in str(token):
      "$token.param_qp_accessions"
    #else
      $token.param_qp_accessions
    #end if
  #end for
#end if
#if $param_name:
  -name     "$param_name"
#end if
#if $param_run:
  -run $param_run
#end if
#if $param_out:
  -out $param_out
#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_qp_accessions" min="0" max="1" title="param_qp_accessions">
      <param name="param_qp_accessions" type="text" size="30" label="A list of cv accessions that should be removed" help="(-qp_accessions) If empty, the usual suspects will be removed!">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_name" type="text" size="30" label="The name of the target run or set that contains the requested quality paramete" help="(-name) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_run" type="data" format="mzml" optional="True" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="(-run) This overrides the name parameter!"/>
    <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="qcml"/>
  </outputs>
  <help>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.


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