annotate QCExtractor.xml @ 1:6c4b0427c053 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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="QCExtractor" name="QCExtractor" version="2.2.0">
  <description>Extracts a table attachment to a given qc parameter.</description>
  <macros>
    <token name="@EXECUTABLE@">QCExtractor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>QCExtractor

#if $param_in:
  -in $param_in
#end if
#if $param_qp:
  -qp     "$param_qp"
#end if
#if $param_run:
  -run $param_run
#end if
#if $param_name:
  -name     "$param_name"
#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) "/>
    <param name="param_qp" type="text" size="30" label="Target attachment qp" help="(-qp) ">
      <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 that defined the run under which the qp for the attachment is aggregated as mzML file" help="(-run) The file is only used to extract the run name from the file name"/>
    <param name="param_name" type="text" size="30" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="(-name) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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>Extracts a table attachment to a given qc parameter.


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