annotate CVInspector.xml @ 9:e97a8b65aa3c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

<?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: [Utilities]-->
<tool id="CVInspector" name="CVInspector" version="2.3.0">
  <description>A tool for visualization and validation of PSI mapping and CV files.</description>
  <macros>
    <token name="@EXECUTABLE@">CVInspector</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>CVInspector

-cv_files
  #for token in $param_cv_files:
    $token
  #end for

#if $rep_param_cv_names:
-cv_names
  #for token in $rep_param_cv_names:
    #if " " in str(token):
      "$token.param_cv_names"
    #else
      $token.param_cv_names
    #end if
  #end for
#end if
#if $param_mapping_file:
  -mapping_file $param_mapping_file
#end if

#if $rep_param_ignore_cv:
-ignore_cv
  #for token in $rep_param_ignore_cv:
    #if " " in str(token):
      "$token.param_ignore_cv"
    #else
      $token.param_ignore_cv
    #end if
  #end for
#end if
#if $param_html:
  -html $param_html
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_cv_files" type="data" format="obo" multiple="true" optional="False" size="30" label="List of ontology files in OBO format" help="(-cv_files) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <repeat name="rep_param_cv_names" min="1" title="param_cv_names">
      <param name="param_cv_names" type="text" size="30" label="List of identifiers (one for each ontology file)" help="(-cv_names) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format" help="(-mapping_file) "/>
    <repeat name="rep_param_ignore_cv" min="0" max="1" title="param_ignore_cv">
      <param name="param_ignore_cv" type="text" size="30" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help="(-ignore_cv) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <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_html" format="html"/>
  </outputs>
  <help>A tool for visualization and validation of PSI mapping and CV files.


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