view CVInspector.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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="CVInspector" name="CVInspector" version="2.0.0">
    <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 $rep_param_cv_names:
    #if &quot; &quot; in str(token):
      &quot;$token.param_cv_names&quot;
    #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 $rep_param_ignore_cv:
    #if &quot; &quot; in str(token):
      &quot;$token.param_ignore_cv&quot;
    #else
      $token.param_ignore_cv
    #end if
  #end for
#end if
#if $param_html:
  -html $param_html
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="" help="(-cv_files) " label="List of ontology files in OBO format" multiple="true" name="param_cv_files" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <repeat min="1" name="rep_param_cv_names" title="param_cv_names">
        <param help="(-cv_names) " label="List of identifiers (one for each ontology file)" name="param_cv_names" size="30" type="text">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param format="xml" help="(-mapping_file) " label="Mapping file in CVMapping (XML) format" name="param_mapping_file" optional="True" type="data"/>
      <repeat max="1" min="0" name="rep_param_ignore_cv" title="param_ignore_cv">
        <param help="(-ignore_cv) " label="A list of CV identifiers which should be ignored" name="param_ignore_cv" size="30" type="text" value="UO PATO BTO">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="html" name="param_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>