comparison ExtractAnnotations.xml @ 3:ab04fda7191e draft default tip

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170

2:0cb8a94dd328

    <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="export" value="METABOLITE"/>
      <param name="db" value="metanetx.chemical"/>
      <output ftype="tsv" name="outputPath">
        <assert_contents>
          <has_n_lines n="146"/>
          <has_n_columns n="2"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="export" value="METABOLITE"/>
      <param name="db" value="metanetx.chemical"/>
      <param name="skip" value="true"/>
      <output ftype="tsv" name="outputPath">
        <assert_contents>
          <has_n_lines n="145"/>
          <has_n_columns n="2"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="export" value="METABOLITE"/>
      <param name="db" value="metanetx.chemical"/>
      <param name="skip" value="true"/>
      <param name="uniq" value="true"/>
      <output ftype="tsv" name="outputPath">
        <assert_contents>
          <has_n_lines n="111"/>
          <has_n_columns n="2"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.
@ATTRIBUTION@]]></help>
  <citations/>
</tool>

3:ab04fda7191e

    <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests/>
  <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.
@ATTRIBUTION@]]></help>
  <citations/>
</tool>