comparison SideCompoundsScan.xml @ 3:3acb02c5eee4 draft default tip

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

2:cb9942e68c8c

    </param>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <output ftype="tsv" name="outputPath">
        <assert_contents>
          <has_n_lines min="1000"/>
          <has_n_columns n="4"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <param name="noReportValue" value="true"/>
      <output ftype="tsv" name="outputPath">
        <assert_contents>
          <has_n_lines min="30"/>
          <has_n_columns n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Scan a network to identify side compounds.
Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources.
Side compounds tend to be ubiquitous and not specific to a particular biochemical or physiological process.Compounds usually considered as side compounds include water, atp or carbon dioxide. By being involved in many reactions and thus connected to many compounds, they tend to significantly lower the average shortest path distances beyond expected metabolic relatedness.
This tool attempts to propose a list of side compounds according to specific criteria:  
- *Degree*: Compounds with an uncommonly high number of neighbors can betray a lack of process specificity.  

3:3acb02c5eee4

    </param>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests/>
  <help><![CDATA[Scan a network to identify side compounds.
Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources.
Side compounds tend to be ubiquitous and not specific to a particular biochemical or physiological process.Compounds usually considered as side compounds include water, atp or carbon dioxide. By being involved in many reactions and thus connected to many compounds, they tend to significantly lower the average shortest path distances beyond expected metabolic relatedness.
This tool attempts to propose a list of side compounds according to specific criteria:  
- *Degree*: Compounds with an uncommonly high number of neighbors can betray a lack of process specificity.