comparison MetaboRank.xml @ 3:21dfe7a69f4b draft default tip

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

2:c3ee474cc203

    <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/>
  </inputs>
  <outputs>
    <data format="tsv" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="sbmlFilePath" value="XF_network.sbml"/>
      <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
      <param name="inputSide" value="XF_network_C_Side.tab"/>
      <output name="output">
        <assert_contents>
          <has_n_lines n="1100"/>
          <has_n_columns n="11"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network.
The MetaboRank takes a metabolic network and a list of compounds of interest, and provide a score of relevance for all of the other compounds in the network.
The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.
It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.
For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker.

3:21dfe7a69f4b

    <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/>
  </inputs>
  <outputs>
    <data format="tsv" name="output"/>
  </outputs>
  <tests/>
  <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network.
The MetaboRank takes a metabolic network and a list of compounds of interest, and provide a score of relevance for all of the other compounds in the network.
The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.
It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.
For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker.