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<tool id="MClust" name="M-Clust" version="0.1.0">
    <description>Get Cluster of proteins</description>
  <command interpreter="Rscript">MClust_all.R -f $input1 -c $input2 -s $Space_String -i $id_column -e $first_experiment -v $outputCSV -d $outputPDF</command>
  <inputs>
    <param format="data" name="input1" type="data" label="Proteins file"/>
    <param format="data" name="input2" type="data" label="Control File"/>
    <param type="integer" name="id_column" label="Column number of Prptein Id" value="1" min="1" />
    <param type="integer" name="first_experiment" label="Column number where the experiments start" value="0" min="0" /> 
    <param type="text" name="Space_String" label="Space String" value="." />
  </inputs>
  <outputs>
    <data format="pdf" name="outputPDF" />
    <data format="tabular" name="outputCSV" />
  </outputs>

  <tests>
    <test>
      <param name="input1" value="EXP11_paraR_log.txt"/>
      <param name="input2" value="EXP11_paraR_log_properties_v1"/>
      <param name="id_column" value="31"/>
      <param name="first_experiment" value="0"/>
      <param name="Space_String" value="."/>
      <output name="outputCSV" file="Clust.csv"/>
      <output name="outputPDF" file="Clust.pdf"/>
    </test>
  </tests>

  <help>
This tool executes a clustering, after a evaluation with ANOVA, works with data with at least three repetitions.
  </help>

  <citations>
    <citation type="bibtex">
      @misc{Concatenate,
        author = {Application, Labis},
        year = 2018,
        title = M-Clust,
        publisher = labisapplications
      }
    </citation>
  </citations>
</tool>