<tool id="region_motif_compare" name="Region Motif Count Compare">
  <description>for comparing the motif counts in different region sets</description>
  <requirements>
    <requirement type="set_environment">RMOTIF_PATH</requirement>
  </requirements>
  <command interpreter="Rscript">
    region_motif_compare.r --args \$RMOTIF_PATH $pwm_file.fields.path $in_tab_1 $in_tab_2 
    $out_enriched 
    $out_depleted 
    $out_plots
  </command>
  <inputs>
    <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
    <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>

    <param name="pwm_file" type="select" label="Using motif database PWM file">
      <options from_data_table="motif_databases"/>
    </param>
  </inputs>

  <outputs>
    <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
    <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
    <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
  </outputs>

  <tests>
    <test>
      <param name="in_tab_1" value="XXX.tab" />
      <param name="in_tab_2" value="XXX.tab" />
      <param name="pwm_file" value="XXX.meme.txt" />
      <output name="out_enriched" file="XXX.tab" />
      <output name="out_depleted" file="XXX.tab" />     
      <output name="out_plots" file="XXX.png" />          
    </test>
  </tests>

  <help>
    This tools reads in two counts file and determines enriched and depleted
    motifs in two different region sets based on poisson calculation with
    gc correction.
  </help>
 
</tool>