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<tool id="dotplot_runner" name="Dotplot ProHits">
  <description></description>
  <command interpreter="python">dotplot_runner.py $saint_file $FDR1 $FDR2 $spec_max $dotplot $heatmap $estimated $stats \$INSTALL_RUN_PATH/</command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="txt" name="saint_file" type="data" label="SAINT Output"/>
    <param type="float" name="FDR1" label="False Discovery Rate 1" value="0.01"/>
    <param type="float" name="FDR2" label="False Discovery Rate 2" value="0.025"/>
    <param type="integer" name="spec_max" label="Maximum spectral count" value="50"/>
  </inputs>
  <outputs>
    <data format="pdf" name="dotplot" label="DotPlot" />    
    <data format="pdf" name="heatmap" label="Heatmap" /> 
    <data format="pdf" name="estimated" label="Estimated" />  
    <data format="pdf" name="stats" label="Stats" />   
  </outputs>
  <stdio>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error: bad bait"
           source="stdout"
           level="fatal"
           description="Error: bad bait"/>
  </stdio> 

  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>
  <help>
**Running ProHits DotPlot**

This runs the biclustering version of the DotPlot tool found at http://prohitstools.mshri.on.ca/. A more interactive version can be found at http://prohits-viz.lunenfeld.ca/. This script will take a long time to run.

INPUTS:

Saint Output: SAINTexpress generated "list.txt" file.

Primary False Discovery Rate

Secondary False Discovery Rate

Maximum Spectral Count

------

**Please cite** 

 * Knight, J.D., Liu, G., Zhang, J., Pasculescu, A., Choi, H., and Gingras, A.-C. (2014) A web-tool for visualizing quantitative protein-protein interaction data. Proteomics, in press. PMID:25422071. 

  </help>
</tool>