<tool id="consolidate_fitnesses" name="Consolidate Fitnesses">
  <description>of transposon insertion locations</description>
  <requirements>
    <requirement type="package" version="1.64">biopython</requirement>
  </requirements>
  <command interpreter="python">
    consol_fit.py  
    -i $input 
    -calctxt $calctxt
    -out $output 
    -out2 $output2 
    -maxweight $maxweight
    -cutoff $cutoff
    -cutoff2 $cutoff2
    -wig $output3
    #if $normalization.calculations  == "yes":
      -normalize $normalization.genes
    #end if
    #if $multiply.choice  == "yes":
      -multiply $multiply.factor
    #end if
    #if $reads.downstream  == "yes":
      -d 1
    #end if
  </command>
  <inputs>
    <param name="input" type="data" label="Fitness file"/>
    <param name="calctxt" type="data" label="the txt file output from calc_fitness"/>
    <conditional name="normalization">
      <param name="calculations" type="select" label="Normalize fitness calculations?">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no">
        <!-- do nothing -->
      </when>
      <when value="yes"> 
        <param name="genes" type="data" label="Genes to normalize by" />
      </when>
    </conditional>
    <param name="cutoff" type="float" value="0.0" label="Cutoff"/>
    <param name="cutoff2" type="float" value="0.0" label="Cutoff2"/>
    <param name="maxweight" type="float" value="75" label="Maximum weight of a transposon gene in normalization calculations"/>
    <conditional name="multiply">
      <param name="choice" type="select" label="Multiply fitness scores by a certain value?">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no">
        <!-- do nothing -->
      </when>
      <when value="yes"> 
        <param name="factor" type="float" value="0.0" label="Multiply by" />
      </when>
    </conditional>
    <conditional name="reads">
      <param name="downstream" type="select" label="Are all reads downstream of the transposon?">
        <option value="no">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no">
        <!-- do nothing -->
      </when>
      <when value="yes"> 
        <!-- do nothing -->
      </when>
    </conditional>
  </inputs>
    <outputs>
        <data format="csv" name="output" />
        <data format="txt" name="output2" />
        <data format="wig" name="output3" />
    </outputs>
  <help>

**What it does**

This tool consolidates the fitness values of transposon insertion mutations generated by Tn-Seq, and is mostly useful for consolidating values produced by a 4-cycle looping trimming pipeline.

</help>
</tool>