<tool id="edu.tamu.cpt.wig.rebase" name="Rebase Wig Analysis Results" version="19.1.0.0">
  <description>against parent features</description>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/wig_rebase.py'
'$parent'
'$wigFile'

'$protein2dna'
--map_by "$map_by"
> '$output']]></command>
  <inputs>
    <param label="Parent GFF3 annotations" name="parent" format="gff3" type="data"/>
    <param label="Wig Results" name="wigFile" format="wig" type="data"/>
    <param label="Map protein translated results to original DNA data" name="protein2dna" type="boolean" truevalue="--protein2dna" falsevalue=""/>
    <param label="Mapping Key" name="map_by" type="text" value="ID"/>
  </inputs>
  <outputs>
    <data format="wig" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="parent" value="T7_CLEAN.gff3"/>
      <param name="wigFile" value="T7_BW_I.wig"/>
      <param name="protein2dna" value="--protein2dna"/>
      <param name="map_by" value="ID"/>
      <output name="output" file="T7_BW_I_REBASE.wig"/>
    </test>
    <test>
      <param name="parent" value="tmhmm.parent.gff3"/>
      <param name="wigFile" value="tmhmm_m.wig"/>
      <param name="protein2dna" value="--protein2dna"/>
      <param name="map_by" value="ID"/>
      <output name="output" file="rebased_m.wig"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Rebases wig results against a set of gff3 annotations which were involved in producing that data.

For example, imagine you take a gff3 file, and export the CDS sequences in
order to analyse in TMHMM. Having done this, you want to view the associated
Wig files in JBrowse with your TMHMM results. This tool will re-map the wig
data to the correct location in the parent genome.

E.g. Given

-  A feature (gp01) runs from 2000-2200
-  A wig file with data from 1-200

The data would be re-mapped and you would receive a wig file with data from 2000-2200.
]]></help>
  <expand macro="citations"/>
</tool>