<tool id="edu.tamu.cpt.gff3.lipoP_to_gff3" name= "LipoP to GFF3" version="1.0">
  <description>Adds LipoP results to GFF3</description>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/lipoP_to_gff3.py

"$lipoIn"
"$gff3In"
--jBrowseOut "$jBrowseOut"
$filterSP2
> $stdout

]]></command>
  <inputs>
    <param label="LipoP Output" name="lipoIn" type="data" format="txt"/>
    <param label="GFF3 for Rebasing" name="gff3In" type="data" format="gff3"/>
    <param label="Output to jBrowse" name="jBrowseOut" type="boolean" truevalue="True" falsevalue="" help="Strip non-cleavage features from GFF3 (for viewing in Apollo)"/>
    <param name="filterSP2" truevalue="--filterSP2" falsevalue="" type="boolean" label="Filter for only SPII Cleavage sites" checked="true"/>
  </inputs>
  <outputs>
    <data format="gff3" name="stdout"/>
  </outputs>
  <tests>
    <test>
      <param name="lipoIn" value="LipoToGFF_In.txt" />
      <param name="gff3In" value="LipoToGFF_In.gff3" />
      <param name="jBrowseOut" value="True" />
      <param name="filterSP2" value="True" />
      <output name="stdout" value="LipoToGFF_Out.gff3" />
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Adds the cleavage sites from a LipoP run to a GFF3 file's feature list. Must use
the .txt output of LipoP (ensure .html is turned off). The most common way this
tool will be utilized is to take a GFF3, use the GFF3 Feature Sequence Export
tool (https://cpt.tamu.edu/galaxy/root?tool_id=edu.tamu.cpt.gff3.export_seq) to 
get a multi-FASTA of the CDSs, run that multi-FASTA through LipoP, and then
recombine the LipoP results with the original GFF3 file with this tool.

Currently, only CleavII results will be added with this tool.

"Output to jBrowse" will remove all gene features that do not have a CleavII 
result from the LipoP, and remove all sub features of the gene except for the 
cleavage sites. This is useful for viewing in Apollo, but should most likely 
not be used if you plan to run this output through more tools.
      ]]></help>
		<expand macro="citations-2020" />
</tool>