<?xml version="1.1"?>
<tool id="edu.tamu.cpt2.phage.disruptin_prox" name="Disruptin Proximity to Lysis Genes Tool" version="1.1">
    <description>identifies lysis gene candidates close to genes encoding endolysin domains and genes encoding transmembrane domains</description>
    <macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements">
      	<requirement type="package" version="3.0.2">intervaltree</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/disruptin_proximity_2_lysis_genes.py
$lgc
$tmhmm
$ipro
$genome
$window
$enzyme
--oa $oa
--ob $ob
--oc $oc
--od $od

]]></command>
    <inputs>
        <param label="Lysis Gene Candidates" name="lgc" type="data" format="fasta" />
	<param label="TMHMM Results" name="tmhmm" type="data" format="gff3" />
        <param label="InterProScan Results" name="ipro" type="data" format="gff3" />
	<param label="Phage Genome" name="genome" type="data" format="gff3" />
        <param label="Adjacency Window Size" name="window" type="integer" value="1000" />
        <param label="Enzyme Domain List" name="enzyme" type="data" format="tabular" />
    </inputs>
    <outputs>
	<data format="gff3" name="oa" label="Protein with endolysin-associated domain and adjacent to lysis gene candidate"/>
        <data format="gff3" name="ob" label="Lysis gene candidates near possible endolysin"/>
        <data format="gff3" name="oc" label="Protein with transmembrane domain and adjacent to lysis gene candidate"/>
        <data format="gff3" name="od" label="Lysis gene candidates near TMD-containing protein"/>
    </outputs>
    <help><![CDATA[
**What it does**
This program is intended to identify protein coding sequences within a certain window (number of base pairs) of genes encoding recognized endolysin domains and others encoding transmembrane domains.
The goal is to identify possible lysis genes or to narrow a list of disruptin candidates.

        ]]></help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
        <citation type="bibtex">
        @unpublished{galaxyTools, 
            author = {A. Holt},
            title = {CPT Galaxy Tools},
            year = {2020},
            note = {https://github.com/tamu-cpt/galaxy-tools/}
        }
        </citation>
    </citations>
</tool>