<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.phage.disruptin_table" name="Disruptin Table Output" version="1.0">
    <description>makes table of disruptin candidates</description>
    <macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
	<command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/Disruptin_hydrophobicity_helicity_table_package.py
$garnier_file
$fasta_file



>$output]]></command>
    <inputs>
        <param label="Garnier csv file" name="garnier_file" type="data" format="tabular" />
		<param label="Candidate fasta file" name="fasta_file" type="data" format="fasta" />
    </inputs>
    <outputs>
		<data format="tabular" name="output"/>
    </outputs>
    <help><![CDATA[
**What it does**
This program takes the parsed output from the garnier tool and the fasta file with disruptin candidate sequences
and compiles information on each of the sequences into a table format. The table includes the sequence and the position for each residue
as well as the charge, hydrophobicity (based on the Kyte Doolittle scale), and secondary structure prediction from
the garnier tool.

        ]]></help>
		<expand macro="citations" />
</tool>