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<?xml version="1.1"?>
<tool id="edu.tamu.cpt2.phage.disruptin_finder" name="Disruptin Finder" version="1.1">
    <description>finds proteins with size and charge criteria</description>
    <macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/disruptin_finder.py
$fasta_file
--thresh_net_charge $thresh_net_charge
--thresh_size $thresh_size
--thresh_charge_ratio $thresh_charge_ratio
--selection_criteria $selection_criteria

> $output]]></command>
    <inputs>
        <param label="Fasta" name="fasta_file" type="data" format="fasta" />
	<param label="Minimum Net Charge" name="thresh_net_charge" type="integer" value="4" />
        <param label="Maximum Length" name="thresh_size" type="integer" value="100" />
	<param label="Minimum Charge to Length Ratio" name="thresh_charge_ratio" type="float" value="0.25" />
		
	<param type="select" label="Type of selection criteria" name="selection_criteria">
		<option value="net">Net charge</option>
		<option value="ratio">Ratio of charged residues to sequence length</option>
		<option value="both" selected="true">Both net charge and ratio</option>
	</param>

    </inputs>
    <outputs>
		<data format="fasta" name="output"/>
    </outputs>
    <help><![CDATA[
**What it does**
This program finds proteins sequences based on given selection criteria: net charge, sequence length, 
and/or number of charged residues per amino acid. Inputs include a multi fasta file of protein sequences,
thresholds for size, charge, and charge-to-size ratio criteria.

This tool returns the selected sequences in a fasta format.

        ]]></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      @unpublished{galaxyTools, 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>