<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>

  </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      @unpublished{galaxyTools, 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>