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<tool id="edu.tamu.cpt.fasta.lipory" name="Identify Lipoboxes" version="19.1.0.0">
  <description> in protein sequences</description>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements">
    <requirement type="package" version="2022.1.18">regex</requirement>
  </expand>
  <command interpreter="python" detect_errors="aggressive"><![CDATA[lipory.py
'$positional_1'
'$positional_2'

--lipobox_mindist '$lipobox_mindist'
--lipobox_maxdist '$lipobox_maxdist'

> '$default']]></command>
  <inputs>
    <param label="Naive orf calls" name="positional_1" type="data" format="gff3"/>
    <param label="Genome" name="positional_2" type="data" format="fasta"/>
    <param label="Minimum distance in codons to start of lipobox" name="lipobox_mindist" type="integer" value="10"/>
    <param label="Maximum distance in codons to start of lipobox" name="lipobox_maxdist" type="integer" value="40"/>
  </inputs>
  <outputs>
    <data format="gff3" name="default" label="Lipoboxes from ${on_string}"/>
  </outputs>
  <tests>
    <test>
      <param name="positional_1" value="T7_LiporyIn.gff3"/>
      <param name="positional_2" value="T7_LiporyIn.fasta"/>
      <param name="lipobox_mindist" value="10"/>
      <param name="lipobox_maxdist" value="60"/>
      <output name="default" value="T7_LiporyOut.gff3"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Identifies possible LipoBoxes from an input GFF3 and FASTA.

**How it works**

Searches in the first 10-40 amino acids of an input protein sequence using regular expressions 
for a 4-amino acid motif based on the consensus sequences described in (**Babu** et al. 2006. *J 
Bacteriol.* 188(8):2761-2773 and **Kongari** *et al.* 2018 *BMC Bioinformatics*. 19:326). The 
amino acids allowed here are relaxed to allow for the diversity of amino acids known to occur in lipoboxes.

Position 1: ILMFTV or only A

Position 2: any residue except REKD or only W

Position 3: GAS 

Position 4: C

      ]]></help>
  <expand macro="citations-2020"/>
</tool>