Mercurial > repos > cpt_testbed > cpt_fixaragorn

<?xml version="1.0"?>
<tool id="edu.tamu.cpt.external.aragorn-gff3" name="Fix tRNA model" version="19.1.0.0">
  <description></description>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
$__tool_directory__/fix-aragorn-gff3.py
@INPUT_GFF@
> $default]]></command>
  <inputs>
      <expand macro="gff3_input" />
  </inputs>
  <outputs>
    <data format="gff3" name="default"/>
  </outputs>
  <tests>
    <test>
      <param name="gff3_data" value="FixAra_In.gff3"/>
      <output name="default" file="FixAra_Out.gff3"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

For an input GFF3 file with tRNAs from the Aragorn or converted from the tRNAscan-SE tools, this tool modifies
the gene model to reflect a gene-tRNA-exon hierarchy. That change is needed
to allow for creation of proper tRNA features in Apollo.
      ]]></help>
		<expand macro="citations" />
</tool>
author	cpt_testbed
date	Fri, 29 Apr 2022 11:32:30 +0000
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