<?xml version="1.0"?>
<tool id="edu.tamu.cpt.genbank.GBKtoFiveCol" name="Genbank to Five Column Format" version="1.0">
    <description></description>
  <macros>
    <import>macros.xml</import>
		<import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/gbk_to_five_col.py
  "$file"

> "$output"

]]></command>
  <inputs>
    <param label="GenBank file" name="file" type="data" format="genbank" />
  </inputs>
  <outputs>
    <data format="tabular" name="output">
    </data>
  </outputs>
  <tests>
      <test>
          <param name="file" value="complex_feature_locs.gbk" />
          <output name="output" value="gbkto5col.tsv" />
      </test>
  </tests>
  <help>
Genbank Format to Five Column Format
====================================

Output format is:

>Feature ID
Line 1
- Column 1: Start location (first nucleotide) of a feature
- Column 2: Stop location (last nucleotide) of a feature
- Column 3: Feature name (for example, 'CDS' or 'mRNA' or 'rRNA' or 'gene' or 'exon')

Line2:
- Column 4: Qualifier name (for example, 'product' or 'number' or 'gene' or 'note')
- Column 5: Qualifier value

Example Output::

    >Feature contig00077
    0	22956	source
    			mol_type	genomic DNA
    			organism	AU1189
    11652	11326	CDS
    11327	11158
    			note	tapemeasure frameshift chaperone
    			product	P2 E' tapemeasure frameshift chaperone
    			gene	gp14
    			translation	MNPIQSDAAAPDLQADAAAIATPAQDDPATHTLDTPLVRGTQTITSITLRKPKSGELRGVSLSDLVSLDVVALSKVLPRISSPMLTEADVASIDPADLVQLGGIFAGFFDAEGREIPTGLPDRVEDPMADIATVFGWTPPVMDAFSLAELMDWRERARVRAGAQ
    11900	11599	CDS
    11600	11408
    11910	11904	RBS

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