<tool id="gfa_to_fa" name="GFA to Fasta" version="0.1.0">
    <description>Convert GFA files to Fasta </description>
    <command detect_errors="exit_code"><![CDATA[
cat '$in_gfa' | python $convert > '$out_fa'
    ]]></command>
    <configfiles>
        <configfile name="convert"><![CDATA[
from __future__ import print_function
import sys
for line in sys.stdin:
    if line.startswith("S"):
        l,h,s,x = line.strip().split()
	print(">" + h)
	print(s)
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="in_gfa" type="data" format="tabular" label="Input GFA file" />
    </inputs>
    <outputs>
        <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" />
    </outputs>
    <tests>
        <test>
            <param name="in_gfa" value="test.gfa"/>
            <output name="out_fa" file="out.fa"/>
        </test>
    </tests>
    <help><![CDATA[
gfa_to_fa converts a GFA file to a Fasta File. The column two from the GFA file is used as sequence header.
    ]]></help>
</tool>