view gfa_to_fa.xml @ 2:e33c82b63727 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 83aed19c6cdf00f3133eb80a69cba0074ca244cc"

<tool id="gfa_to_fa" name="GFA to FASTA" version="0.1.2">
    <description>Convert Graphical Fragment Assembly files to FASTA format </description>
    <command detect_errors="exit_code"><![CDATA[
cat '$in_gfa' | python '$convert' > '$out_fa'
    ]]></command>
    <configfiles>
        <configfile name="convert"><![CDATA[
from __future__ import print_function
import sys
for line in sys.stdin:
    if line.startswith("S"):
        l,h,s = line.strip().split('\t')[:3]
        print(">" + h)
        print(s)
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="in_gfa" type="data" format="tabular,gfa1" label="Input GFA file" />
    </inputs>
    <outputs>
        <data name="out_fa" format="fasta" label="${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[
This tool converts a GFA file (Graphical Fragment Assembly) to a FASTA file. The second column from the GFA file is used as the sequence header.

More information about the GFA file format can be found here_

.. _here: http://gfa-spec.github.io/GFA-spec/GFA1.html
    ]]></help>
</tool>