--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gfa_to_fa.xml	Wed Jun 19 06:40:02 2019 -0400
@@ -0,0 +1,37 @@
+<tool id="gfa_to_fa" name="GFA to FASTA" version="0.1.0">
+    <description>Convert Graphical Fragment Assembly files to FASTA format </description>
+    <command detect_errors="exit_code"><![CDATA[
+cat '$in_gfa' | python '$convert' > '$out_fa'
+    ]]></command>
+    <configfiles>
+        <configfile name="convert"><![CDATA[
+from __future__ import print_function
+import sys
+for line in sys.stdin:
+    if line.startswith("S"):
+        l,h,s,x = line.strip().split()
+	print(">" + h)
+	print(s)
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="in_gfa" type="data" format="tabular" label="Input GFA file" />
+    </inputs>
+    <outputs>
+        <data name="out_fa" format="fasta" label="${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[
+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>
+