Mercurial > repos > erasmus-medical-center > gfa_to_fa

diff gfa_to_fa.xml @ 1:810d464f9359 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 1a253e02d30317fb231294b55291df79b1cda568
author erasmus-medical-center
date Tue, 17 Jul 2018 13:35:44 -0400
parents a9447e4a5634
children a54fa2c9503f
line wrap: on
line diff
--- a/gfa_to_fa.xml	Tue Jul 17 10:31:08 2018 -0400
+++ b/gfa_to_fa.xml	Tue Jul 17 13:35:44 2018 -0400
@@ -1,20 +1,18 @@
 <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>
+cat '$in_gfa' | python $convert > '$out_fa'
+    ]]></command>
     <configfiles>
         <configfile name="convert"><![CDATA[
 from __future__ import print_function
-import sys		
+import sys
 for line in sys.stdin:
     if line.startswith("S"):
         l,h,s,x = line.strip().split()
 	print("> " + h)
 	print(s)
-]]>
-        </configfile>
+        ]]></configfile>
     </configfiles>
     <inputs>
         <param name="in_gfa" type="data" format="tabular" label="Input GFA file" />