Mercurial > repos > iuc > gfa_to_fa

changeset 2:e33c82b63727 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 83aed19c6cdf00f3133eb80a69cba0074ca244cc"
author iuc
date Wed, 03 Mar 2021 17:17:49 +0000
parents 8e9d604e92f4
children
files gfa_to_fa.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/gfa_to_fa.xml	Tue Jan 21 18:55:34 2020 -0500
+++ b/gfa_to_fa.xml	Wed Mar 03 17:17:49 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="gfa_to_fa" name="GFA to FASTA" version="0.1.1">
+<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' > '$out_fa'
@@ -9,13 +9,13 @@
 import sys
 for line in sys.stdin:
     if line.startswith("S"):
-        l,h,s,x = line.strip().split()
+        l,h,s = line.strip().split('\t')[:3]
         print(">" + h)
         print(s)
         ]]></configfile>
     </configfiles>
     <inputs>
-        <param name="in_gfa" type="data" format="tabular" label="Input GFA file" />
+        <param name="in_gfa" type="data" format="tabular,gfa1" label="Input GFA file" />
     </inputs>
     <outputs>
         <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" />