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comparison 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
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0:a9447e4a5634 1:810d464f9359
1 <tool id="gfa_to_fa" name="GFA to Fasta" version="0.1.0"> 1 <tool id="gfa_to_fa" name="GFA to Fasta" version="0.1.0">
2 <description>Convert GFA files to Fasta </description> 2 <description>Convert GFA files to Fasta </description>
3 <command detect_errors="exit_code"><![CDATA[ 3 <command detect_errors="exit_code"><![CDATA[
4 cat $in_gfa | python $convert > '$out_fa' 4 cat '$in_gfa' | python $convert > '$out_fa'
5 ]]> 5 ]]></command>
6 </command>
7 <configfiles> 6 <configfiles>
8 <configfile name="convert"><![CDATA[ 7 <configfile name="convert"><![CDATA[
9 from __future__ import print_function 8 from __future__ import print_function
10 import sys 9 import sys
11 for line in sys.stdin: 10 for line in sys.stdin:
12 if line.startswith("S"): 11 if line.startswith("S"):
13 l,h,s,x = line.strip().split() 12 l,h,s,x = line.strip().split()
14 print("> " + h) 13 print("> " + h)
15 print(s) 14 print(s)
16 ]]> 15 ]]></configfile>
17 </configfile>
18 </configfiles> 16 </configfiles>
19 <inputs> 17 <inputs>
20 <param name="in_gfa" type="data" format="tabular" label="Input GFA file" /> 18 <param name="in_gfa" type="data" format="tabular" label="Input GFA file" />
21 </inputs> 19 </inputs>
22 <outputs> 20 <outputs>