Mercurial > repos > iuc > gfa_to_fa

comparison gfa_to_fa.xml @ 2:43f7a0890015 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 17:17:23 +0000
parents bb94cb83d936
children
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1:bb94cb83d936 2:43f7a0890015
1 <tool id="gfa_to_fa" name="GFA to FASTA" version="0.1.1"> 1 <tool id="gfa_to_fa" name="GFA to FASTA" version="0.1.2">
2 <description>Convert Graphical Fragment Assembly files to FASTA format </description> 2 <description>Convert Graphical Fragment Assembly files to FASTA format </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 ]]></command> 5 ]]></command>
6 <configfiles> 6 <configfiles>
7 <configfile name="convert"><![CDATA[ 7 <configfile name="convert"><![CDATA[
8 from __future__ import print_function 8 from __future__ import print_function
9 import sys 9 import sys
10 for line in sys.stdin: 10 for line in sys.stdin:
11 if line.startswith("S"): 11 if line.startswith("S"):
12 l,h,s,x = line.strip().split() 12 l,h,s = line.strip().split('\t')[:3]
13 print(">" + h) 13 print(">" + h)
14 print(s) 14 print(s)
15 ]]></configfile> 15 ]]></configfile>
16 </configfiles> 16 </configfiles>
17 <inputs> 17 <inputs>
18 <param name="in_gfa" type="data" format="tabular" label="Input GFA file" /> 18 <param name="in_gfa" type="data" format="tabular,gfa1" label="Input GFA file" />
19 </inputs> 19 </inputs>
20 <outputs> 20 <outputs>
21 <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" /> 21 <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" />
22 </outputs> 22 </outputs>
23 <tests> 23 <tests>