Mercurial > repos > erasmus-medical-center > gfa_to_fa
comparison gfa_to_fa.xml @ 0:a9447e4a5634 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
| author | erasmus-medical-center |
|---|---|
| date | Tue, 17 Jul 2018 10:31:08 -0400 |
| parents | |
| children | 810d464f9359 |
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| -1:000000000000 | 0:a9447e4a5634 |
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| 1 <tool id="gfa_to_fa" name="GFA to Fasta" version="0.1.0"> | |
| 2 <description>Convert GFA files to Fasta </description> | |
| 3 <command detect_errors="exit_code"><![CDATA[ | |
| 4 cat $in_gfa | python $convert > '$out_fa' | |
| 5 ]]> | |
| 6 </command> | |
| 7 <configfiles> | |
| 8 <configfile name="convert"><![CDATA[ | |
| 9 from __future__ import print_function | |
| 10 import sys | |
| 11 for line in sys.stdin: | |
| 12 if line.startswith("S"): | |
| 13 l,h,s,x = line.strip().split() | |
| 14 print("> " + h) | |
| 15 print(s) | |
| 16 ]]> | |
| 17 </configfile> | |
| 18 </configfiles> | |
| 19 <inputs> | |
| 20 <param name="in_gfa" type="data" format="tabular" label="Input GFA file" /> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" /> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="in_gfa" value="test.gfa"/> | |
| 28 <output name="out_fa" file="out.fa"/> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help><![CDATA[ | |
| 32 gfa_to_fa converts a GFA file to a Fasta File. The column two from the GFA file is used as sequence header. | |
| 33 ]]></help> | |
| 34 </tool> | |
| 35 |