Mercurial > repos > erasmus-medical-center > gfa_to_fa
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gfa_to_fa.xml Tue Jul 17 10:31:08 2018 -0400 @@ -0,0 +1,35 @@ +<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> + <configfiles> + <configfile name="convert"><![CDATA[ +from __future__ import print_function +import sys +for line in sys.stdin: + if line.startswith("S"): + l,h,s,x = line.strip().split() + print("> " + h) + print(s) +]]> + </configfile> + </configfiles> + <inputs> + <param name="in_gfa" type="data" format="tabular" label="Input GFA file" /> + </inputs> + <outputs> + <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" /> + </outputs> + <tests> + <test> + <param name="in_gfa" value="test.gfa"/> + <output name="out_fa" file="out.fa"/> + </test> + </tests> + <help><![CDATA[ +gfa_to_fa converts a GFA file to a Fasta File. The column two from the GFA file is used as sequence header. + ]]></help> +</tool> +