Mercurial > repos > iracooke > protk_proteogenomics
view gff3_to_fasta.xml @ 1:a85c8de9630a draft
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author | iracooke |
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date | Thu, 26 Mar 2015 20:16:00 -0400 |
parents | 28067ed4ea0e |
children | 68d8c9e521d7 |
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<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.0"> <requirements> <container type="docker">iracooke/protk-1.4.1</container> <requirement type="package" version="1.4">protk</requirement> </requirements> <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description> <command> augustus_to_proteindb.rb $gff_file -o $output $coords </command> <stdio> <exit_code range="1:" level="fatal" description="Failure" /> </stdio> <inputs> <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" /> <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" /> </inputs> <outputs> <data format="fasta" name="output" /> </outputs> <tests> <!-- Just test that the tool runs and produces vaguely correct output --> <test> <param name="gff_file" value="augustus_sample.gff" format="gff3"/> <output name="output" file="augustus_sample.fasta" format="fasta"/> </test> </tests> <help> **What it does** Extract proteins from gff3 and encode genomic coordinates in the fasta header. Currently this only works with gff3 generated using the Augustus gene finder ---- **References** </help> </tool>