Mercurial > repos > iracooke > protk_proteogenomics
comparison gff3_to_fasta.xml @ 0:28067ed4ea0e draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 20:11:34 -0400 |
| parents | |
| children | 68d8c9e521d7 |
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| -1:000000000000 | 0:28067ed4ea0e |
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| 1 <tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.0"> | |
| 2 <requirements> | |
| 3 <container type="docker">iracooke/protk-1.4.1</container> | |
| 4 <requirement type="package" version="1.4">protk</requirement> | |
| 5 </requirements> | |
| 6 | |
| 7 <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description> | |
| 8 | |
| 9 <command> | |
| 10 augustus_to_proteindb.rb $gff_file -o $output $coords | |
| 11 </command> | |
| 12 | |
| 13 | |
| 14 | |
| 15 | |
| 16 <stdio> | |
| 17 <exit_code range="1:" level="fatal" description="Failure" /> | |
| 18 </stdio> | |
| 19 | |
| 20 <inputs> | |
| 21 <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" /> | |
| 22 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" /> | |
| 23 </inputs> | |
| 24 | |
| 25 <outputs> | |
| 26 <data format="fasta" name="output" /> | |
| 27 </outputs> | |
| 28 | |
| 29 <tests> | |
| 30 <!-- Just test that the tool runs and produces vaguely correct output --> | |
| 31 <test> | |
| 32 <param name="gff_file" value="augustus_sample.gff" format="gff3"/> | |
| 33 <output name="output" file="augustus_sample.fasta" format="fasta"/> | |
| 34 </test> | |
| 35 </tests> | |
| 36 | |
| 37 | |
| 38 <help> | |
| 39 | |
| 40 **What it does** | |
| 41 | |
| 42 Extract proteins from gff3 and encode genomic coordinates in the fasta header. | |
| 43 Currently this only works with gff3 generated using the Augustus gene finder | |
| 44 | |
| 45 ---- | |
| 46 | |
| 47 **References** | |
| 48 | |
| 49 | |
| 50 </help> | |
| 51 | |
| 52 </tool> |