Mercurial > repos > iracooke > protk_proteogenomics
diff gff3_to_fasta.xml @ 2:68d8c9e521d7 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:34:50 -0400 |
| parents | 28067ed4ea0e |
| children |
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--- a/gff3_to_fasta.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/gff3_to_fasta.xml Tue Oct 20 20:34:50 2015 -0400 @@ -1,40 +1,29 @@ -<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> +<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.1"> + <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">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> - - + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + <command> + augustus_to_proteindb.rb $gff_file -o $output $coords + </command> + <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** @@ -42,11 +31,5 @@ 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>