Mercurial > repos > iracooke > proteindb_from_gff3
changeset 0:af52f95e857e draft
Uploaded
| author | iracooke |
|---|---|
| date | Tue, 18 Mar 2014 20:29:57 -0400 |
| parents | |
| children | c2e169ff9e63 |
| files | README.md proteindb_from_gff3.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 4 files changed, 56 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Mar 18 20:29:57 2014 -0400 @@ -0,0 +1,3 @@ +# Create protein database from gff3 including encoding genome coordinates into the fasta header + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteindb_from_gff3.xml Tue Mar 18 20:29:57 2014 -0400 @@ -0,0 +1,43 @@ +<tool id="proteindb_from_gff3" name="Extract proteins from gff3" version="1.0.0"> + <requirements> + <requirement type="package" version="1.2.6">protk</requirement> + </requirements> + + <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description> + + <command> + augustus_to_proteindb.rb $fasta_file -o $output $coords + </command> + + + + + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + + <inputs> + <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> + <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" /> + </inputs> + + <outputs> + <data format="fasta" name="output" /> + </outputs> + + + <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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Mar 18 20:29:57 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Proteomics datatypes"> + <repository changeset_revision="25f42af5b73d" name="proteomics_datatypes" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Mar 18 20:29:57 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="protk" version="1.2.6"> + <repository changeset_revision="1b21ba7de3e7" name="package_protk_1_2_6" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>