Mercurial > repos > iracooke > sixframe_translate
changeset 0:d3850859bc50 draft
Uploaded
| author | iracooke |
|---|---|
| date | Sat, 14 Jun 2014 18:22:33 -0400 |
| parents | |
| children | 10465e20d9a2 |
| files | .gitignore README README.md repository_dependencies.xml sixframe_translate.xml |
| diffstat | 5 files changed, 55 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.gitignore Sat Jun 14 18:22:33 2014 -0400 @@ -0,0 +1,1 @@ +*.tar.bz2 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Sat Jun 14 18:22:33 2014 -0400 @@ -0,0 +1,4 @@ +Requirements: +This package uses protk, msgfplus and proteowizard, which must be installed separately. + +For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Jun 14 18:22:33 2014 -0400 @@ -0,0 +1,3 @@ +# Translate Nucleotide sequences to Protein + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sat Jun 14 18:22:33 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Proteomics datatypes"> + <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sixframe_translate.xml Sat Jun 14 18:22:33 2014 -0400 @@ -0,0 +1,43 @@ +<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.0.0"> + <requirements> + <requirement type="package" version="1.3">protk</requirement> + </requirements> + + <description>Translates DNA/RNA to protein</description> + + <command> + sixframe.rb $fasta_file -o $output $strip_header $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="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" /> + <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" /> + </inputs> + + <outputs> + <data format="fasta" name="output" /> + </outputs> + + + <help> + +**What it does** + +Generates 6 frame translations suitable for proteogenomics workflows + +---- + +**References** + + + </help> + +</tool>