Mercurial > repos > iracooke > tpp_prophets
changeset 11:8512f117b10b draft
Uploaded
| author | iracooke |
|---|---|
| date | Sat, 14 Jun 2014 18:26:00 -0400 |
| parents | 0ad9b29c22e5 |
| children | 4c66453a168e |
| files | .gitignore README README.md repository_dependencies.xml sixframe_translate.xml |
| diffstat | 5 files changed, 8 insertions(+), 47 deletions(-) [+] |
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--- a/.gitignore Sat Jun 14 18:25:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -*.tar.bz2 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Sat Jun 14 18:26:00 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
--- a/README.md Sat Jun 14 18:25:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -# Translate Nucleotide sequences to Protein - -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sat Jun 14 18:26:00 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>
--- a/sixframe_translate.xml Sat Jun 14 18:25:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -<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>