Mercurial > repos > iracooke > sixframe_translate

changeset 0:d3850859bc50 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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>