Mercurial > repos > iracooke > tpp_prophets

changeset 11:8512f117b10b draft

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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>