Mercurial > repos > iracooke > sixframe_translate

changeset 4:cbf4291587c5 draft

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Uploaded
author simonalpha
date Mon, 05 Jan 2015 17:28:25 -0500
parents efd982d2db59
children 5de1f2d753fc
files .gitignore README.md repository_dependencies.xml sixframe_translate.xml tool_dependencies.xml
diffstat 5 files changed, 57 insertions(+), 1 deletions(-) [+]
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--- a/.gitignore	Mon Jan 05 17:28:09 2015 -0500
+++ /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.md	Mon Jan 05 17:28:25 2015 -0500
@@ -0,0 +1,3 @@
+# Translate Nucleotide sequences to Protein
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Jan 05 17:28:25 2015 -0500
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Proteomics datatypes">
+    <repository changeset_revision="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+ </repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sixframe_translate.xml	Mon Jan 05 17:28:25 2015 -0500
@@ -0,0 +1,44 @@
+<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.0.0">
+	<requirements>
+            <container type="docker">simonalpha/protk:1.4.0</container>
+	    <requirement type="package" version="1.2.6">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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 05 17:28:25 2015 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="protk" version="1.2.6">
+         <repository changeset_revision="2b59cbe74904" name="package_protk_1_2_6" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>