Mercurial > repos > iracooke > sixframe_translate

changeset 1:6bd1bfae1119 draft

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Uploaded
author iracooke
date Tue, 18 Mar 2014 01:21:42 -0400
parents a4aa55f893e9
children 477026629d1b
files sixframe_translate.xml
diffstat 1 files changed, 43 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sixframe_translate.xml	Tue Mar 18 01:21:42 2014 -0400
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+<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.0.0">
+	<requirements>
+	    <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>
+
+
+	<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="" />
+
+
+	<stdio>
+		<exit_code range="1:"   level="fatal"   description="Failure" />
+	</stdio>
+
+	<inputs>	
+		<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+	</inputs>
+
+	<outputs>
+		<data format="fasta" name="output" />
+	</outputs>
+
+
+  <help>
+
+**What it does**
+
+Generates 6 frame translations suitable for proteogenomics workflows
+
+----
+
+**References**
+
+
+  </help>
+
+</tool>