# HG changeset patch
# User nedias
# Date 1476245097 14400
# Node ID 04de7d352a3db8c51f791d02d8cfcb5ce58845f0
# Parent  0095bf758b19bd26cc3174108a8ea41260f43a11
Uploaded

diff -r 0095bf758b19 -r 04de7d352a3d orf_tool.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orf_tool.xml	Wed Oct 12 00:04:57 2016 -0400
@@ -0,0 +1,32 @@
+<tool id="orf_tool" name="Open Reading Frame Extract Tool" version="0.1.0">
+    <description>from given fasta RNA sequence</description>
+    <requirements>
+        <requirement type="package" version="1.64">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command interpreter="python">entry.py --version</version_command>
+    <command interpreter="python">
+entry.py -i "$input_file" -a "$output_all" -d "$output_dest" -f "$ext" -l "$length"
+    </command>
+    <inputs>
+      <param name="input_file" type="data" label="Input File" format="fasta,fastq,sam,bam" help="FASTA, FASTQ, or SFF format." />
+      <param name="ext" type="select" value="fasta" label="Input file type">
+	<option value="fasta">Fasta</option>
+	<option value="fastq">Fastq</option>
+	<option value="sam">Sam</option>
+	<option value="bam">Bam</option>
+      </param>
+      <param name="length" type="integer" value="100" max="100" min="1"  label="Length" help="Percentage of the max match." />
+    </inputs>
+    <outputs>
+        <data name="output_all" format_source="input_file" metadata_source="input_file" label="$input_file.name all matches">
+        </data>
+        <data name="output_dest" format_source="input_file" metadata_source="input_file" label="$input_file.name designated matches">
+        </data>
+    </outputs>
+</tool>