diff codon_usage.xml @ 28:e85a1feaaf38 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/codon_usage.xml	Wed Dec 12 08:12:25 2018 -0500
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<tool name="Codon Usage" id="codon_usage" version="0.2.0">
+  <description>for each sequence in a file</description>
+  <requirements>
+    <requirement type="package" version="3.6.0">python</requirement>
+    <requirement type="package" version="1.72">biopython</requirement>
+    <requirement type="package" version="0.23.4">pandas</requirement>
+  </requirements> 
+  
+  <command>
+<![CDATA[
+  python '$__tool_directory__/codon_usage.py' -i $input -t $input_type -o $output -c $codon_table
+]]>
+  </command>
+  <inputs>
+    <param name="input" format="fasta" type="data" label="Source file"/>
+
+    <param name="input_type" type="select" format="text">
+			<label>Indicate the input file format</label>
+			<option value="fasta">Fasta</option>
+			<option value="gbk">gbk</option>
+		</param>
+
+    <param name="codon_table" type="select" format="text">
+			<label>Choose the proper codon table for your organism)</label>
+        <option value="Archaeal"> Archaeal</option>
+        <option value="Bacterial">Bacterial</option>
+        <option value="Standard">Standard</option>
+		</param>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <help>
+This tool compute codon usage of an annotated genome [preferably Prokaryotes].
+  </help>
+</tool>