diff Project_RM/codon_usage.xml @ 6:1c2b04d72f9d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Project_RM/codon_usage.xml	Sun Dec 09 06:14:35 2018 -0500
@@ -0,0 +1,44 @@
+<tool id="codon_usage" name="Codon Usage" version="0.1.0">
+  <description>for each sequence in a file</description>
+  <requirements>
+    <requirement type="python module">biopython</requirement>
+    <requirement type="python module">pandas</requirement>
+  </requirements> 
+  
+  <command interpreter="python">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>
+
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file1" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>
+
+  <help>
+This tool compute codon usage of an annotated genome [preferably Prokaryotes].
+  </help>
+</tool>