diff trams.xml @ 3:1f00946b18c2 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trams.xml	Wed Dec 12 09:09:45 2012 -0500
@@ -0,0 +1,23 @@
+<tool id="trams" name="TRAMS">
+  <description>Tool for Rapid Annotation of Microbial SNPs</description>
+  <command interpreter="python">trams.py $input1 $input2 $ref_format $annot $overl $sum</command>
+  <inputs>
+    <param name="input1" type="data" format="tabular" label="SNP table" />
+    <param name="input2" type="data" format="txt" label="Reference genome" help="Reference genome file, should be genbank or embl file." />
+    <param name="ref_format" type="select">
+     <label>Reference file type</label>
+      <option value="gb">Genbank</option>
+      <option value="embl">EMBL</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="annot" format="tabular" label="${tool.name} on ${on_string}: SNP annotation file" />
+    <data name="overl" format="tabular" label="${tool.name} on ${on_string}: Overlap file" />
+    <data name="sum" format="txt" label="${tool.name} on ${on_string}: Summary file" />
+  </outputs>
+  <help>
+
+This tool annotates SNPs from a SNP table and a genbank file.
+
+  </help>
+</tool>