--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/seq2meme.xml	Tue Mar 13 23:34:52 2012 -0400
@@ -0,0 +1,21 @@
+<tool id="seq2meme" name="create-motif-file">
+  <description>from fasta file</description>
+  <command interpreter="python">seq2meme.py $input $output $motifName $psuedocont $background </command>
+  <inputs>
+     <param name="input" type="data" format="txt" label="Sequence file" help="all sequences should be the same length"/>    
+      <param name="motifName" size="20" type="text" value="motif1" label="Motif name (no space allowed)"/>
+      <param name="psuedocont" size="10" type="float" value="1.0" label="Psuedocount"/>
+    <param name="background" size="40" type="text" value="A,0.25,C,0.25,G,0.25,T,0.25" label="Background frequency"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="$motifName-meme"/>
+  </outputs>
+  <help>
+
+**Description**
+
+Generate a MEME motif format file from a set of sequences. Input could be raw sequences (one sequence per line) or fasta format (one identifier line and one sequence line).
+
+
+  </help>
+</tool>