Mercurial > repos > xuebing > seq_to_meme

changeset 0:8147a2451531

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Uploaded
author xuebing
date Sat, 31 Mar 2012 21:50:00 -0400
parents
children 54f508fcdc40
files seq_to_meme.xml
diffstat 1 files changed, 21 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seq_to_meme.xml	Sat Mar 31 21:50:00 2012 -0400
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+<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>