# HG changeset patch
# User xuebing
# Date 1333283033 14400
# Node ID 7ffb2ec6f557bbc741bd3871cce2266b3a338555
# Parent  cd88406c2436e3f75470ae4c2a76487a34d45251
Uploaded

diff -r cd88406c2436 -r 7ffb2ec6f557 splicesite_maxent.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/splicesite_maxent.xml	Sun Apr 01 08:23:53 2012 -0400
@@ -0,0 +1,65 @@
+<tool id="maxent" name="splice site score">
+  <description>using max entropy model</description>
+  <command interpreter="perl">$script $input > $out_file1 </command>
+  <inputs>
+    <param name="input" format="txt" type="data" label="Sequence file" help="fasta or raw sequence (one sequence per line)"/>
+    <param name="script" type="select" label="Select model">
+        <option value="maxent_score5.pl" selected="true">5' splice site</option>
+        <option value="maxent_score3.pl">3' splice site</option>
+    </param>
+    
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool computes splice site scores using a max entropy model. See more details here: 
+
+http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
+
+-----
+
+**Example input for 5' splice site sequence**
+
+3 exonic and 6 intronic nucleotides flanking the junction::
+
+    CTGGTGAGT
+    AAGGTACAG
+
+or fasta format::
+
+    >seq1
+    CTGGTGAGT
+    >seq2
+    AAGGTACAG
+
+Output::
+
+    CTGGTGAGT	10.10
+    AAGGTACAG	8.04
+
+or fasta format::
+
+    >seq1   CTGGTGAGT	10.10
+    >seq2   AAGGTACAG	8.04
+
+
+-----
+
+**Example input for 3' splice site sequence**
+
+3 exonic and 20 intronic nucleotides flanking the junction::
+
+    CCTGCATCCTCTGTTCCCAGGTG
+    TTTCTTCCCTCCGGGAACAGTGG
+
+Output::
+
+    CCTGCATCCTCTGTTCCCAGGTG	10.47
+    TTTCTTCCCTCCGGGAACAGTGG	6.22
+
+  </help>
+</tool>