# HG changeset patch
# User mmseq
# Date 1313423679 14400
# Node ID 4fa2b9a7b5eb5f1e0e67847bd4cf113740d0ad42
# Parent  5b5fdffd8bd1017459722857d3e8ac06d64587e3
Uploaded

diff -r 5b5fdffd8bd1 -r 4fa2b9a7b5eb mmseq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mmseq.xml	Mon Aug 15 11:54:39 2011 -0400
@@ -0,0 +1,32 @@
+<tool id="mmseq" name="MMSEQ">
+  <description>Estimation of transcript expression</description>
+  <command interpreter="bash">mmseq.sh $input1 $input2 $output1 $output2 $output3</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data" label="Reference genome"/>
+    <param format="bam" name="input2" type="data" label="Sorted bam file"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output1"/>
+    <data format="tabular" name="output2"/>
+    <data format="tabular" name="output3"/>
+  </outputs>
+  <help>
+
+**About MMSEQ**
+
+MMSEQ_ is a novel RNA seq analysis method for estimating haplotype, isoform and gene specific expression.
+
+.. _MMSEQ: http://www.bgx.org.uk/software/mmseq.html
+
+--------
+
+**Input formats**::
+
+MMSEQ accepts sorted BAM file as input. The SAM files obtained as a result of Bowtie alignment can be converted to BAM files and sorted using the SAMTools.
+
+--------
+
+**Outputs**::
+
+  </help>
+</tool>