# HG changeset patch
# User mmseq
# Date 1313423569 14400
# Node ID 5b5fdffd8bd1017459722857d3e8ac06d64587e3
# Parent  8429299dfc9acf61f0ec371c8aae48b87930e5dc
Deleted selected files

diff -r 8429299dfc9a -r 5b5fdffd8bd1 mmseq.sh
--- a/mmseq.sh	Mon Aug 15 11:52:30 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-TEMP=bam.hits
-bam2hits $1 $2 > $TEMP 2> /dev/null
-mmseq $TEMP output > /dev/null
-mv output.mmseq $3
-mv output.gene.mmseq $4
-mv output.amalgamated.mmseq $5
diff -r 8429299dfc9a -r 5b5fdffd8bd1 mmseq.xml
--- a/mmseq.xml	Mon Aug 15 11:52:30 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<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>