Mercurial > repos > mmseq > mmseq
changeset 2:5b5fdffd8bd1
Deleted selected files
| author | mmseq |
|---|---|
| date | Mon, 15 Aug 2011 11:52:49 -0400 |
| parents | 8429299dfc9a |
| children | 4fa2b9a7b5eb |
| files | mmseq.sh mmseq.xml |
| diffstat | 2 files changed, 0 insertions(+), 40 deletions(-) [+] |
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--- 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
--- 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>