Mercurial > repos > mmseq > mmseq
changeset 6:feda458ea8c5
Uploaded mmseq analysis pipeline xml file
author | mmseq |
---|---|
date | Mon, 15 Aug 2011 12:00:16 -0400 |
parents | 5868599b6b91 |
children | 227e5fcd9200 |
files | mmseq.xml |
diffstat | 1 files changed, 32 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mmseq.xml Mon Aug 15 12:00:16 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>