Mercurial > repos > mmseq > mmseq
view mmseq.xml @ 3:4fa2b9a7b5eb
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author | mmseq |
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date | Mon, 15 Aug 2011 11:54:39 -0400 |
parents | 8429299dfc9a |
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<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>