annotate mmseq.xml @ 3:4fa2b9a7b5eb

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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

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**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.

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**Outputs**::

  </help>
</tool>