Mercurial > repos > mmseq > mmseq
comparison 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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2:5b5fdffd8bd1 | 3:4fa2b9a7b5eb |
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1 <tool id="mmseq" name="MMSEQ"> | |
2 <description>Estimation of transcript expression</description> | |
3 <command interpreter="bash">mmseq.sh $input1 $input2 $output1 $output2 $output3</command> | |
4 <inputs> | |
5 <param format="fasta" name="input1" type="data" label="Reference genome"/> | |
6 <param format="bam" name="input2" type="data" label="Sorted bam file"/> | |
7 </inputs> | |
8 <outputs> | |
9 <data format="tabular" name="output1"/> | |
10 <data format="tabular" name="output2"/> | |
11 <data format="tabular" name="output3"/> | |
12 </outputs> | |
13 <help> | |
14 | |
15 **About MMSEQ** | |
16 | |
17 MMSEQ_ is a novel RNA seq analysis method for estimating haplotype, isoform and gene specific expression. | |
18 | |
19 .. _MMSEQ: http://www.bgx.org.uk/software/mmseq.html | |
20 | |
21 -------- | |
22 | |
23 **Input formats**:: | |
24 | |
25 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. | |
26 | |
27 -------- | |
28 | |
29 **Outputs**:: | |
30 | |
31 </help> | |
32 </tool> |