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author jjohnson
date Wed, 06 Feb 2013 09:56:58 -0500
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1 <tool id="tophatstatsPE" name="Tophat Stats PE" version="1.0">
2 <description>Calculate mapping statistics from Tophat BAM files.</description>
3 <command interpreter="perl">tophatstatsPE.pl $hits $fastq > $output</command>
4 <inputs>
5 <param name="hits" type="data" format="bam" label="BAM file produced by Tophat"/>
6 <param name="fastq" type="data" format="fastq" label="Fastq file used to produce the BAM file" />
7 </inputs>
8 <outputs>
9 <data format="txt" name="output" />
10 </outputs>
11 <tests>
12 </tests>
13 <help>
14 **Tophat Stats PE**
15
16 This tool generates mapping statics from BAM files produced by
17 Tophat. For paired-end experiments only one of the read files (R1
18 or R2) needs to be provided.
19
20 **Example output:**
21
22 ::
23
24 Input files: /galaxy/database/files/001/dataset_1682.dat /galaxy/database/files/001/dataset_1680.dat
25 73538 total read pairs in fastq file
26 14429 (19.62%) read pairs with only one read in the pair mapped (14262 with unique alignments)
27 36461 (49.58%) read pairs mapped with correct orientation and insert size (36366 with unique alignments)
28 12169 (16.55%) read pairs mapped with correct orientation but wrong insert size (12063 with unique alignments)
29 0.458333333333333 (0.00%) read pairs mapped with wrong orientation but correct insert size (0 with unique alignments)
30 10478.5416666667 (14.25%) read pairs with no mapping
31
32
33 **Credit**
34
35 John Garbe, University of Minnesota
36
37 </help>
38 </tool>