Mercurial > repos > devteam > samtools_flagstat
comparison samtools_flagstat.xml @ 0:13c4ad597626 draft
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Mon, 26 Aug 2013 14:22:51 -0400 |
| parents | |
| children | a3dd61e7bec1 |
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| -1:000000000000 | 0:13c4ad597626 |
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| 1 <tool id="samtools_flagstat" name="flagstat" version="1.0.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 4 </requirements> | |
| 5 <description>provides simple stats on BAM files</description> | |
| 6 <command>samtools flagstat "$input1" > "$output1" | |
| 7 </command> | |
| 8 <inputs> | |
| 9 <param name="input1" type="data" format="bam" label="BAM File to Convert" /> | |
| 10 </inputs> | |
| 11 <outputs> | |
| 12 <data name="output1" format="txt" /> | |
| 13 </outputs> | |
| 14 <tests> | |
| 15 <test> | |
| 16 <param name="input1" value="3unsorted.bam" ftype="bam" /> | |
| 17 <output name="output1" file="samtools_flagstat_out1.txt" /> | |
| 18 </test> | |
| 19 </tests> | |
| 20 <help> | |
| 21 | |
| 22 **What it does** | |
| 23 | |
| 24 This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file. | |
| 25 | |
| 26 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | |
| 27 | |
| 28 ------ | |
| 29 | |
| 30 **Citation** | |
| 31 | |
| 32 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ | |
| 33 | |
| 34 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* | |
| 35 | |
| 36 </help> | |
| 37 </tool> |