Mercurial > repos > devteam > samtools_flagstat
annotate samtools_flagstat.xml @ 1:f92f13ccee76 draft
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
author | devteam |
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date | Thu, 27 Mar 2014 14:05:16 -0400 |
parents | 1bbde47ebd2a |
children | 728e2ed819a1 |
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1
f92f13ccee76
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
devteam
parents:
0
diff
changeset
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1 <tool id="samtools_flagstat" name="flagstat" version="1.0.1"> |
0 | 2 <requirements> |
1
f92f13ccee76
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
devteam
parents:
0
diff
changeset
|
3 <requirement type="package" version="0.1.19">samtools</requirement> |
0 | 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> |