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comparison samtools_flagstat.xml @ 4:10b658bef71a draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:54:34 -0400
parents 480404be9626
children 28eb6a47be96
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3:480404be9626 4:10b658bef71a
1 <tool id="samtools_flagstat" name="flagstat" version="1.0.3"> 1 <tool id="samtools_flagstat" name="Flagstat" version="2.0">
2 <requirements> 2 <description>tabulate descriptive stats for BAM datset</description>
3 <requirement type="package" version="1.1">samtools</requirement> 3 <macros>
4 </requirements> 4 <import>macros.xml</import>
5 <description>provides simple stats on BAM files</description> 5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
6 <command>samtools flagstat "$input1" > "$output1" 9 <command>samtools flagstat "$input1" > "$output1"
7 </command> 10 </command>
8 <inputs> 11 <inputs>
9 <param name="input1" type="data" format="bam" label="BAM File to Convert" /> 12 <param name="input1" type="data" format="bam" label="BAM File to Convert" />
10 </inputs> 13 </inputs>
11 <outputs> 14 <outputs>
12 <data name="output1" format="txt" /> 15 <data name="output1" format="txt" />
13 </outputs> 16 </outputs>
14 <tests> 17 <tests>
15 <test> 18 <test>
16 <param name="input1" value="3unsorted.bam" ftype="bam" /> 19 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
17 <output name="output1" file="samtools_flagstat_out1.txt" /> 20 <output name="output1" file="samtools_flagstat_out1.txt" />
18 </test> 21 </test>
19 </tests> 22 </tests>
20 <help> 23 <help>
21 24
22 **What it does** 25 **What it does**
23 26
24 This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file. 27 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
25 28
26 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml 29 200 + 0 in total (QC-passed reads + QC-failed reads)
27 30 0 + 0 secondary
28 ------ 31 0 + 0 supplementary
29 32 0 + 0 duplicates
30 **Citation** 33 25 + 0 mapped (12.50%:nan%)
31 34 200 + 0 paired in sequencing
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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_ 35 100 + 0 read1
33 36 100 + 0 read2
34 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* 37 0 + 0 properly paired (0.00%:nan%)
35 38 0 + 0 with itself and mate mapped
39 25 + 0 singletons (12.50%:nan%)
40 0 + 0 with mate mapped to a different chr
41 0 + 0 with mate mapped to a different chr (mapQ>=5)
42
36 </help> 43 </help>
44 <expand macro="citations"></expand>
37 </tool> 45 </tool>