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38 lines
1.2 KiB
XML
38 lines
1.2 KiB
XML
<tool id="samtools_flagstat" name="flagstat" version="1.0.0">
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<requirements>
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<requirement type="package">samtools</requirement>
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</requirements>
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<description>provides simple stats on BAM files</description>
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<command>samtools flagstat "$input1" > "$output1"
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</command>
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<inputs>
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<param name="input1" type="data" format="bam" label="BAM File to Convert" />
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</inputs>
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<outputs>
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<data name="output1" format="txt" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="3unsorted.bam" ftype="bam" />
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<output name="output1" file="samtools_flagstat_out1.txt" />
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</test>
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</tests>
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<help>
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**What it does**
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This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
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.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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------
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**Citation**
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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>`_
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If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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</help>
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</tool>
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