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1 <tool id="samtools_flagstat" name="flagstat" version="1.0.3">
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2 <requirements>
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3
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3 <requirement type="package" version="1.1">samtools</requirement>
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4 </requirements>
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5 <description>provides simple stats on BAM files</description>
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6 <command>samtools flagstat "$input1" > "$output1"
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7 </command>
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8 <inputs>
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9 <param name="input1" type="data" format="bam" label="BAM File to Convert" />
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10 </inputs>
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11 <outputs>
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12 <data name="output1" format="txt" />
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13 </outputs>
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14 <tests>
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15 <test>
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16 <param name="input1" value="3unsorted.bam" ftype="bam" />
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17 <output name="output1" file="samtools_flagstat_out1.txt" />
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18 </test>
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19 </tests>
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20 <help>
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21
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22 **What it does**
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23
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24 This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
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25
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26 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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27
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28 ------
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29
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30 **Citation**
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31
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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>`_
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33
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34 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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35
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36 </help>
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37 </tool>
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