Mercurial > repos > xuebing > sharplabtool
comparison tools/samtools/samtools_flagstat.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="samtools_flagstat" name="flagstat" version="1.0.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package">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 </help> | |
| 29 </tool> |