/tools/samtools/samtools_flagstat.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 29 lines · 25 code · 4 blank · 0 comment · 0 complexity · 01cd42218f46a97a1f53f3392bee37fc MD5 · raw file

  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. **What it does**
  22. This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
  23. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
  24. </help>
  25. </tool>