view samtools_flagstat.xml @ 6:6757453c6af9 draft

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<tool id="samtools_0_1_18_mpileup" name="mpileup" version="1.0.0">
  <requirements>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <description>creates mpileup for VarScan2</description>
  <command>samtools mpileup "$input1" "$input2" > "$output1"
  </command>
  <inputs>
    <param name="input1" type="data" format="bam" label="BAM File" />
    <param name="input2" type="data" format="bam" label="BAM File" />
  </inputs>
  <outputs>
    <data name="output1" format="txt" />
  </outputs>
<!--
  <tests>
    <test>
      <param name="input1" value="unsorted.bam" ftype="bam" />
      <output name="output1" file="samtools_flagstat_out1.txt" />
    </test>
  </tests>
-->
  <help>

This tool runs the mpileup command of samtools 0.1.18
with flags -q 1 -B

  </help>
</tool>