view phe_samtools_mpileup.xml @ 15:b13db9e677b4 draft default tip

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<tool id="phe_samtools_mpileup" name="PHE MPileup" version="1.0">
  <description>PHE SNP and indel caller</description>
  <requirements>
      <requirement type="package" version="1.1">samtools</requirement>
      <requirement type="package" version="1.2">bcftools</requirement>
  </requirements>
  <stdio>
    <!-- Assume anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />
  </stdio>
  <command interpreter="bash">
    phe_samtools_mpileup.sh $input_bam $ref_file $outvcf
  </command>
  <inputs>
    <param name="input_bam" type="data" format="bam" label="BAM file" />
    <param name="ref_file" type="data" format="fasta" label="Using reference file" />
  </inputs>
  <outputs>
    <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" />
  </outputs>
  <tests>
      <test>
        <param name="input_bam" value="in_short.bam" ftype="bam" />
        <param name="ref_file" value="ref.fa" ftype="fasta" />
        <output name="outvcf" file="out.vcf" ftype="vcf" />
      </test>
  </tests>
  <help>

**Citation**

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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

  </help>
</tool>