annotate bam_to_sam.xml @ 0:dc20f447c0e2 draft

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<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3">
  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <description>converts BAM format to SAM format</description>
  <command interpreter="python">
    bam_to_sam.py
      --input1=$input1
      --output1=$output1
      $header
  </command>
  <inputs>
    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
    <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
  </inputs>
  <outputs>
    <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
  </outputs>
  <tests>
    <test>
      <!--
      Bam-to-Sam command:
      samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
      -->
      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
      <param name="header" value="" />
      <output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
    </test>
    <test>
      <!--
      Bam-to-Sam command:
      samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
      bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
      -->
      <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
      <param name="header" value="" />
      <output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
    </test>
    <test>
      <!--
      Bam-to-Sam command:
      samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
      -->
      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
      <param name="header" value="--header" />
      <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
    </test>
  </tests>
  <help>

**What it does**

This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.

.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml

------

**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;`_

  </help>
</tool>