root/galaxy-central/tools/samtools/bam_to_sam.xml @ 3

<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0">
  <requirements>
    <requirement type="package">samtools</requirement>
  </requirements>
  <description>converts BAM format to SAM format</description>
  <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command>
  <inputs>
    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
  </inputs>
  <outputs>
    <data name="output1" format="sam" />
  </outputs>
  <tests>
    <test>
      <!--
      Bam-to-Sam command:
      samtools view -o test-data/3.bam bam_to_sam_out1.sam
      -->
      <param name="input1" value="1.bam" ftype="bam" />
      <output name="output1" file="bam_to_sam_out1.sam" />
    </test>
    <test>
      <!--
      Bam-to-Sam command:
      samtools view -o test-data/1.sam bam_to_sam_out2.sam
      -->
      <param name="input1" value="3.bam" ftype="bam" />
      <param name="output1" file="bam_to_sam_out2.sam" />
    </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

  </help>
</tool>