root/galaxy-central/tools/samtools/sam_to_bam.xml

<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0">
  <description>converts SAM format to BAM format</description>
  <requirements>
    <requirement type="package">samtools</requirement>
  </requirements>
  <command interpreter="python">
sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} 
#if $source.index_source == "history":
--ref_file=$source.ref_file
#else
--ref_file="None"
#end if
--output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR}
  </command>
  <inputs>
    <conditional name="source">
      <param name="index_source" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <param name="input1" type="data" format="sam" label="SAM File to Convert">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
        </param>
      </when>
      <when value="history">
        <param name="input1" type="data" format="sam" label="Convert SAM file" />
        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="output1" format="bam"/>
  </outputs>
  <tests>
    <test>
      <!--
      Sam-to-Bam command:
      samtools faidx chr_m.fasta
      samtools view -bt chr_m.fasta.fai -o unsorted.bam test-data/3.sam
      samtools sort unsorted.bam sam_to_bam_out1
      chr_m.fasta is the reference file
      -->
      <param name="index_source" value="history" /> 
      <param name="input1" value="3.sam" ftype="sam" />
      <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
      <output name="output1" file="sam_to_bam_out1.bam" />
    </test>
    <test>
      <!--
      Sam-to-Bam command:
      samtools view -bt chr_m.fasta.fai -o unsorted.bam test-data/3.sam
      samtools sort unsorted.bam sam_to_bam_out2
      chr_m.fasta is the reference file and the index chr_m.fasta.fai 
      should be in the same directory
      -->
      <param name="index_source" value="cached" />
      <param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" />
      <param name="output1" file="sam_to_bam_out2.bam" />
    </test>
  </tests>
  <help>

**What it does**

This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.

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

  </help>
</tool>