comparison bwa.xml @ 12:bd3a1e0de84c draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a

11:546ada4a9f43

      @read_group_options@

      "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
    #end if

    | samtools view -Sb - > temporary_bam_file.bam &&

    samtools sort -f temporary_bam_file.bam ${bam_output}
]]>
  </command>

  <inputs>
    <expand macro="reference_source_conditional" />

12:bd3a1e0de84c

      @read_group_options@

      "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
    #end if

    | samtools sort -O bam -o '$bam_output'
]]>
  </command>

  <inputs>
    <expand macro="reference_source_conditional" />