comparison bwa-mem.xml @ 11:546ada4a9f43 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf

10:6069ffa8b240

<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="0.7.12">
  <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
  <macros>
    <import>read_group_macros.xml</import>
    <import>bwa_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <command>
<![CDATA[
    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&

        ## The following shell commands decide which of the BWA indexing algorithms (IS or BWTSW) will be run
        ## depending on the size of the input FASTA dataset
        ( size=`stat -c %s "${reference_source.ref_file}" 2>/dev/null`; ## Linux
          if [ $? -ne 0 ]; then
              size=\$(stat -f %z "${reference_source.ref_file}"); ## OSX
          fi &&
          if [ "\$size" -lt 2000000000 ]; then
              echo "Reference genome size is \$size bytes, generating BWA index with is algorithm";
              bwa index -a is "${reference_fasta_filename}";
          else
              echo "Reference genome size is \$size bytes, generating BWA index with bwtsw algorithm";
              bwa index -a bwtsw "${reference_fasta_filename}";
          fi
        ) &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    ## Begin BWA-MEM command line

    bwa mem
    -t "\${GALAXY_SLOTS:-1}"

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

  <inputs>

    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
        <option value="cached">Use a built-in genome index</option>
        <option value="history">Use a genome from history and build index</option>
      </param>
      <when value="cached">
        <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
          <options from_data_table="bwa_mem_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history">
        <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
      </when>
    </conditional>
    <conditional name="fastq_input">
      <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
        <option value="paired">Paired</option>
        <option value="single">Single</option>
        <option value="paired_collection">Paired Collection</option>

      <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
    </test>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
      <param name="fastq_input_selector" value="paired"/>
      <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
      <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
      <param name="rg_selector" value="set"/>
      <param name="ID" value="rg1"/>

11:546ada4a9f43

<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.1">
  <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
  <macros>
    <import>read_group_macros.xml</import>
    <import>bwa_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <command>
<![CDATA[
    @set_reference_fasta_filename@

    ## Begin BWA-MEM command line

    bwa mem
    -t "\${GALAXY_SLOTS:-1}"

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

  <inputs>
    <expand macro="reference_source_conditional" />
    <conditional name="fastq_input">
      <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
        <option value="paired">Paired</option>
        <option value="single">Single</option>
        <option value="paired_collection">Paired Collection</option>

      <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
    </test>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
      <param name="index_a" value="is"/>
      <param name="fastq_input_selector" value="paired"/>
      <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
      <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
      <param name="rg_selector" value="set"/>
      <param name="ID" value="rg1"/>