comparison bwa-mem.xml @ 2:b4dfb5470bf3 draft

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

1:8955a9521def

<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="0.4.2">
  <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>
    #set $reference_fasta_filename = "localref.fa"

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

        ## The following shell commands decide with of the BWA indexing algorithms (IS or BWTSW) will be run
        ## depending ob the size of the input FASTA dataset
           (
            size=`stat -c %s "${reference_fasta_filename}" 2&gt;/dev/null`;                  ## Linux
            if [ $? -eq 0 ];
            then
              if [ "\$size" -lt 2000000000 ];
              then
                bwa index -a is "${reference_fasta_filename}";
                echo "Generating BWA index with is algorithm";
              else
                bwa index -a bwtsw "${reference_fasta_filename}";
                echo "Generating BWA index with bwtsw algorithm";
              fi;
            fi;

            eval \$(stat -s "${reference_fasta_filename}" 2&gt;/dev/null);                   ## OSX
            if [ -n "\$st_size" ];
            then
              if [ "\$st_size" -lt 2000000000 ];
              then
                bwa index -a is "${reference_fasta_filename}";
                echo "Generating BWA index with is algorithm";
              else
                bwa index -a bwtsw "${reference_fasta_filename}";
                echo "Generating BWA index with bwtsw algorithm";
              fi;
            fi;
            ) &amp;&amp;

    #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}"

      #end if
    #end if

    #if str( $analysis_type.analysis_type_selector ) == "pacbio":
      -x pacbio
    #elif str( $analysis_type.analysis_type_selector ) == "full":
      #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":    ## Algorithmic options
        -k "${analysis_type.algorithmic_options.k}"
        -w "${analysis_type.algorithmic_options.w}"
        -d "${analysis_type.algorithmic_options.d}"

    #else:
      "${reference_fasta_filename}"
      "${fastq_input.fastq_input1}"
    #end if

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

    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>

    <conditional name="analysis_type">
      <param name="analysis_type_selector" type="select" label="Select analysis mode">
        <option value="illumina">1.Simple Illumina mode</option>
        <option value="pacbio">2.PacBio mode (-x pacbio)</option>
        <option value="full">3.Full list of options</option>
      </param>
      <when value="illumina">
        <!-- do nothing -->
      </when>
      <when value="pacbio">
        <!-- do nothing. all magic happens within <command> tag -->
      </when>
      <when value="full">
        <conditional name="algorithmic_options">
          <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.">

      <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"/>

2:b4dfb5470bf3

<?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}"

      #end if
    #end if

    #if str( $analysis_type.analysis_type_selector ) == "pacbio":
      -x pacbio
    #elif str( $analysis_type.analysis_type_selector ) == "ont2d":
      -x ont2d
    #elif str( $analysis_type.analysis_type_selector ) == "intractg":
      -x intractg
    #elif str( $analysis_type.analysis_type_selector ) == "full":
      #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":    ## Algorithmic options
        -k "${analysis_type.algorithmic_options.k}"
        -w "${analysis_type.algorithmic_options.w}"
        -d "${analysis_type.algorithmic_options.d}"

    #else:
      "${reference_fasta_filename}"
      "${fastq_input.fastq_input1}"
    #end if

    | samtools sort -O bam -o '$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>

    <conditional name="analysis_type">
      <param name="analysis_type_selector" type="select" label="Select analysis mode">
        <option value="illumina">1.Simple Illumina mode</option>
        <option value="pacbio">2.PacBio mode (-x pacbio)</option>
        <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
        <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
        <option value="full">5.Full list of options</option>
      </param>
      <when value="illumina">
        <!-- do nothing -->
      </when>
      <when value="pacbio">
        <!-- do nothing. all magic happens within <command> tag -->
      </when>
      <when value="ont2d">
        <!-- do nothing. all magic happens within <command> tag -->
      </when>
      <when value="intractg">
        <!-- do nothing. all magic happens within <command> tag -->
      </when>
      <when value="full">
        <conditional name="algorithmic_options">
          <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.">

      <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"/>