<tool id="bwa_mem2" name="BWA-MEM2"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
    <macros>
        <import>read_group_macros.xml</import>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="xrefs"/>
    <command><![CDATA[
@pipefail@
@set_reference_fasta_filename@

## Begin BWA-MEM command line

bwa-mem2 mem
#if str( $output_sort ) == "unsorted":
    -t 1
#else
    -t "\${GALAXY_SLOTS:-1}"
#end if
## Verbosity is set to 1 (errors only)
-v 1

#if str( $fastq_input.fastq_input_selector ) == "paired_iv":
    ## For interleaved fastq files set -p option
    -p
    ## check that insert statistics is used
    #if str( $fastq_input.iset_stats ):
      -I '${fastq_input.iset_stats}'
    #end if
#end if

#if str( $analysis_type.analysis_type_selector ) not in ["illumina", "full"]:
    -x '$analysis_type.analysis_type_selector'
#elif str( $analysis_type.analysis_type_selector ) == "full":
    ## Algorithmic options
    #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":
        -k '${analysis_type.algorithmic_options.k}'
        -w '${analysis_type.algorithmic_options.w}'
        -d '${analysis_type.algorithmic_options.d}'
        -r '${analysis_type.algorithmic_options.r}'
        -y '${analysis_type.algorithmic_options.y}'
        -c '${analysis_type.algorithmic_options.c}'
        -D '${analysis_type.algorithmic_options.D}'
        -W '${analysis_type.algorithmic_options.W}'
        -m '${analysis_type.algorithmic_options.m}'
        ${analysis_type.algorithmic_options.S}
        ${analysis_type.algorithmic_options.P}
        ${analysis_type.algorithmic_options.e}
    #end if

    ## Scoring options
    #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set":
        -A '${analysis_type.scoring_options.A}'
        -B '${analysis_type.scoring_options.B}'
        -O '${analysis_type.scoring_options.O}'
        -E '${analysis_type.scoring_options.E}'
        -L '${analysis_type.scoring_options.L}'
        -U '${analysis_type.scoring_options.U}'
    #end if

    ## IO options
    #if str( $analysis_type.io_options.io_options_selector ) == "set":
        -T '${analysis_type.io_options.T}'
        -h '${analysis_type.io_options.h}'
        ${analysis_type.io_options.a}
        ${analysis_type.io_options.C}
        ${analysis_type.io_options.V}
        ${analysis_type.io_options.Y}
        ${analysis_type.io_options.M}
        ${analysis_type.io_options.five}
        ${analysis_type.io_options.q}
    #end if

#end if

## Handle read group options...
@define_read_group_helpers@
#if str( $fastq_input.fastq_input_selector ) == "paired":
    #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
#else:
    #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
#end if
@set_use_rg_var@
@set_read_group_vars@
#if $use_rg
    @set_rg_string@
    -R '$rg_string'
#end if

#if str( $fastq_input.fastq_input_selector ) == "paired":
    ## check that insert statistics is used
    #if str( $fastq_input.iset_stats ):
        -I '${fastq_input.iset_stats}'
    #end if

    '${reference_fasta_filename}'
    '${fastq_input.fastq_input1}' '${fastq_input.fastq_input2}'
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
    ## check that insert statistics is used
    #if str( $fastq_input.iset_stats ):
        -I '${fastq_input.iset_stats}'
    #end if

    '${reference_fasta_filename}'
    '${fastq_input.fastq_input1.forward}' '${fastq_input.fastq_input1.reverse}'
#else:
    '${reference_fasta_filename}'
    '${fastq_input.fastq_input1}'
#end if

#if str( $output_sort ) == "coordinate":
        | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
#elif str( $output_sort ) == "name":
        | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
#else
        | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output'
#end if


    ]]></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>
                <option value="paired_iv">Paired Interleaved</option>
            </param>
            <when value="paired">
                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
                <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
                <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
                    <sanitizer invalid_char="">
                        <valid initial="string.digits"><add value=","/> </valid>
                    </sanitizer>
                </param>
            </when>
            <when value="single">
                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
            </when>
            <when value="paired_collection">
                <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
                <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
                    <sanitizer invalid_char="">
                        <valid initial="string.digits"><add value=","/> </valid>
                    </sanitizer>
                </param>
            </when>
            <when value="paired_iv">
                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
                <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
                    <sanitizer invalid_char="">
                        <valid initial="string.digits"><add value=","/> </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>

        <expand macro="read_group_conditional" />

        <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.">
                        <option value="set">Set</option>
                        <option value="do_not_set" selected="True">Do not set</option>
                    </param>
                    <when value="set">
                        <param name="k" type="integer" value="19" label="Minimum seed length" help="-k; default=19"/>
                        <param name="w" type="integer" value="100" label="Band width for banded alignment" help="-w; default=100"/>
                        <param name="d" type="integer" value="100" label="Off-diagonal X-dropoff" help="-d; default=100"/>
                        <param name="r" type="float" value="1.5" label="Look for internal seeds inside a seed longer than -k * THIS VALUE" help="-r; default=1.5; This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy" />
                        <param name="y" type="integer" value="20" label="Seed occurrence for the 3rd round seeding" help="-y; default=20" />
                        <param name="c" type="integer" value="500" label="Skip seeds with more than that many occurrences" help="-c; default=500"/>
                        <param name="D" type="float" value="0.5" label="Drop chains shorter than this fraction of the longest overlapping chain" help="-D; default=0.5"/>
                        <param name="W" type="integer" value="0" label="Discard a chain if seeded bases shorter than THIS VALUE" help="-W; default=0"/>
                        <param name="m" type="integer" value="50" label="Perform at most this many rounds of mate rescues for each read" help="-m; default=50"/>
                        <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Skip mate rescue" help="-S"/>
                        <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip pairing; mate rescue performed unless -S also in use" help="-P"/>
                        <param name="e" type="boolean" truevalue="-e" falsevalue="" label="Discard full-length exact matches" help="-e"/>
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>

                <conditional name="scoring_options">
                    <param name="scoring_options_selector" type="select" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options.">
                        <option value="set">Set</option>
                        <option value="do_not_set" selected="True">Do not set</option>
                    </param>
                    <when value="set">
                        <param name="A" type="integer" value="1" label="Score for a sequence match" help="-A; scales options -T, -d, -B, -O, -E, -L, and -U unless overridden; default=1"/>
                        <param name="B" type="integer" value="4" label="Penalty for a mismatch" help="-B; default=4"/>
                        <param name="O" type="text" value="6,6" label="Gap open penalties for deletions and insertions" help="-O; default=6,6">
                            <sanitizer invalid_char="">
                                <valid initial="string.digits"><add value=","/> </valid>
                            </sanitizer>
                        </param>
                        <param name="E" type="text" value="1,1" label="Gap extension penalties; a gap of size k cost &#39;-O + -E*k&#39;. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" help="-E; default=1,1">
                            <sanitizer invalid_char="">
                                <valid initial="string.digits"><add value=","/> </valid>
                            </sanitizer>
                        </param>
                        <param name="L" type="text" value="5,5" label="Penalties for 5&#39;-end and 3&#39;-end clipping" help="-L; default=5,5; When performing Smith-Waterman extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best Smith-Waterman score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best Smith-Waterman score; clipping penalty is not deduced">
                            <sanitizer invalid_char="">
                                <valid initial="string.digits"><add value=","/> </valid>
                            </sanitizer>
                        </param>
                        <param name="U" type="integer" value="17" label="Penalty for an unpaired read pair" help="-U; default=17"/>
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>

                <conditional name="io_options">
                    <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
                        <option value="set">Set</option>
                        <option value="do_not_set" selected="True">Do not set</option>
                    </param>
                    <when value="set">
                        <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
                        <param argument="-q" type="boolean" truevalue="-q" falsevalue="" label="Don't lower MAPQ for split alignment" help="By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score."/>
                        <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
                        <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
                        <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
                        <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
                        <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
                        <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" />
                        <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard&lt;1.96 compatibility" />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>
            </when>
        </conditional>
        <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can extend the run time of the tool significantly (cause it requires running on only a single thread).">
            <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
            <option value="name">Sort by read names  (i.e., the QNAME field) </option>
            <option value="unsorted">Not sorted (sorted as input)</option>
        </param>
    </inputs>

    <outputs>
        <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
            <expand macro="dbKeyActionsBwaMem" />
            <change_format>
                <when input="output_sort" value="name" format="qname_sorted.bam" />
                <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <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="analysis_type_selector" value="illumina"/>
            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
        </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="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
            <param name="analysis_type_selector" value="illumina"/>
            <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="4" />
        </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.gz" value="bwa-mem-fastq1.fq.gz"/>
            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
            <param name="analysis_type_selector" value="illumina"/>
            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
        </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"/>
            <param name="PL" value="CAPILLARY"/>
            <param name="LB" value="AARDVARK-1" />
            <param name="analysis_type_selector" value="illumina"/>
            <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="4" />
        </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="analysis_type_selector" value="illumina"/>
            <param name="output_sort" value="unsorted"/>
            <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="4" />
        </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="analysis_type_selector" value="illumina"/>
            <param name="output_sort" value="name"/>
            <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="4" />
        </test>
        <test>
            <param name="reference_source_selector" value="cached" />
            <param name="ref_file" value="mtgenome"/>
            <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="analysis_type_selector" value="illumina"/>
            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[
**What is does**
BWA-MEM2 is the new version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.

The Galaxy implementation takes fastq files as input and produces output in BAM format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).

-----

**Indices: Selecting reference genomes for BWA**

Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:

  1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.
  2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa mem`.

If your genome of interest is not listed here you have two choices:

  1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
  2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.

-----

**Galaxy-specific option**

Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:

  1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]
  2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  <reference index> <PacBio dataset in fastq format>
  3. *Full list of options*: Allows access to all options through Galaxy interface.

-----

**Bam sorting mode**

The generated bam files can be sorted according to three criteria: coordinates, names and input order.

In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file. 

When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field). 

Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.


@RG@

@info@
    ]]></help>
    <expand macro="citations" />
</tool>