<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="@TOOL_VERSION@" profile="22.05">
    <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="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
@pipefail@
@set_reference_fasta_filename@

## Begin BWA-MEM command line

bwa 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" help="Please note that minimap2 is recommended over BWA as the aligner for long-read or contig data, for which it outperforms BWA in speed and typically in accuracy (see tool help below).">
                <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>
        <!-- `samtools sort` in the new update adds PG lines to the output so the lines_diff is changed from "2" to "4" -->
        <test expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired_collection"/>
                <param name="fastq_input1">
                    <collection type="paired">
                        <element name="forward" value="bwa-mem-fastq1.fq" />
                        <element name="reverse" value="bwa-mem-fastq2.fq" />
                    </collection>
                </param>
            </conditional>
            <conditional name="analysis_type">
                <param name="analysis_type_selector" value="illumina"/>
            </conditional>
            <param name="output_sort" value="name"/>
            <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[

**What it does**

This Galaxy tool wraps the bwa-mem module of the BWA_ read mapping tool. For more details about the different modules of the BWA package see the `BWA manual`_.

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

From http://arxiv.org/abs/1303.3997:

BWA-MEM is an alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human.
It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment.
The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.

-----

@ref_genomes@

-----

**Analysis modes**

The tool supports different preconfigured analysis modes optimized for different types of input data. Alternatively, it allows you to take full control over all available options.

The preconfigured modes are:

  1. *Simple Illumina mode*

     This corresponds to the simplest possible and standard bwa mem application in which it aligns single or paired-end data to a reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]
  2. *PacBio mode*

     This mode is adjusted specifically for mapping of long PacBio subreads. It is running bwa mame with the `-x pacbio` option.
  3. *Nanopore 2D-reads mode*

     This mode is running bwa mem with the `-x ont2d` option.
  4. *Intra-sepcies contigs mode*

     This mode is running bwa mem with the `-x intractg` option.

.. class:: infomark

   Please note: minimap2_ is recommended over and outperforms BWA-MEM for most types of input data except for Illumina short reads. For Illumina short-read mapping you may also consider using `BWA-MEM2`_, which is about twice as fast as BWA-MEM.

-----

**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@

@links@
.. _minimap2: https://github.com/lh3/minimap2
.. _`BWA-MEM2`: https://github.com/bwa-mem2/bwa-mem2
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp324</citation>
        <citation type="doi">10.1093/bioinformatics/btp698</citation>
        <citation type="bibtex">@misc{1303.3997,
            Author = {Heng Li},
            Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
            Year = {2013},
            Eprint = {arXiv:1303.3997},
            url = {http://arxiv.org/abs/1303.3997},
            }</citation>
    </citations>
</tool>