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<tool id="bwa_mem" name="Map with BWA-MEM" version="0.7.7">
  <requirements>
    <requirement type="package" version="0.7.7">bwa</requirement>
  </requirements>
  <description></description>
  <parallelism method="basic"></parallelism>
  <version_command>bwa 2&gt;&amp;1 | grep "Version: " | sed -e 's/Version: //'</version_command>
  <command interpreter="python">
    bwa_mem.py
      --threads="\${GALAXY_SLOTS:-1}"
      --fileSource="${genomeSource.refGenomeSource}"
      #if $genomeSource.refGenomeSource == "history":
        ##build index on the fly
        --ref="${genomeSource.ownFile}"
        --dbkey="${dbkey}"
      #else:
        ##use precomputed indexes
        --ref="${genomeSource.indices.fields.path}"
      #end if

      ## input file(s)
      --fastq="${paired.fastq}"
      #if $paired.sPaired == "paired":
        --rfastq="${paired.rfastq}"
      #end if

      ## output file
      --output="${output}"

      ## run parameters
      --genAlignType="${paired.sPaired}"
      --params="${params.source_select}"
      #if $params.source_select != "pre_set":
        --minEditDistSeed="${params.minEditDistSeed}"
        --bandWidth="${params.bandWidth}"
        --offDiagonal="${params.offDiagonal}"
        --internalSeeds="${params.internalSeeds}"
        --seedsOccurrence="${params.seedsOccurrence}"
        --mateRescue="${params.mateRescue}"
        --skipPairing="${params.skipPairing}"
        --seqMatch="${params.seqMatch}"
        --mismatch="${params.mismatch}"
        --gapOpen="${params.gapOpen}"
        --gapExtension="${params.gapExtension}"
        --clipping="${params.clipping}"
        --unpairedReadpair="${params.unpairedReadpair}"
        --interPairEnd="${params.interPairEnd}"
        --minScore="${params.minScore}"
        --mark="${params.mark}"

        #if $params.readGroup.specReadGroup == "yes"
          --rgid="${params.readGroup.rgid}"
          --rgsm="${params.readGroup.rgsm}"
          --rgpl="${params.readGroup.rgpl}"
          --rglb="${params.readGroup.rglb}"
          --rgpu="${params.readGroup.rgpu}"
          --rgcn="${params.readGroup.rgcn}"
          --rgds="${params.readGroup.rgds}"
          --rgdt="${params.readGroup.rgdt}"
          --rgfo="${params.readGroup.rgfo}"
          --rgks="${params.readGroup.rgks}"
          --rgpg="${params.readGroup.rgpg}"
          --rgpi="${params.readGroup.rgpi}"
        #end if
      #end if

      ## suppress output SAM header
      --suppressHeader="${suppressHeader}"
  </command>

  <inputs>
    <conditional name="genomeSource">
      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="indices" type="select" label="Select a reference genome">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <conditional name="paired">
      <param name="sPaired" type="select" label="Is this library mate-paired?">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single">
        <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
      </when>
      <when value="paired">
        <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
        <param name="rfastq" type="data" format="fastqsanger,fastqillumina" label="Reverse FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
      </when>
    </conditional>
    <conditional name="params">
      <param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List">
        <option value="pre_set">Commonly Used</option>
        <option value="full">Full Parameter List</option>
      </param>
      <when value="pre_set" />
      <when value="full">
        <param name="minEditDistSeed" type="integer" value="19" label="Minimum seed length" />
        <param name="bandWidth" type="integer" value="100" label="Band width for banded alignment" />
        <param name="offDiagonal" type="integer" value="100" label="off-diagonal X-dropoff" />
        <param name="internalSeeds" type="float" value="1.5" label="look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]" />
        <param name="seedsOccurrence" type="integer" value="10000" label="skip seeds with more than INT occurrences" />
        <param name="mateRescue" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skip seeds with more than INT occurrences" />
        <param name="skipPairing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skpe pairing, mate rescue performed unless -S also in use" />
        <param name="seqMatch" type="integer" value="1" label="score of a sequence match" />
        <param name="mismatch" type="integer" value="4" label="penalty for a mismatch" />
        <param name="gapOpen" type="integer" value="6" label="gap open penalty" />
        <param name="gapExtension" type="text" value="None" label="gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]" />
        <param name="clipping" type="integer" value="5" label="penalty for clipping" />
        <param name="unpairedReadpair" type="integer" value="17" label="penalty for an unpaired read pair" />
        <param name="interPairEnd" type="boolean" truevalue="True" falsevalue="False" checked="False" label="first query file consists of interleaved paired-end sequences" />
        <param name="minScore" type="integer" value="30" label="minimum score to output" />
        <param name="mark" type="boolean" truevalue="True" falsevalue="False" checked="False" label="mark shorter split hits as secondary (for Picard/GATK compatibility)" />

        <conditional name="readGroup">
          <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
            <option value="yes">Yes</option>
            <option value="no" selected="True">No</option>
          </param>
          <when value="yes">
            <param name="rgid" type="text" size="25" label="[Essential]Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG 
tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group 
IDs may be modified when merging SAM files in order to handle collisions." />
            <param name="rgpl" type="text" size="25" label="[Essential]Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, 
SOLID, HELICOS, IONTORRENT and PACBIO" />
            <param name="rglb" type="text" size="25" label="[Essential]Library name (LB)" help="Required if RG specified" />
            <param name="rgsm" type="text" size="25" label="[Essential]Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
            <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
            <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
            <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
            <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" />
            <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each 
flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by 
various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
            <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" />
            <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
            <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
          </when>
          <when value="no" />
        </conditional>
      </when>
    </conditional>
    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
  </inputs>

  <outputs>
    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
      <actions>
        <conditional name="genomeSource.refGenomeSource">
          <when value="indexed">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="bwa_indexes" column="1">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                <filter type="param_value" ref="genomeSource.indices" column="0"/>
              </option>
            </action>
          </when>
          <when value="history">
            <action type="metadata" name="dbkey">
              <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>
  </outputs>

  <tests>
    <test>
    </test>
    <test>
    </test>
    <test>
    </test>
  </tests>
  <help>
**What it does**

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. BWA-MEM, which is the latest algorithm, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

------

**Input formats**

BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or Illumina FASTQ format (galaxy type *fastqillumina*). Use the FASTQ Groomer to prepare your files.

------

**License and citation**

This tool uses `BWA`_, which is licensed separately. Please cite |Li2013|_.

.. _BWA: http://bio-bwa.sourceforge.net/
.. |Li2013| replace:: Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio.GN]
.. _Li2013: http://arxiv.org/abs/1303.3997
  </help>
</tool>