Mercurial > repos > iuc > bwa_mem2
diff bwa-mem2.xml @ 0:82217dccdbcf draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
| author | iuc |
|---|---|
| date | Fri, 08 Oct 2021 10:19:48 +0000 |
| parents | |
| children | b4a22d90cce9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-mem2.xml Fri Oct 08 10:19:48 2021 +0000 @@ -0,0 +1,399 @@ +<tool id="bwa_mem2" name="BWA-MEM2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>- map medium and long reads (> 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 "250" and "250,25" will work while "250,,10" 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 "250" and "250,25" will work while "250,,10" 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 "250" and "250,25" will work while "250,,10" 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 '-O + -E*k'. 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'-end and 3'-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 >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<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>