Mercurial > repos > devteam > bwa_0_7_10
changeset 5:86c73f0eb389 draft default tip
Uploaded
| author | devteam |
|---|---|
| date | Thu, 06 Nov 2014 14:52:29 -0500 |
| parents | d04dfa7de2dc |
| children | |
| files | bwa-mem.xml |
| diffstat | 1 files changed, 69 insertions(+), 76 deletions(-) [+] |
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--- a/bwa-mem.xml Thu Nov 06 14:52:14 2014 -0500 +++ b/bwa-mem.xml Thu Nov 06 14:52:29 2014 -0500 @@ -1,5 +1,10 @@ <?xml version="1.0"?> -<tool id="bwa_mem_0_7_10" name="BWA-MEM" version="bwa-0.7.10-r837-dirty_galaxy_0.1"> +<tool id="bwa_mem_0_7_10" name="BWA-MEM" version="bwa-0.7.10-r837-dirty_galaxy_0.2"> + + <macros> + <import>bwa_macros.xml</import> + </macros> + <requirements> <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> <requirement type="package" version="1.1">samtools</requirement> @@ -56,8 +61,8 @@ #if str( $fastq_input.fastq_input_selector ) == "paired_iv": ## For interleaved fastq files set -p option -p - #if str( $fastq_input.iv_stats.iv_stats_selector ) == "True": ## check that insert statistics is used - -I "${fastq_input.iv_stats.iset_stats}" + #if str( $fastq_input.iset_stats ): ## check that insert statistics is used + -I "${fastq_input.iset_stats}" #end if #end if @@ -118,23 +123,37 @@ #if str( $fastq_input.fastq_input_selector ) == "paired": - #if str( $fastq_input.paired_stats.paired_stats_selector ) == "True": ## check that insert statistics is used - -I "${fastq_input.paired_stats.iset_stats}" + #if str( $fastq_input.iset_stats ): ## check that insert statistics is used + -I "${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": + + #if str( $fastq_input.iset_stats ): ## check that insert statistics is used + -I "${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 - | samtools view -Sb - > $bam_output + | samtools view -Sb - > temporary_bam_file.bam && + + samtools sort -f temporary_bam_file.bam ${bam_output} </command> @@ -155,71 +174,52 @@ </param> </when> <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> + <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> <option value="paired_iv">Paired Interleaved</option> </param> <when value="paired"> <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> - - <!-- PE stat selection block 1: If you make any changes in this conditional block, copy them to PE stat selection block 2 below as well --> - - <conditional name="paired_stats"> - <param name="paired_stats_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Specify insert size statistics?" help="-I; if you choose to not specify, it will be inferred from the data"/> - <when value="set"> - - <param name="iset_stats" type="text" value="250" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths in the form mean,sd,min,max" help="-I; 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="do_not_set"> - <!-- do nothing --> - </when> - </conditional> - - <!-- end of PE stat selection block 1 --> - + <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd 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" label="Select fastq dataset" help="Specify dataset with single reads"/> </when> + <when value="paired_collection"> + <param name="fastq_input1" format="fastqsanger" 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" size="10" label="Enter mean, standerd 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" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> - - <!-- PE stat selection block 2: If you make any changes in this conditional block, copy them to PE stat selection block 1 above as well --> - - <conditional name="iv_stats"> - <param name="iv_stats_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Specify insert size statistics?" help="-I; if you choose to not specify, it will be inferred from the data"/> - <when value="set"> - - <param name="iset_stats" type="text" value="250" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths in the form mean,sd,min,max" help="-I; 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="do_not_set"> - <!-- do nothing --> - </when> - </conditional> - - <!-- end of PE stat selection block 2 --> - + <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> + <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd 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> + <conditional name="rg"> - <param name="rg_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Specify readgroup information?" help="Specifying readgroup information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details"/> + <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying readgroup information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details"> + <option value="set">Set</option> + <option value="do_not_set" selected="True">Do not set</option> + </param> <when value="set"> <param name="ID" type="text" value="readgroup1" size="20" label="Specify readgroup ID" help="This value must be unique among multiple samples in your experiment"> <sanitizer invalid_char=""> @@ -252,7 +252,10 @@ </when> <when value="full"> <conditional name="algorithmic_options"> - <param name="algorithmic_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e 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"/> @@ -271,8 +274,12 @@ <!-- do nothing --> </when> </conditional> + <conditional name="scoring_options"> - <param name="scoring_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U 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; default=1"/> <param name="B" type="integer" value="4" label="penalty for mismatch" help="-B; default=4"/> @@ -297,8 +304,12 @@ <!-- do nothing --> </when> </conditional> + <conditional name="io_options"> - <param name="io_options_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M 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="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 this many hits with score >80% of the max score, output all in XA tag" help="-h; default=5"/> @@ -418,31 +429,13 @@ (4 sigma from the mean if absent) and min of the insert size distribution. FR orientation only. [inferred] ------- -.. class:: warningmark - -**An important note on Read Groups** - -One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do thid directly in BWA MEM interface using the -**Specify readgroup information?** widget. If you are not familiar with readgroups you shold know that this is effectively a way to tag reads with an additional ID. -This allows you to combine BAM files from, for example, multiple BWA MEM runs into a single dataset. This significantly simplifies downstream processing as -instead of dealing with multiple datasets you only have to handle only one. This is possible because the readgroup information allows you to identify -data from different experiments even if they are combined in one file. Many downstream analysis tools such as varinat callers (e.g., FreeBayes or Naive Varinat Caller -present in Galaxy) are aware of readgtroups and will automatically generate calls for each individual sample even if they are combined within a single file. +@dataset_collections@ ------ - -.. class:: infomark - -**More info** +@RG@ -To obtain more information about BWA MEM and ask questions use these resources: +@info@ - 1. https://biostar.usegalaxy.org/ - 2. https://www.biostars.org/ - 3. https://github.com/lh3/bwa - 4. http://bio-bwa.sourceforge.net/ </help>