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author | iuc |
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date | Mon, 19 Dec 2016 15:18:40 -0500 |
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<tool id="samblaster" name="samblaster" version="0.1.24"> <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description> <requirements> <requirement type="package" version="0.1.24">samblaster</requirement> <requirement type="package" version="0.6.5">sambamba</requirement> </requirements> <version_command>samblaster --version</version_command> <command detect_errors="exit_code"><![CDATA[ #if $input.is_of_type('sam'): #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input #else: #set stream="'%s'" % $input #end if sambamba view -t \${GALAXY_SLOTS:-4} -h <(sambamba sort -t \${GALAXY_SLOTS:-4} -n $stream -o /dev/stdout) | samblaster $output $discordantFile $splitterFile $unmappedFile $acceptDupMarks $excludeDups $removeDups $addMateTags $compatibility_mode --maxSplitCount '$maxSplitCount' --maxUnmappedBases '$maxUnmappedBases' --minIndelSize '$minIndelSize' --minNonOverlap '$minNonOverlap' --minClipSize '$minClipSize' #if $output != "-o /dev/null": && sambamba sort -o output.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam output.sam) #end if #if $discordantFile: && sambamba sort -o discordant.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam discordant.sam) #end if #if $splitterFile: && sambamba sort -o splitter.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam splitter.sam) #end if ]]></command> <inputs> <param argument="--input" type="data" format="bam,sam"/> <param argument="--output" label="Output bam file for all input alignments" type="boolean" checked="true" truevalue="-o output.sam" falsevalue="-o /dev/null"/> <param argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d discordant.sam" falsevalue=""/> <param argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s splitter.sam" falsevalue=""/> <param argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/> <param argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/> <param argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/> <param argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/> <param argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/> <param name="compatibility_mode" argument="-M" label="Run in compatibility mode?" help="Both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM -M option." type="boolean" truevalue="-M" falsevalue="" /> <param argument="--maxSplitCount" label="Maximum number of split alignments for a read to be included in splitter file." type="integer" value="2"/> <param argument="--maxUnmappedBases" label="Maximum number of un-aligned bases between two alignments to be included in splitter file." type="integer" value="50" min="1"/> <param argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/> <param argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="integer" value="20" min="1"/> <param argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/> </inputs> <outputs> <data name="output_bam" format="bam" label="samblaster alignments on ${on_string}" from_work_dir="output.bam"> <filter>output</filter> </data> <data name="discordant_bam" format="bam" label="samblaster discordant alignments on ${on_string}" from_work_dir="discordant.bam"> <filter>discordantFile</filter> </data> <data name="splitter_bam" format="bam" label="samblaster split alignments on ${on_string}" from_work_dir="splitter.bam"> <filter>splitterFile</filter> </data> <data name="unmapped_fastq" format="fastqsanger" label="samblaster unmapped fastq on ${on_string}" from_work_dir="unmapped.fastq"> <filter>unmappedFile</filter> </data> </outputs> <tests> <test> <param name="input" value="sr.input.bam"/> <param name="output" value="true"/> <param name="discordandFile" value="false"/> <param name="splitterFile" value="true"/> <param name="unmappedFile" value="true"/> <output name="output_bam" file="output.bam" compare="sim_size"/> <output name="splitter_bam" file="splitters.bam" compare="sim_size"/> <output name="unmapped_fastq"> <assert_contents> <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" /> </assert_contents> </output> </test> <test> <param name="input" value="sr.input.sam.gz" ftype="sam"/> <param name="output" value="true"/> <param name="discordandFile" value="false"/> <param name="splitterFile" value="true"/> <param name="unmappedFile" value="true"/> <output name="output_bam" file="output.bam" compare="sim_size"/> <output name="splitter_bam" file="splitters.bam" compare="sim_size"/> <output name="unmapped_fastq"> <assert_contents> <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ *samblaster* ============ Summary ------- *samblaster* is a fast and flexible program for marking duplicates in **read-id grouped** paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, *samblaster* will require approximately 20MB of memory per 1M read pairs. Usage ----- See the `SAM File Format Specification <http://samtools.sourceforge.net/SAMv1.pdf>`__ for details about the SAM alignment format. By default, samblaster marks duplicates with SAM FLAG 0x400. The **--removeDups** option will instead remove duplicate alignments from the output file. **ALIGNMENT TYPE DEFINITIONS:** Below, we will use the following definitions for alignment types. Starting with *samblaster* release 0.1.22, these definitions are affected by the use of the **-M** option. By default, *samblaster* will use the current definitions of alignment types as specified in the `SAM Specification <http://samtools.sourceforge.net/SAMv1.pdf>`__. Namely, alignments marked with FLAG 0x100 are considered *secondary*, while those marked with FLAG 0x800 are considered *supplemental*. If the **-M** option is specified, alignments marked with either FLAG 0x100 or 0x800 are considered *supplemental*, and no alignments are considered *secondary*. A *primary* alignment is always one that is neither *secondary* nor *supplemental*. Only *primary* and *supplemental* alignments are used to find chimeric (split-read) mappings. The **-M** flag is used for backward compatibility with older SAM/BAM files in which "chimeric" alignments were marked with FLAG 0x100, and should also be used with output from more recent runs of *bwa mem* using its **-M** option. **DISCORDANT READ PAIR IDENTIFICATION:** A **discordant** read pair is one which meets all of the following criteria: 1. Both side of the read pair are mapped (neither FLAG 0x4 or 0x8 is set). 2. The *properly paired* FLAG (0x2) is not set. 3. *Secondary* or *supplemental* alignments are never output as discordant, although a discordant read pair can have such alignments associated with them. 4. Duplicate read pairs that meet the above criteria will be output as discordant unless the **-e** option is used. **UNMAPPED/CLIPPED READ IDENTIFICATION:** An **unmapped** or **clipped** read is a *primary* alignment that is unaligned over all or part of its length respectively. The lack of a full alignment may be caused by a SV breakpoint that falls within the read. Therefore, *samblaster* will optionally output such reads to a FASTQ file for re-alignment by a tool, such as `YAHA <https://github.com/GregoryFaust/yaha/>`__, geared toward finding split-read mappings. *samblaster* applies the following strategy to identify and output unmapped/clipped reads: 1. An **unmapped** read has the *unmapped read* FLAG set (0x4). 2. A **clipped** read is a mapped read with a CIGAR string that begins or ends with at least **--minClipSize** unaligned bases (CIGAR code S and/or H), and is not from a read that has one or more *supplemental* alignments. 3. In order for *samblaster* to output the entire sequence for clipped reads, the input SAM file must have soft clipped primary alignments. 4. *samblaster* will output unmapped/clipped reads into a FASTQ file if QUAL information is available in the input file, and a FASTA file if not. 5. Unmapped/clipped reads that are part of a duplicate read pair will be output unless the **-e** option is used. **Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab, University of Virginia <http://faculty.virginia.edu/irahall/>`__ **Please cite:** `Faust, G.G. and Hall, I.M., “\ *SAMBLASTER*: fast duplicate marking and structural variant read extraction,” *Bioinformatics* Sept. 2014; **30**\ (17): 2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__ **Also see:** `SAMBLASTER\_Supplemental.pdf <https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__ for additonal discussion and statistics about the duplicates marked by *samblaster* vs. *Picard* using the NA12878 sample dataset. Click the preceeding link or download the file from this repository. **Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab, University of Virginia <http://faculty.virginia.edu/irahall/>`__ **Please cite:** `Faust, G.G. and Hall, I.M., “\ *SAMBLASTER*: fast duplicate marking and structural variant read extraction,” *Bioinformatics* Sept. 2014; **30**\ (17): 2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__ **Also see:** `SAMBLASTER\_Supplemental.pdf <https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__ for additonal discussion and statistics about the duplicates marked by *samblaster* vs. *Picard* using the NA12878 sample dataset. Click the preceeding link or download the file from this repository. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btu314</citation> </citations> </tool>