| Next changeset 1:cf4ad98037d9 (2024-10-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687 |
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samblaster.xml test-data/output.bam test-data/splitters.bam test-data/sr.input.bam test-data/sr.input.sam.gz |
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| diff -r 000000000000 -r aa72470e14f7 samblaster.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samblaster.xml Mon Dec 19 15:18:40 2016 -0500 |
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| b'@@ -0,0 +1,211 @@\n+<tool id="samblaster" name="samblaster" version="0.1.24">\n+ <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>\n+ <requirements>\n+ <requirement type="package" version="0.1.24">samblaster</requirement>\n+ <requirement type="package" version="0.6.5">sambamba</requirement>\n+ </requirements>\n+ <version_command>samblaster --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $input.is_of_type(\'sam\'):\n+ #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h \'%s\')" % $input\n+ #else:\n+ #set stream="\'%s\'" % $input\n+ #end if\n+ sambamba view -t \\${GALAXY_SLOTS:-4} -h <(sambamba sort -t \\${GALAXY_SLOTS:-4} -n $stream -o /dev/stdout) |\n+ samblaster\n+ $output\n+ $discordantFile\n+ $splitterFile\n+ $unmappedFile\n+ $acceptDupMarks\n+ $excludeDups\n+ $removeDups\n+ $addMateTags\n+ $compatibility_mode\n+ --maxSplitCount \'$maxSplitCount\'\n+ --maxUnmappedBases \'$maxUnmappedBases\'\n+ --minIndelSize \'$minIndelSize\'\n+ --minNonOverlap \'$minNonOverlap\'\n+ --minClipSize \'$minClipSize\'\n+ #if $output != "-o /dev/null":\n+ && sambamba sort -o output.bam -l 6 -t \\${GALAXY_SLOTS:-4} <(sambamba view -S -f bam output.sam)\n+ #end if\n+ #if $discordantFile:\n+ && sambamba sort -o discordant.bam -l 6 -t \\${GALAXY_SLOTS:-4} <(sambamba view -S -f bam discordant.sam)\n+ #end if\n+ #if $splitterFile:\n+ && sambamba sort -o splitter.bam -l 6 -t \\${GALAXY_SLOTS:-4} <(sambamba view -S -f bam splitter.sam)\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param argument="--input" type="data" format="bam,sam"/>\n+ <param argument="--output" label="Output bam file for all input alignments" type="boolean" checked="true" truevalue="-o output.sam" falsevalue="-o /dev/null"/>\n+ <param argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d discordant.sam" falsevalue=""/>\n+ <param argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s splitter.sam" falsevalue=""/>\n+ <param argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/>\n+ <param argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/>\n+ <param argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/>\n+ <param argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/>\n+ <param argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/>\n+ <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="" />\n+ <param argument="--maxSplitCount" label="Maximum number of split alignments for a read to be included in splitter file." type="integer" value="2"/>\n+ <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"/>\n+ <param argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/>\n+ <param argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="'..b'upplemental*. If the\n+**-M** option is specified, alignments marked with either FLAG 0x100 or\n+0x800 are considered *supplemental*, and no alignments are considered\n+*secondary*. A *primary* alignment is always one that is neither\n+*secondary* nor *supplemental*. Only *primary* and *supplemental*\n+alignments are used to find chimeric (split-read) mappings. The **-M**\n+flag is used for backward compatibility with older SAM/BAM files in\n+which "chimeric" alignments were marked with FLAG 0x100, and should also\n+be used with output from more recent runs of *bwa mem* using its **-M**\n+option.\n+\n+**DISCORDANT READ PAIR IDENTIFICATION:** A **discordant** read pair is\n+one which meets all of the following criteria:\n+\n+1. Both side of the read pair are mapped (neither FLAG 0x4 or 0x8 is\n+ set).\n+2. The *properly paired* FLAG (0x2) is not set.\n+3. *Secondary* or *supplemental* alignments are never output as\n+ discordant, although a discordant read pair can have such alignments\n+ associated with them.\n+4. Duplicate read pairs that meet the above criteria will be output as\n+ discordant unless the **-e** option is used.\n+\n+**UNMAPPED/CLIPPED READ IDENTIFICATION:** An **unmapped** or **clipped**\n+read is a *primary* alignment that is unaligned over all or part of its\n+length respectively. The lack of a full alignment may be caused by a SV\n+breakpoint that falls within the read. Therefore, *samblaster* will\n+optionally output such reads to a FASTQ file for re-alignment by a tool,\n+such as `YAHA <https://github.com/GregoryFaust/yaha/>`__, geared toward\n+finding split-read mappings. *samblaster* applies the following strategy\n+to identify and output unmapped/clipped reads:\n+\n+1. An **unmapped** read has the *unmapped read* FLAG set (0x4).\n+2. A **clipped** read is a mapped read with a CIGAR string that begins\n+ or ends with at least **--minClipSize** unaligned bases (CIGAR code S\n+ and/or H), and is not from a read that has one or more *supplemental*\n+ alignments.\n+3. In order for *samblaster* to output the entire sequence for clipped\n+ reads, the input SAM file must have soft clipped primary alignments.\n+4. *samblaster* will output unmapped/clipped reads into a FASTQ file if\n+ QUAL information is available in the input file, and a FASTA file if\n+ not.\n+5. Unmapped/clipped reads that are part of a duplicate read pair will be\n+ output unless the **-e** option is used.\n+\n+\n+**Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab,\n+University of Virginia <http://faculty.virginia.edu/irahall/>`__\n+\n+**Please cite:** `Faust, G.G. and Hall, I.M., \xe2\x80\x9c\\ *SAMBLASTER*: fast\n+duplicate marking and structural variant read extraction,\xe2\x80\x9d\n+*Bioinformatics* Sept. 2014; **30**\\ (17):\n+2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__\n+\n+**Also see:** `SAMBLASTER\\_Supplemental.pdf\n+<https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__\n+for additonal discussion and statistics about the duplicates marked by\n+*samblaster* vs. *Picard* using the NA12878 sample dataset. Click the\n+preceeding link or download the file from this repository.\n+**Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab,\n+University of Virginia <http://faculty.virginia.edu/irahall/>`__\n+\n+**Please cite:** `Faust, G.G. and Hall, I.M., \xe2\x80\x9c\\ *SAMBLASTER*: fast\n+duplicate marking and structural variant read extraction,\xe2\x80\x9d\n+*Bioinformatics* Sept. 2014; **30**\\ (17):\n+2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__\n+\n+**Also see:** `SAMBLASTER\\_Supplemental.pdf\n+<https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__\n+for additonal discussion and statistics about the duplicates marked by\n+*samblaster* vs. *Picard* using the NA12878 sample dataset. Click the\n+preceeding link or download the file from this repository.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu314</citation>\n+ </citations>\n+</tool>\n' |
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