# HG changeset patch # User rnateam # Date 1448293324 18000 # Node ID 55b539a509f09a3b22b8b51ee16c2669b8f3ee7d # Parent f5bb8374099962a9cc56102b5ee1c8d949fc927b add flexbar_no_split diff -r f5bb83740999 -r 55b539a509f0 flexbar_no_split.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar_no_split.xml Mon Nov 23 10:42:04 2015 -0500 @@ -0,0 +1,345 @@ + + + + + + + + + + + flexible adapter removal (no barcodes version) + + + flexbar + + + flexbar --version + + + + flexbar + + --threads \${GALAXY_SLOTS:-1} + + --reads $reads + + --reads2 $reads2 + + #if $reads.ext == "fastqsanger": + --format sanger + #end if + #if $reads.ext == "fastqsolexa": + --format solexa + #end if + #if $reads.ext == "fastqillumina": + --format i1.3 + #end if + #if $reads.ext == "csfasta": + --color-space + #end if + #if $reads.ext == "fastqcssanger": + --color-space + #end if + + + --max-uncalled $maxUncalled + --min-read-length $minReadLen + + #if $trimEnds.select == "on": + --pre-trim-left $trimEnds.trimLeft + --pre-trim-right $trimEnds.trimRight + #end if + + #if $cTrimPhred.select == "on": + --pre-trim-phred $cTrimPhred.trimPhred + #end if + + #if $cTrimLen.select == "on": + --post-trim-length $cTrimLen.trimLen + #end if + + + #if $cAdapters.select == "on": + + #if $cAdapters.ccAdapters.select == "data": + --adapters $cAdapters.ccAdapters.adaptersData + #end if + + #if $cAdapters.ccAdapters.select == "seq": + --adapter-seq $cAdapters.ccAdapters.adapterSeq + #end if + + --adapter-trim-end $cAdapters.aTrimEnd + + #if $cAdapters.caTailLen.select == "yes": + --adapter-tail-length $cAdapters.caTailLen.aTailLen + #end if + + $cAdapters.aReadSet + + --adapter-min-overlap $cAdapters.aMinOverlap + --adapter-threshold $cAdapters.aThresh + + #if $cAdapters.caAlignScores.select == "yes": + --adapter-match $aMatch + --adapter-mismatch $aMismatch + --adapter-gap $aGap + #end if + #end if + + + #if $cOutput.select == "show": + $cOutput.fastaOutput + $cOutput.lenDist + $cOutput.singleReads + #end if + + #if $cLogging.select == "show": + $cLogging.logLevel + $cLogging.numTags + $cLogging.remTags + $cLogging.rndTags + #end if + + > $output; + + mv flexbar_1.fastq $output_1; + mv flexbar_2.fastq $output_2; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Description** + +A restricted version of the flexbar tool for use in workflows. This version is missing the ability to demultiplex barcoded runs. It is restricted to handling paired-end reads. For that reason there is always two fastq outputs, allowing the tool to be incorporated into workflows. + +Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. Flexbar is available on the project_ page. + +.. _project: https://github.com/seqan/flexbar + +------ + +**Trim-end modes** + +**Any:** longer side of read remains after overlap removal + +**Left:** right side remains after removal, align before or at read end + +**Right:** left part remains after removal, align after or at read start + +**Left tail:** consider first n bases of reads in alignment + +**Right tail:** use only last n bases, see tail-length options + +------ + +**Documentation** + +Further documentation is available on the `manual`__ wiki page and via the command line help screen. + +.. __: https://github.com/seqan/flexbar/wiki + +------ + +**Reference** + +Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905. + + + +