# HG changeset patch # User jtilman # Date 1363627108 -3600 # Node ID 621fa3daa2a1cc96b5761a9e659afd439cd84450 # Parent 702ac01fbef89675613c90371d6de8542d780b69 Updated tool definition for Flexbar 2.33 release diff -r 702ac01fbef8 -r 621fa3daa2a1 flexbar.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.pl Mon Mar 18 18:18:28 2013 +0100 @@ -0,0 +1,34 @@ +#!/usr/bin/env perl + +# Flexbar wrapper for Galaxy tool definition, version 2.33 +# Author: Johannes Roehr + +use warnings; +use strict; + +my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV]; + +my $call = join " ", @ARGV[0..($#ARGV - 4)]; + +system $call .' --target FlexbarTargetFile > '. $outFile and exit 1; + + +foreach(){ + + my $fileType; + + $fileType = $1 if /\.(\w+)$/; + $fileType = $format if /\.\w*fast\w$/; + $fileType = 'fasta' if /\.fasta$/; + $fileType = 'tabular' if $fileType eq 'lengthdist'; + + my $file = $_; + + s/_//g; + + my $name = "primary_". $id ."_". $_ ."_visible_". $fileType; + + rename $file, $name; + rename $name, $folder; +} + diff -r 702ac01fbef8 -r 621fa3daa2a1 flexbar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.xml Mon Mar 18 18:18:28 2013 +0100 @@ -0,0 +1,423 @@ + + + + + + + flexible barcode and adapter removal + + + flexbar + + + flexbar --version + + + + flexbar.pl flexbar + + --threads $threads + + --reads $reads + + #if $cReads2.select == "on": + #if $cReads2.reads2.ext == $reads.ext: + --reads2 $cReads2.reads2 + #end if + #end if + + + #if $reads.ext == "fasta": + --format fasta + #end if + #if $reads.ext == "fastq": + --format fastq + #end if + #if $reads.ext == "fastqsanger": + --format fastq-sanger + #end if + #if $reads.ext == "fastqsolexa": + --format fastq-solexa + #end if + #if $reads.ext == "fastqillumina": + --format fastq-i1.3 + #end if + #if $reads.ext == "csfasta": + --format csfasta + #end if + #if $reads.ext == "fastqcssanger": + --format csfastq + #end if + + + --max-uncalled $maxUncalled + --min-readlength $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 $cBarcodes.select == "on": + --barcodes $cBarcodes.barcodes + + #if $cBarcodes.cbReads.select == "yes": + --barcode-reads $cBarcodes.cbReads.bReads + #end if + + #if $cBarcodes.cbReads.select == "no": + $cBarcodes.cbReads.bKeep + #end if + + --barcode-trim-end $cBarcodes.bTrimEnd + + #if $cBarcodes.cbTailLen.select == "yes": + --barcode-tail-length $cBarcodes.cbTailLen.bTailLen + #end if + + #if $cBarcodes.cbMinOverlap.select == "yes": + --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap + #end if + + --barcode-threshold $cBarcodes.bThresh + + #if $cBarcodes.cbAlignScores.select == "yes": + --barcode-match $bMatch + --barcode-mismatch $bMismatch + --barcode-gap $bGap + #end if + #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 + + --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 $cLogging.select == "show": + $cLogging.logLevel + $cLogging.singleReads + $cLogging.lenDist + $cLogging.fastaOutput + $cLogging.numTags + $cLogging.remTags + $cLogging.rndTags + #end if + + + $output $output.id $__new_file_path__ $reads.ext + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Description** + +Flexbar is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases 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://sourceforge.net/projects/flexbar + +------ + +**Trim-end modes** + +**Any:** longer part of read remains + +**Left:** align before or at read end, right part remains + +**Right:** align after or at read start, left part remains + +**Left tail:** consider first n bases, see tail-length options + +**Right tail:** use only last n bases of reads in alignment + +------ + +**Documentation** + +Further documentation is available on the `manual`__ wiki page and via the command line help screen. + +.. __: http://sourceforge.net/p/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. + + + + +