# HG changeset patch # User jtilman # Date 1363625156 14400 # Node ID 702ac01fbef89675613c90371d6de8542d780b69 # Parent 9523892524673a5414f602572d72c46e7d4c3da0 Deleted selected files diff -r 952389252467 -r 702ac01fbef8 flexbar.pl --- a/flexbar.pl Fri Feb 22 05:31:55 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -#!/usr/bin/env perl - -# Flexbar wrapper for Galaxy tool definition, version 2.32 -# 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 952389252467 -r 702ac01fbef8 flexbar.xml --- a/flexbar.xml Fri Feb 22 05:31:55 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,417 +0,0 @@ - - - - - - - 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 - #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. - - - - -