Mercurial > repos > rnateam > bctools
changeset 10:17603d9eee69 draft
Uploaded
author | rnateam |
---|---|
date | Tue, 17 Nov 2015 11:35:45 -0500 |
parents | b994884d5541 |
children | f5bb83740999 |
files | flexbar_split_RYYR_bcs.xml |
diffstat | 1 files changed, 107 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar_split_RYYR_bcs.xml Tue Nov 17 11:35:45 2015 -0500 @@ -0,0 +1,107 @@ + +<!-- Flexbar tool definition for Galaxy, version 2.5 --> +<!-- Author: Johannes Roehr --> +<!-- Modified by Daniel Maticzka as specialized tool for splitting binary barcodes. --> + + +<tool id="flexbar_split_RYYR_bcs" name="Split by binary barcodes" version="2.5"> + + <description>using RYYR IUPAC pattern.</description> + + <requirements> + <requirement type="package" version="2.5">flexbar</requirement> + </requirements> + + <version_command>flexbar --version</version_command> + + <command> + + 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 + + --barcodes $__tool_directory__/RYYR_bcs.fa + + --barcode-reads $bReads + + --barcode-threshold $bThresh + + --max-uncalled $maxUncalled + --min-read-length $minReadLen + + > $output; + + mv flexbar_barcode_repA_1.fastq $output_repA_1; + mv flexbar_barcode_repA_2.fastq $output_repA_2; + mv flexbar_barcode_repB_1.fastq $output_repB_1; + mv flexbar_barcode_repB_2.fastq $output_repB_2; + + </command> + + + <inputs> + + <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> + + <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/> + + <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/> + + <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/> + + <param name="maxUncalled" size="4" type="integer" value="0" label="Max uncalled" optional="false" help="allowed uncalled bases per read"/> + + <param name="minReadLen" size="4" type="integer" value="18" label="Minimum read length" optional="false" help="shorter reads are discarded"/> + + </inputs> + + <stdio> + <exit_code range="1:" level="fatal" description="Error!" /> + </stdio> + + <outputs> + <data format="txt" name="output" metadata_source="reads"/> + <data format="fastq" name="output_repA_1"/> + <data format="fastq" name="output_repA_2"/> + <data format="fastq" name="output_repB_1"/> + <data format="fastq" name="output_repB_2"/> + </outputs> + + + <help> + +**Description** + +This tool splits paired-end reads according to an external set of barcode reads in RY IUPAC format according to patterns RYYR and YRRY using Flexbar. + +.. _project: https://github.com/seqan/flexbar + +------ + +**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. + + </help> + +</tool>