view flexbar_split_RYYR_bcs.xml @ 43:ec95b7f878de draft

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<!-- 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 (replicate A) and YRRY (replicate B) 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>