view bbduk.xml @ 5:5127e62d11fb draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"

<tool id="bbmap_bbduk" name="bbduk" version="@VERSION@">
    <description> Compares reads to the kmers in a reference dataset, optionally
allowing an edit distance</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[
        bbduk.sh
        in1=${reads[0]} 
        in2=${reads[1]} 
        ref=${bbduk_adapters} 
        out1=${pair_id}_1.trimmed.fastq.gz 
        out2=${pair_id}_2.trimmed.fastq.gz 
        stats=${pair_id}.stats.txt 
        threads=${task.cpus} 
        minlen=${params.bbduk_minlen} 
        qtrim=${params.bbduk_qtrim} 
        trimq=${params.bbduk_trimq} 
        ktrim=${params.bbduk_ktrim} 
        k=${params.bbduk_k} 
        mink=${params.bbduk_mink} 
        hdist=${params.bbduk_hdist} 
        ${params.bbduk_trimbyoverlap} 
        ${params.bbduk_trimpairsevenly}
    ]]>    </command>

    <inputs>
        <param name="ref" type="data" format="fasta,fasta.gz" label="Reference assembly"/>
        <param name="reads" type="data" format="fastq,fastq.gz" label="Long reads"/>
    </inputs>

    <outputs>
        <data name="assembly" format="fasta" />
    </outputs>
    <help><![CDATA[
    “Duk” stands for Decontamination Using Kmers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation, subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass. Specifically, any combination of operations is possible in a single pass, with the exception of kmer-based operations (kmer trimming, kmer masking, or kmer filtering); at most 1 kmer-based operation can be done in a single pass. BBDuk2 allows multiple kmer-based operations in a single pass, and is otherwise equivalent to BBDuk.

    BBDuk’s parameters are described in its shellscript (bbduk.sh). This file provides usage examples of various common tasks.      
    ]]>    </help>
    <expand macro="citations" />

</tool>