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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
author thanhlv
date Wed, 18 Mar 2020 21:24:20 +0000
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5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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1 <tool id="bbmap_bbduk" name="bbduk" version="@VERSION@">
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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2 <description> Compares reads to the kmers in a reference dataset, optionally
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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3 allowing an edit distance</description>
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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4 <macros>
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5 <import>macros.xml</import>
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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10 <command detect_errors="exit_code"><![CDATA[
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11 bbduk.sh
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12 in1=${reads[0]}
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13 in2=${reads[1]}
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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14 ref=${bbduk_adapters}
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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15 out1=${pair_id}_1.trimmed.fastq.gz
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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16 out2=${pair_id}_2.trimmed.fastq.gz
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17 stats=${pair_id}.stats.txt
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18 threads=${task.cpus}
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19 minlen=${params.bbduk_minlen}
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20 qtrim=${params.bbduk_qtrim}
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21 trimq=${params.bbduk_trimq}
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22 ktrim=${params.bbduk_ktrim}
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23 k=${params.bbduk_k}
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24 mink=${params.bbduk_mink}
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25 hdist=${params.bbduk_hdist}
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26 ${params.bbduk_trimbyoverlap}
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27 ${params.bbduk_trimpairsevenly}
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28 ]]> </command>
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29
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30 <inputs>
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31 <param name="ref" type="data" format="fasta,fasta.gz" label="Reference assembly"/>
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32 <param name="reads" type="data" format="fastq,fastq.gz" label="Long reads"/>
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33 </inputs>
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34
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35 <outputs>
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36 <data name="assembly" format="fasta" />
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37 </outputs>
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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38 <help><![CDATA[
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39 “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.
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40
5127e62d11fb "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
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41 BBDuk’s parameters are described in its shellscript (bbduk.sh). This file provides usage examples of various common tasks.
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42 ]]> </help>
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43 <expand macro="citations" />
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44
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45 </tool>