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<?xml version="1.0"?>
<tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0">
    <description>alignment with pipelign</description>
    <macros>
        <token name="@VERSION@">0.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">pipelign</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        pipelign -d files -c -i '$inFile' -o '$outFile' -t $lenThr -a $alphabet
            -p $simPer -r $run -e $merge -q \${GALAXY_SLOTS:-1}
            -s $mIterateLong -m $mIterateMerge -w $ambigPer
            $keepOrphans $keepBadSeqs $excludeClusters
    ]]></command>
    <inputs>
        <param argument="--inFile" type="data" format="fasta" label="Input sequence file" />
        <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" />
        <param argument="--alphabet" type="select" label="Alphabet for input sequences">
            <option value="dna">DNA</option>
            <option value="rna">RNA</option>
            <option value="aa">Amino Acids</option>
        </param>
        <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" />
        <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" />
        <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" help="Default: 0.8" />
        <param argument="--run" type="select" label="Parallelization version">
            <option value="J">Joblib</option>
            <option value="G">GNU</option>
        </param>
        <param argument="--merge" type="select" label="Merge strategy">
            <option value="P">Parallel</option>
            <option value="C">Consensus</option>
        </param>
        <param argument="--mIterateLong" type="integer" value="1" label="Number of iterations to refine long alignments" help="Default: 1" />
        <param argument="--mIterateMerge" type="integer" value="1" label="Number of iterations to refine merged alignment" help="Default: 1" />
        <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" help="Default: 0.1" />
        <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" />
    </inputs>
    <outputs>
        <data name="outFile" format="fasta" />
    </outputs>
    <tests>
        <test>
            <param name="inFile" value="pipelign-in1.fasta" />
            <output name="outFile" file="pipelign-out1.fasta" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

-------------------

A pipeline for automated multiple sequence alignment, particularly of viral sequences.

]]>
    </help>
    <citations>
        <citation type="bibtex">
            @UNPUBLISHED{spond,
                                author = "A.S.Md.M. Hossain, S.D.W.Frost",
                                title = "Pipelign: an alignment pipeline for viral sequences.",
                                year = "2019",
                                note = "https://github.com/asmmhossain/pipelign/",
                                url = "https://github.com/asmmhossain/pipelign/"}
        </citation>
    </citations>
</tool>