<?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
            --outDir files
            --clearExistingDirectory
            --inFile '$inFile'
            --outFile '$outFile'
            --lenThr $lenThr
            --alphabet $alphabet
            --simPer $simPer
            --merge $merge
            --thread \${GALAXY_SLOTS:-1}
            --mIterateLong $mIterateLong
            --mIterateMerge $mIterateMerge
            --ambigPer $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" />
        <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" min="1" label="Number of iterations to refine long alignments" />
        <param argument="--mIterateMerge" type="integer" value="1" min="1" label="Number of iterations to refine merged alignment" />
        <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" />
        <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">
                <assert_contents>
                    <has_line line="&gt;K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1" />
                    <has_line line="&gt;K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1" />
                    <has_line line="&gt;K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1" />
                    <has_line line="&gt;K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1" />
                    <has_line line="&gt;K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1" />
                    <has_line line="&gt;K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1" />
                    <has_line line="&gt;K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1" />
                    <has_line line="&gt;K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1" />
                </assert_contents>
            </output>
        </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>