<tool id="maftoaxt" name="mafToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        Convert file from MAF to axt format
    </description>
    <macros>
        <token name="@TOOL_VERSION@">469</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">ucsc-maftoaxt</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        mafToAxt
            '$in_maf'
            #if $tar_seq.tarSeq == "customTar"
                '$tar_seq.targetSeq'
            #else
                first
            #end if
            '$querySeq'
            '$out'
            $stripDb
        ]]></command>
        <inputs>
            <param name="in_maf" format="maf" type="data" label="MAF dataset" />

            <conditional name="tar_seq">
                <param name="tarSeq" type="select" label="Select target sequence" optional="false" help="Which sequence from the MAF file should be used as the target sequence. ">
                    <option value="" selected="true">Use the first sequence of the block as the target</option>
                    <option value="customTar">Specify the target sequence by name</option>
                </param>
                <when value="customTar">
                    <param optional="false" name="targetSeq" type="text" label="Name of sequence that should be used as target sequence" help="Must be present in the MAF file." />
                </when>
                <when value="" />
            </conditional>

            <param name="querySeq" type="text" optional="false" label="Name of sequence that should be used as the query sequence" help="Must be present in the MAF file." />
            <param argument="-stripDb" type="boolean" truevalue="-stripDb" falsevalue="" label="Strip names from start to the first period" help="'hg38.chr19' becomes 'chr19'" />

        </inputs>
        <outputs>
            <data name="out" format="axt" />
        </outputs>
        <tests>
            <test>
                <param name="in_maf" value="1.maf"/>
                <param name="querySeq" value="panTro1"/>
                <output name="out" file="1.axt"/>
            </test>
            <test>
                <param name="in_maf" value="1.maf"/>
                <param name="tarSeq" value="customTar"/>
                <param name="targetSeq" value="panTro1"/>
                <param name="querySeq" value="rn3"/>
                <output name="out" file="2.axt"/>
            </test>
        </tests>
        <help><![CDATA[
    **What it does**

    `mafToAxt`_ is a tool to convert `MAF`_ dataset to `axt`_ format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction.

    For implementation details see mafToAxt's `source code`_.

    .. _mafToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
    .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
    .. _MAF: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
    .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/mafToAxt/mafToAxt.c
        ]]>    </help>
        <citations>
            <citation type="doi">10.1093/bib/bbs038</citation>
        </citations>
    </tool>