<tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        Chain together axt alignments
    </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-axtchain</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    axtChain
        -faQ
        -faT
        #if $minScore
            -minScore='$minScore'
        #end if
        #if $scoreScheme
            -scoreScheme='$scoreScheme'
        #end if
        #if str($linear_gap_options.linear_gap) == "linear_gap_file"
            -linearGap='${linear_gap_options.lineargap_input}'
        #else
            -linearGap=$linear_gap_options.linear_gap
        #end if
        '$in_axt'
        '$in_target'
        '$in_query'
        '$out'
    ]]></command>
    <inputs>
        <param name="in_axt" format="axt" type="data" label="Alignments" />
        <param name="in_target" format="fasta" type="data" label="Target sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. hg38.chr1"/>
        <param name="in_query" format="fasta" type="data" label="Query sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. mm39.chr1"/>

        <conditional name="linear_gap_options">
            <param label="Specify type of linear gap costs to use" name="linear_gap" type="select">
                <option selected="true" value="loose">loose (chicken/human linear gap costs)</option>
                <option value="medium">medium (mouse/human linear gap costs)</option>
                <option value="linear_gap_file">Provide a dataset with linear gap costs</option>
            </param>
            <when value="medium" />
            <when value="loose" />
            <when value="linear_gap_file">
                <param name="lineargap_input" type="data" format="tabular" label="Read the linear gap costs from" help="See help for a sample file"/>
            </when>
        </conditional>

        <param argument="-minScore" type="integer" optional="true" label="Minimum score for chain" help="Default 1000" />
        <param argument="-scoreScheme" type="data" format="tabular" optional="true" label="Read the scoring matrix from a blastz-format file" />
    </inputs>
    <outputs>
        <data name="out" format="chain" />
    </outputs>
    <tests>
        <test>
            <param name="in_axt" value="hg38.chrM.mm39.chrM.axt" />
            <param name="in_target" value="hg38.chrM.fasta" />
            <param name="in_query" value="mm39.chrM.fasta" />
            <conditional name="linear_gap_options">
                <param name="linear_gap" value="medium" />
            </conditional>
            <output name="out" file="hg38.chrM.mm39.chrM.chain" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`axtChain`_ is a tool to chain together alignments in `axt`_ format. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously.

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

linearGap defaults:

loose::

    tablesize   11
    smallSize   111
    position    1       2       3       11      111     2111    12111   32111   72111   152111  252111
    qGap        325     360     400     450     600     1100    3600    7600    15600   31600   56600
    tGap        325     360     400     450     600     1100    3600    7600    15600   31600   56600
    bothGap     625     660     700     750     900     1400    4000    8000    16000   32000   57000

medium::

    tableSize   11
    smallSize   111
    position  	1   	2		3   	11  	111  	2111  	12111  32111   72111  152111  252111
    qGap    	350 	425 	450  	600  	900  	2900  	22900  57900  117900  217900  317900
    tGap    	350 	425 	450  	600  	900  	2900  	22900  57900  117900  217900  317900
    bothGap 	750 	825 	850 	1000 	1300  	3300  	23300  58300  118300  218300  318300


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