<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy1" profile="20.01">
    <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description>
    <macros>
        <import>macros_last.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        #if $db_opts.db_opts_input == 'lastdb'
            ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
        #end if

        last-split

        -f $output_format
        #if $db_opts.db_opts_input == 'db'
            -g '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
        #else if $db_opts.db_opts_input == 'lastdb'
            -g 'db_files/lastdb'
        #end if

        -d $lastsplit_opt.d
        -c $lastsplit_opt.c
        -t $lastsplit_opt.t
        -M $lastsplit_opt.M
        -S $lastsplit_opt.S
        -m $lastsplit_opt.m
        $lastsplit_opt.no_split
        -b \${GALAXY_MEMORY_MB:-2G}

        '$last_align'

        >'$outfile'
    ]]></command>

    <inputs>
        <expand macro="input_db" />
        <param name="last_align" type="data" format="maf" label="LASTal data file" />
        <param name="output_format" argument="-f" type="select" multiple="false" label="Output format">
            <option value="MAF">MAF</option>
            <option value="MAF+" selected="true">MAF+</option>
        </param>
        <section name="lastsplit_opt" title="Last-split options" expanded="false">
            <param argument="-d" type="select" multiple="false" label="RNA direction">
                <option value="0">Reverse</option>
                <option value="1" selected="true">Forward</option>
                <option value="2">Mixed</option>
            </param>    
            <param argument="-c" type="float" value="0.004" label="Cis-splice probability per base"/>
            <param argument="-t" type="float" value="0.00001" label="Trans-splice probability per base"/>
            <param argument="-M" type="float" value="7" label="Mean of ln[intron length]"/>
            <param argument="-S" type="float" value="1.7" label="Standard deviation of ln[intron length]"/>
            <param argument="-m" type="float" value="1" label="Maximum mismap probability"/>
            <!--<param name="score" argument="-s" type="int" value="lastal e" label="Minimum alignement score"/>-->
            <param name="no_split" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Write original, not split, alignement."/>
        </section>
    </inputs>

    <outputs>
        <data name="outfile" format="maf" label="LAST split from  ${on_string}" />
    </outputs>

    <tests>
        <test>
            <conditional name="db_opts">
                <param name="db_opts_input" value="db"/>
                <param name="database" value="humdb"/>
            </conditional>
            <param name="last_align" ftype="maf" value="last_align_gen.maf"/>
            <output name="outfile" ftype="maf" file="last_split.maf"  lines_diff="2"/>
        </test>
    </tests>

    <help>@LAST_HELP@</help>
    <citations><expand macro="citations"/></citations>
</tool>