<macros>
    <token name="@discosnp_single_reads@"><![CDATA[
        #for $input in $input_type_options.list_reads
            #set $filename = str($input) + "." + $input.ext
            ln -sf '${input}' '${filename}' &&
            echo '${filename}' >> input.lst &&
        #end for
    ]]></token>
    <token name="@discosnp_paired_reads@"><![CDATA[
        #for $i, $paired in enumerate( $input_type_options.list_paired_reads )

            #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext
            ln -sf '${paired.forward}' '${filenameFWD}' &&

            #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext
            ln -sf '${paired.reverse}' '${filenameREV}' &&

            echo '${filenameFWD}' > "paired_${i}.lst" &&
            echo '${filenameREV}' >> "paired_${i}.lst" &&
            echo "paired_${i}.lst" >> input.lst &&

        #end for
    ]]></token>
    <token name="@lordec_inputs@"><![CDATA[
        -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
        -i '${program_type_choice.i}'
        -k ${program_type_choice.k}
        -s ${program_type_choice.s}
    ]]></token>
    <xml name="lordec_inputs">
        <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
        <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
        <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
        <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
    </xml>
    <xml name="citations">
        <citations>
            <yield/>
            <citation type="doi">10.1186/s13742-015-0105-2</citation>
        </citations>
    </xml>
</macros>