bed_gff_or_vcf_to_bigwig_converter.xml

<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.1" hidden="true">
    <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
    <requirements>
        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
        <requirement type="package" version="2.27.1">bedtools</requirement>
    </requirements>
    <command>
<![CDATA[
        ## Remove comments and sort by chromosome. Remove anything after ##FASTA in gff files.

        #if $input.is_of_type("gff"):
            sed -e '/^\#\#FASTA$/,\$d' '$input' | grep -v '^#' |
        #else:
            grep -v '^#' '$input' |
        #end if

        sort -k1,1 |

        ## Generate coverage bedgraph.
        bedtools genomecov -bg -i stdin -g '$chromInfo'

        ## Only use split option for bed and gff/gff3/gtf.
        #if $input.ext in [ 'bed', 'gff', 'gff3', 'gtf' ]:
            -split
        #end if

        ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this
        ## should only be used on systems with large RAM.
        ## | wigToBigWig stdin '$chromInfo' '$output'

        ## This can be used anywhere.
        > temp.bg && bedGraphToBigWig temp.bg '$chromInfo' '$output'
]]>
    </command>
    <inputs>
        <param format="bed,gff,vcf" name="input" type="data" label="Choose input file"/>
    </inputs>
    <outputs>
        <data format="bigwig" name="output"/>
    </outputs>
    <help>
    </help>
</tool>