<tool id="hicup_filter" name="Hicup Filter" version="0.1.0">
        <description>classifies read pairs, identifying valid Hi-C di-tags.</description>

    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <expand macro="stdio" />

    <command><![CDATA[    
        hicup_filter --digest '$digest'
        #if $advanced_options.longest:
            --longest '$advanced_options.longest'
        #end if
        #if $advanced_options.shortest:
            --shortest '$advanced_options.shortest'
        #end if
        #for $file in $inputFiles:
            $file
        #end for
        && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects
        && mv *filt.sam dataset.filt.sam
        && mv hicup_filter_summary* hicup_filter_summary.txt
        && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam
        && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam  hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam 
        && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam
        && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam 
        && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam
        && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam
        #if $advanced_options.longest or $advanced_options.shortest: 
        && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam
        #end if
       
        && mv *filter_piechart.svg filter_piechart.svg
    ]]></command>
    <inputs>
        <param name="inputFiles" type="data" multiple="true" format="bam,sam" label="Input"/>
        <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/>
        <section name="advanced_options" title="Advanced options">
            <expand macro="filter_longest_shortest" />
        </section>
    </inputs>
    <outputs>
        <expand macro="filter_output" />
    </outputs>
    <tests>
        <test>
            <param name="digest" value="digester_file.txt" ftype="txt" />
            <param name="inputFiles" value="result.pair.sam" ftype="sam" />
            <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/>
            <output name="dataset_filt" file="dataset.filt.sam" lines_diff="8" />
            <output name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" />
            <output name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" />
            <output name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" />
            <output name="invalid_filter" file="dataset.invalid.filter.sam"  lines_diff="8" />
            <output name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" />
            <output name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" />
            <output name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" />
        </test>
    </tests>
    <help><![CDATA[

    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/

    To get more information about the filter visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Filter
    ]]></help>
    <expand macro="citation_hicup" />
</tool>