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<?xml version="1.0"?>
<tool id="hg_gc_percent" name="hgGcPercent" version="1.0">
    <description>Calculates GC percentages of a twoBit file</description>

    <macros>
        <import>ucsc_macros.xml</import>
    </macros>

    <expand macro="requirements_twobit">
        <requirement type="package" version="340">ucsc_gcpercent</requirement>
        <requirement type="package" version="340">ucsc_bigwig</requirement>
    </expand>

    <command detect_errors="exit_code">
<![CDATA[
    ## This tool generates a bigWig file instead of a gzip wiggle file in order
    ## to facilitate testing. Support for comparing gzip files will be added to
    ## Galaxy in 17.05: https://github.com/galaxyproject/galaxy/pull/3550

    twoBitInfo "${twobit_input}" "${twobit_input}.chromInfo" &&

    hgGcPercent -doGaps -noDots -verbose=0 -wigOut
        -win=${window_size}
        -overlap=${overlap}
        -file=stdout

        #if str($region_type.region_type_selector) == "chrom":
            -chr="${region_type.chrom_name}"
        #end if

        db_placeholder "${twobit_input}" |

        wigToBigWig stdin "${twobit_input}.chromInfo" "${bw_output}"
]]>
    </command>
    <inputs>
        <param name="twobit_input" type="data" format="twobit" label="twoBit input file" />

        <param name="window_size" type="integer" min="1" value="5"
            label="Window size"
            help="Size of the sliding window for calculating GC percentages (-win)" />

        <param name="overlap" type="integer" min="0" value="0"
            label="Overlap size"
            help="Size of overlap for the sliding window (-overlap)" />

        <conditional name="region_type">
            <param name="region_type_selector" type="select"
                    label="Choose the analysis region">
                <option value="all" selected="true">All scaffolds</option>
                <option value="chrom">Chromosome</option>
            </param>

            <when value="all"></when>

            <when value="chrom">
                <param name="chrom_name" type="text" label="Sequence name"
                        help="Process only this sequence in the twoBit file" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="bw_output" format="bigwig" />
    </outputs>
    <tests>
        <test>
            <!-- Test hgGcPercent with default settings -->
            <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
            <output name="bw_output" file="contigs_gc5Base.bw" />
        </test>
        <test>
            <!-- Test hgGcPercent with custom window and overlap -->
            <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
            <param name="window_size" value="100" />
            <param name="overlap" value="10" />
            <output name="bw_output" file="contigs_gc100Base_10overlap.bw" />
        </test>
        <test>
            <!-- Test hgGcPercent with only one chromosome -->
            <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
            <param name="region_type_selector" value="chrom" />
            <param name="chrom_name" value="contig12" />
            <output name="bw_output" file="contig12_gc5Base.bw" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

hgGcPercent uses a sliding window to calculate the GC percentages
of a genome assembly.

    ]]></help>

    <expand macro="citations" />
</tool>