<tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>compute a background model for cHi-C / HiChIP data</description>
    <macros>
        <token name="@BINARY@">chicViewpointBackgroundModel</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            ln -s '$m' '${counter}_matrix.$m.ext' &&
        #end for
        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])

        @BINARY@
            --matrices $m
            --averageContactBin $averageContactBin
            --fixateRange $fixateRange
            --referencePoints '$referencePoints'
            $truncateZeros
            --threads @THREADS@
            --outFileName background.txt
    ]]>    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_multiple_macro" />
        <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
        <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' />
        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' />
        <param argument='--truncateZeros' type='boolean' truevalue='--truncateZeros' falsevalue="" checked="false" label="Truncate zeros" help="Set this parameter if you want truncate zeros to fight over dispersion." />
    </inputs>
    <outputs>
        <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
            <param name="referencePoints" value="cHi-C/referencePoints.bed" />
            <output name="background" ftype="tabular">
                <assert_contents>
                    <has_text text="-500000" />
                    <has_text text="-498000" />
                    <has_n_columns n="5" />
                    <has_text text="nbinom" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
            <param name="truncateZeros" value="True" />
            <param name="referencePoints" value="cHi-C/referencePoints.bed" />
            <output name="background" ftype="tabular">
                <assert_contents>
                    <has_text text="476000" />
                    <has_text text="491000" />
                    <has_n_columns n="5" />
                    <has_text text="nbinom" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Compute a background model for cHi-C data analysis
==================================================

chicViewpointBackgroundModel computes for all given samples with all reference points a background model. For all relative distances to a reference point
a negative binomial distribution is fitted. Moreover, for each relative distance to a reference point the average value for this location is computed. Both
background models are used, the first one for p-value and significance computation, the second one to filter out interactions with a less x-fold over mean.

The background distributions are fixed at `--fixateRange` i.e. all distances lower / higher than this value use the fixed background distribution.

For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]>    </help>
    <expand macro="citations" />
</tool>