<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>Runs Dekker's iterative correction over a hic matrix.</description>
    <macros>
        <token name="@BINARY@">hicCorrectMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        ln -s '$matrix' temp_matrix.npz.h5 &&

        hicCorrectMatrix
            $mode.mode_selector
            --matrix temp_matrix.npz.h5

            ## special: --chromosomes is optional, but if given needs at least one argument
            #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomes ])
            #if chroms
                --chromosomes "$chroms"
            #end if

            #if $mode.mode_selector == 'correct':

                --iterNum $mode.iterNum
                --outFileName corrected_matrix.npz.h5

                #if $mode.filterThreshold_low and $mode.filterThreshold_large:
                    --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
                #end if

                #if $mode.inflationCutoff:
                    --inflationCutoff $mode.inflationCutoff
                #end if

                #if $mode.transCutoff:
                    --transCutoff $mode.transCutoff
                #end if

                #if $mode.sequencedCountCutoff:
                    --sequencedCountCutoff $mode.sequencedCountCutoff
                #end if

                $mode.skipDiagonal
                $mode.perchr

            #elif $mode.mode_selector == 'merge_failed':
                --plotName diagnostic_plot.png
                --outMatrixFile corrected_matrix.npz.h5
                #if $mode.xMax:
                    --xMax $mode.xMax
                #end if
                #if $mode.filterThreshold_low and $mode.filterThreshold_large:
                    --filterThreshold '$mode.filterThreshold_low' '$mode.filterThreshold_large'
                #end if
            #else:
                --plotName diagnostic_plot.png
                #if $mode.xMax:
                    --xMax $mode.xMax
                #end if
            #end if

]]>
    </command>
    <inputs>
        <param argument="--matrix" name="matrix" type="data" format="h5"
            label="Hi-C matrix" />

        <conditional name="mode">
            <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">
                <option value="diagnostic_plot">Diagnostic plot</option>
                <option value="correct">Correct matrix</option>
            </param>
            <when value="diagnostic_plot">
                <expand macro="xMax" />
            </when>
            <when value="correct">
                <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500"
                    label="Number of iterations" />

                <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true"
                    label="Inflation cutoff" value=""
                    help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
                    For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/>

                <param argument="--transCutoff" name="transCutoff" type="float" optional="true"
                    label="Trans region cutoff" value=""
                    help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/>

                <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float"
                    label="Sequenced count cutoff"
                    help="Each bin receives a value indicating the fraction that is covered by reads.
                        A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/>

                <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false"
                    label="Skip diagonal counts"/>

                <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
                    label="Normalize each chromosome separately" />
                <expand macro="filterThreshold" />

            </when>
        </conditional>

        <repeat name="chromosomes" min="0"
            title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
                    The order of the given chromosomes will be kept for the resulting corrected matrix">
            <param name="chromosome" type="text" value="" >
                <validator type="empty_field" />
            </param>
        </repeat>

    </inputs>
    <outputs>
        <data name="outFileName"  from_work_dir="corrected_matrix.npz.h5" format="h5">
            <filter>mode['mode_selector'] == "correct"</filter>
        </data>
        <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
            <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="small_test_matrix.h5" ftype="h5"/>
            <param name="mode_selector" value="correct"/>
            <repeat name="chromosomes">
                <param name="chromosome" value="chrUextra"/>
            </repeat>
            <repeat name="chromosomes">
                <param name="chromosome" value="chr3LHet"/>
            </repeat> 
            <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix" ftype="h5" value="small_test_matrix.h5"/>
            <param name="mode_selector" value="diagnostic_plot"/>
            <repeat name="chromosomes">
                <param name="chromosome" value="chrUextra"/>
            </repeat>
            <repeat name="chromosomes">
                <param name="chromosome" value="chr3LHet"/>
            </repeat> 
            <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Runs Dekker's iterative correction over a Hi-C matrix.

correct:         Run the iterative correction.

diagnostic_plot:  Plots a histogram of the coverage per bin together with the
modified z-score based on the median absolute deviation
method (see Boris Iglewicz and David Hoaglin 1993, Volume
16: How to Detect and Handle Outliers The ASQC Basic
References in Quality Control: Statistical Techniques,
Edward F. Mykytka, Ph.D., Editor.

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