<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>computes viewpoints with the given reference points and a background model.</description>
    <macros>
        <token name="@BINARY@">chicViewpoint</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re

        #for $m in $matrix_h5_cooler_multiple:
            #set identifier = @ESCAPE_IDENTIFIER_M@
            ln -s '$m' '$identifier' &&
        #end for
        #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])

        @BINARY@
            --matrices $m
            --range $rangeUpstream $rangeDownstream
            --referencePoints '$referencePoints'
            --averageContactBin $averageContactBin
            --fixateRange $fixateRange
            --threads @THREADS@
            --backgroundModelFile '$backgroundModelFile'
            --outFileName interactionFiles.hdf5

    ]]>    </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 create viewpoints." />
        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />

        <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
        <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." />
    </inputs>
    <outputs>
        <data name="interactionFileNames" from_work_dir="interactionFiles.hdf5" format="h5" label="${tool.name} interaction file" />
    </outputs>
    <tests>
        <test>
            <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_chicViewpoint.bed" />
            <param name="backgroundModelFile" value="cHi-C/background.txt" />
            <param name="fixateRange" value="500000" />
            <param name="rangeUpstream" value="200000" />
            <param name="rangeDownstream" value="200000" />
            <output name="interactionFileNames" ftype="h5">
                <assert_contents>
                    <has_h5_attribute key="averageContactBin" value="5" />
                    <has_h5_attribute key="fixateRange" value="500000" />
                    <!-- <has_h5_attribute key="range" value="200000,200000" /> -->
                    <has_h5_attribute key="resolution" value="1000" />
                    <has_h5_attribute key="type" value="interactions" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Compute viewpoints for all given reference points
=================================================

Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files
are named by the name of the reference point, the sample name and  the location of the reference point:

gene_matrix_name_chr_start_end.txt

If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis.

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>