<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
    <macros>
        <token name="@BINARY@">chicAggregateStatistic</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re
        
        @BINARY@
        
            --interactionFile '$interactionFile'
            --outFileName aggregatedFile.hdf5
            #if $targetFormat_conditional.targetFormat_selector == 'hdf5':
                --targetFile '$targetFormat_conditional.targetFileHDF' 
            #else:
                --targetFile '$targetFormat_conditional.targetFileBED'
            #end if
            --threads @THREADS@

    ]]>    </command>
    <inputs>

    <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" />
     <conditional name="targetFormat_conditional">
            <param name="targetFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
                <option value="hdf5">Target file from chicSignificantInteractions (h5 / hdf5)</option>
                <option value="bed" selected="True">Regions of interest (bed)</option>
            </param>
            <when value="hdf5">
                <param name="targetFileHDF" type="data" format="h5" label="The target data file created by chicSignificantInteractions" />
            </when>
            <when value="bed">
                <param name="targetFileBED" type="data" format="bed" label="Regions of interest" help="BED file which stores a list of regions that are used to aggregate the data for the differntial test." />
            </when>
        </conditional>
     </inputs>
    <outputs>
          <data name="aggregatedFile" from_work_dir="aggregatedFile.hdf5" format="h5" label="Aggregated file" />
    </outputs>
    <tests>
        <test>
            <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
            <conditional name="targetFormat_conditional">
                <param name="targetFormat_selector" value="hdf5" />
                <param name="targetFileHDF" value="cHi-C/chicSignificantInteractions/targetFile_dual.hdf5" />
            </conditional>
            <output name="aggregatedFile" ftype="h5">
                <assert_contents>
                    <has_h5_attribute key="type" value="aggregate" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />

            <conditional name="targetFormat_conditional">
                <param name="targetFormat_selector" value="bed" />
                <param name="targetFileBED" value="cHi-C/target_list.bed" />
            </conditional>
            <output name="aggregatedFile" ftype="h5">
                <assert_contents>
                    <has_h5_attribute key="type" value="aggregate" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Aggregate statistic for differential testing
============================================

chicAggregateStatistic is a preprocessing tool for chicDifferentialTest. It takes two consecutive viewpoint files and one target file and creates one
file containing all locations which should be tested for differential interactions. Either one target file for two consecutive viewpoint files or one
target file for all viewpoints is accepted.

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>