<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <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
        mkdir interactionFiles &&
        mkdir targetFolder &&
        mkdir aggregatedFilesFolder &&


        #for $file in $interactionFiles:
            #set identifier = @ESCAPE_IDENTIFIER_FILE@
            ln -s '$file' 'interactionFiles/$identifier' &&
        #end for

        #for $file in $targetFiles:
            #set identifier = @ESCAPE_IDENTIFIER_FILE@
            ln -s '$file' 'targetFolder/$identifier' &&
        #end for

        #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
            #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
            #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])

        #end if
        @BINARY@
            #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
                --interactionFile $interactonfileslist
                --targetFile $targetfileslist
            #else:
                --interactionFile $batchmode_conditional.interactionFilesOrderFile
                --interactionFileFolder interactionFiles
                --targetFileFolder targetFolder
                --targetFile $batchmode_conditional.targetFilesOrderFile
                --batchMode
                --writeFileNamesToFile aggregatedFilesBatch.txt
            #end if

            --outputFolder aggregatedFilesFolder
            -suffix aggregated.txt
            --threads @THREADS@

    ]]></command>
    <inputs>
        <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
        <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/>

        <conditional name="batchmode_conditional">
            <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
                <option value="optionBatchmode">Batch processing</option>
                <option value="optionSinglemode" selected="True">Single file processing</option>
            </param>
            <when value="optionBatchmode">
                <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
                <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order"/>

            </when>
            <when value="optionSinglemode">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
            <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
        </collection>
        <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
            <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt"/>

            <conditional name="batchmode_conditional">
                <param name="batchmode_selector" value='optionBatchmode'/>
                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
                <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
            </conditional>

            <output_collection name="aggregatedFilesCollection" type="list" count="6">
                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>

                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/>
                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/>

                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/>
                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/>
            </output_collection>

            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
        </test>
        <test>
            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt"/>

            <conditional name="batchmode_conditional">
                <param name="batchmode_selector" value='optionSinglemode'/>
            </conditional>

            <output_collection name="aggregatedFilesCollection" type="list" count="2">
                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
            </output_collection>
        </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>