--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chicAggregateStatistic.xml	Mon Dec 16 15:35:06 2019 -0500
@@ -0,0 +1,126 @@
+<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 $batchmode_conditional.targetFilesOrderFile
+                --batchMode
+                --writeFileNamesToFile aggregatedFilesBatch.txt
+            #end if
+            
+            --outputFolder aggregatedFilesFolder
+            -suffix aggregated.bed
+            --threads @THREADS@
+
+    ]]></command>
+    <inputs>
+        <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
+        <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/>
+
+        <conditional name="batchmode_conditional">
+            <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
+                <option value="optionBatchmode">Batch processing</option>
+                <option value="optionSinglemode" selected="True">Single file processing</option>
+            </param>
+            <when value="optionBatchmode">
+                <param name='interactionFilesOrderFile' type="data" format="tabular" label="Interaction file order"/> 
+                <param name='targetFilesOrderFile' type="data" format="tabular" label="Target file order"/> 
+
+            </when>
+            <when value="optionSinglemode">              
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
+            <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
+        </collection>
+        <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${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.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed"/>
+            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed"/>
+            
+            <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.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/>
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/>
+
+                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" ftype="interval" lines_diff="4"/>
+                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed" ftype="interval" lines_diff="4"/>
+               
+                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" ftype="interval" lines_diff="4"/>
+                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed" 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.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed"/>
+            <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed"/>
+            
+            <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.bed" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" ftype="interval" lines_diff="4"/>
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed" 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>