# HG changeset patch
# User iuc
# Date 1597400352 14400
# Node ID d6f5e51e97ece3f8a653a03a3c00885d9eaf6fe3
# Parent  63588847a75a9ef385ebf209121cd25539a82059
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"

diff -r 63588847a75a -r d6f5e51e97ec chicAggregateStatistic.xml
--- a/chicAggregateStatistic.xml	Tue Mar 24 13:47:20 2020 -0400
+++ b/chicAggregateStatistic.xml	Fri Aug 14 06:19:12 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
     <macros>
         <token name="@BINARY@">chicAggregateStatistic</token>
@@ -12,15 +12,27 @@
         mkdir aggregatedFilesFolder &&
 
 
-        #for $file in $interactionFiles:
-            #set identifier = @ESCAPE_IDENTIFIER_FILE@
-            ln -s '$file' 'interactionFiles/$identifier' &&
-        #end for
+        #if $tar_input_conditional.tar_input_selector == 'tar_input':
+            ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 
+            tar -C interactionFiles -xvf viewpoints.tar &&
+            
+            #if $targetFiles:
+                ln -s '$tar_input_conditional.targetFiles' targetFiles.tar && 
+                tar -C targetFolder -xvf targetFiles.tar &&
+            #end if
+        #else:
+            #for $file in $tar_input_conditional.interactionFiles:
+                #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                ln -s '$file' 'interactionFiles/$identifier' &&
+            #end for
 
-        #for $file in $targetFiles:
-            #set identifier = @ESCAPE_IDENTIFIER_FILE@
-            ln -s '$file' 'targetFolder/$identifier' &&
-        #end for
+            #for $file in $targetFiles:
+                #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                ln -s '$file' 'targetFolder/$identifier' &&
+            #end for
+
+        #end if
+
 
         #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
             #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
@@ -44,10 +56,31 @@
             -suffix aggregated.txt
             --threads @THREADS@
 
+        #if $tar:
+            && cd aggregatedFilesFolder
+            && tar -cvf ../aggregatedFilesFolder.tar *
+            && cd ..
+            && rm -rf aggregatedFilesFolder
+        #end if
+
     ]]></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="tar_input_conditional">
+            <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
+                <option value="tar_input">Tar file</option>
+                <option value="interval_input" selected="True">Interval files</option>
+            </param>
+            <when value="tar_input">
+                <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
+                <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false"/>
+            </when>
+            <when value="interval_input">
+                <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
+                <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/>
+            </when>
+        </conditional>
+        
 
         <conditional name="batchmode_conditional">
             <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
@@ -62,14 +95,21 @@
             <when value="optionSinglemode">
             </when>
         </conditional>
+        <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
+                help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
+   
     </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>
+        <data name="aggregatedFilesFolderTar" from_work_dir="aggregatedFilesFolder.tar" format="tar" label="Aggregated files tar.gz">
+            <filter>tar</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -108,6 +148,44 @@
                 <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>
+
+        <test>
+            <conditional name="tar_input_conditional">
+                <param name="tar_input_selector" value='interval_input'/>
+                <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>
+
+            <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>
+
+            <param name='tar' value='True'/>
+
+            <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
+            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
+        </test>
+
+         <test>
+            <conditional name="tar_input_conditional">
+                <param name="tar_input_selector" value='tar_input'/>
+                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/>
+                <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar"/>
+            </conditional>
+
+            <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>
+
+            <param name='tar' value='True'/>
+
+            <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
+            <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r 63588847a75a -r d6f5e51e97ec test-data/cHi-C/chicAggregateStatistic/batch_mode.tar
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diff -r 63588847a75a -r d6f5e51e97ec test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png
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