# HG changeset patch
# User iuc
# Date 1597399965 14400
# Node ID 78b70d78a5963701ccc2717560893fa964ba44f1
# Parent  8fb5845264586412341cd73eb0868f7119774498
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"

diff -r 8fb584526458 -r 78b70d78a596 chicViewpoint.xml
--- a/chicViewpoint.xml	Tue Mar 24 14:32:20 2020 -0400
+++ b/chicViewpoint.xml	Fri Aug 14 06:12:45 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>computes viewpoints with the given reference points and a background model.</description>
     <macros>
         <token name="@BINARY@">chicViewpoint</token>
@@ -27,6 +27,13 @@
             --backgroundModelFile '$backgroundModelFile'
             --outputFolder interactionFiles
             $writeFileNamesToFile
+        
+        #if $tar:
+            && cd interactionFiles
+            && tar -cvf ../viewpoints.tar .
+            && cd ..
+            && rm -rf interactionFiles
+        #end if
 
     ]]></command>
     <inputs>
@@ -47,6 +54,9 @@
         
         <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt'  falsevalue="" checked="false" label="Save interaction file names (batch processing)"
                     help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
+        <param name='tar' type='boolean' checked="false" 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="interactionFilesCollection" type="list" label="Interaction files">
@@ -55,6 +65,9 @@
         <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
             <filter>writeFileNamesToFile</filter>
         </data>
+        <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar">
+            <filter>tar</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -103,6 +116,21 @@
             <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
 
         </test>
+        <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"/>
+            <param name="writeFileNamesToFile" value="True"/>
+            <param name='tar' value='True'/>
+
+            <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' />
+            <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
+
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicAggregateStatistic/batch_mode.tar
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2.tar
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicPlotViewpoint/batchMode/plots.tar
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicSignificantInteractions/significantFilesFolder.tar
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicSignificantInteractions/targetFolder.tar
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicViewpoint/output_1.tar
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diff -r 8fb584526458 -r 78b70d78a596 test-data/cHi-C/chicViewpoint/viewpoints.tar
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