# HG changeset patch
# User iuc
# Date 1597399178 14400
# Node ID 38fa8a72ece64f8c0d44c604b75a55c4733eb525
# Parent  7668fac6cc3a9f52f2acc893096819d9dbcf4254
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"

diff -r 7668fac6cc3a -r 38fa8a72ece6 chicSignificantInteractions.xml
--- a/chicSignificantInteractions.xml	Tue Mar 24 13:42:40 2020 -0400
+++ b/chicSignificantInteractions.xml	Fri Aug 14 05:59:38 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>computes viewpoints with the given reference points and a background model</description>
     <macros>
         <token name="@BINARY@">chicSignificantInteractions</token>
@@ -12,12 +12,17 @@
         mkdir targetFolder &&
         mkdir significantFilesFolder &&
 
-        #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 &&
+        #else:
+            #for $file in $tar_input_conditional.interactionFiles:
+                #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                                    
+                ln -s '$file' 'interactionFiles/$identifier' &&
+            #end for
+        #end if
+    
         #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
             #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
         #end if
@@ -53,9 +58,36 @@
             --fixateRange $fixateRange
             -suffix significant_interactions.txt
             --threads @THREADS@
+
+            #if $tar:
+                && cd targetFolder
+                && tar -cvf ../targetFolder.tar *
+                && cd ..
+                && rm -rf targetFolder
+
+                && cd significantFilesFolder
+                && tar -cvf ../significantFilesFolder.tar *
+                && cd ..
+                && rm -rf significantFilesFolder
+
+            #end if
     ]]></command>
     <inputs>
+        <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"/>
+            </when>
+            <when value="interval_input">
         <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
+            </when>
+        </conditional>
+
+
+
         <conditional name="batchmode_conditional">
             <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
                 <option value="optionBatchmode">Batch processing</option>
@@ -96,6 +128,8 @@
         <param argument="--fixateRange" type="integer" value="500000"  label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
         <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues'  falsevalue="" checked="false" label="Truncate zeros by setting them to one."
                     help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision."/>
+        <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="significantFilesCollection" type="list" label="Significant files">
@@ -110,10 +144,19 @@
         <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names">
             <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
         </data>
+        <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar">
+            <filter>tar</filter>
+        </data>
+        <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar">
+            <filter>tar</filter>
+        </data>
     </outputs>
     <tests>
         <test>
-            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
+            <conditional name="tar_input_conditional">
+                <param name="tar_input_selector" value='interval_input'/>
+                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
+            </conditional>
             <conditional name="batchmode_conditional">
                 <param name="batchmode_selector" value='optionBatchmode'/>
                 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
@@ -149,7 +192,10 @@
             <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.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"/>
+            <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/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
+            </conditional>
             <conditional name="batchmode_conditional">
                 <param name="batchmode_selector" value='optionSinglemode'/>
                 <param name="computeSampleNumber" value="1"/>
@@ -174,6 +220,66 @@
                 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/>
                 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.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_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.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="computeSampleNumber" value='2'/>
+            </conditional>
+            <param name="pvalue" value='0.2'/>
+
+            <conditional name="filter_conditional">
+                <param name="filter_selector" value='optionLoosePvalue'/>
+                <param name="loosePvalue" value='0.5'/>
+            </conditional>
+
+            <param name="backgroundModelFile" value="cHi-C/background.txt"/>
+            <param name="rangeUpstream" value="200000"/>
+            <param name="rangeDownstream" value="200000"/>
+
+            <param name='tar' value='True'/>
+
+            <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
+            <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
+
+            <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
+            <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.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/viewpoints.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="computeSampleNumber" value='2'/>
+            </conditional>
+            <param name="pvalue" value='0.2'/>
+
+            <conditional name="filter_conditional">
+                <param name="filter_selector" value='optionLoosePvalue'/>
+                <param name="loosePvalue" value='0.5'/>
+            </conditional>
+
+            <param name="backgroundModelFile" value="cHi-C/background.txt"/>
+            <param name="rangeUpstream" value="200000"/>
+            <param name="rangeDownstream" value="200000"/>
+
+            <param name='tar' value='True'/>
+
+            <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
+            <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
+
+            <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
+            <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
         </test>
 
     </tests>
diff -r 7668fac6cc3a -r 38fa8a72ece6 test-data/cHi-C/chicAggregateStatistic/batch_mode.tar
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diff -r 7668fac6cc3a -r 38fa8a72ece6 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2.tar
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diff -r 7668fac6cc3a -r 38fa8a72ece6 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar
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diff -r 7668fac6cc3a -r 38fa8a72ece6 test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png
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diff -r 7668fac6cc3a -r 38fa8a72ece6 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png
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diff -r 7668fac6cc3a -r 38fa8a72ece6 test-data/cHi-C/chicSignificantInteractions/significantFilesFolder.tar
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diff -r 7668fac6cc3a -r 38fa8a72ece6 test-data/cHi-C/chicViewpoint/viewpoints.tar
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