# HG changeset patch
# User iuc
# Date 1597399355 14400
# Node ID ac7999229ac60bbcb1e12d0bc3d83de933645d66
# Parent  dbf82dd7bdb3920a00692a2f13292dabe4ac5e3a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"

diff -r dbf82dd7bdb3 -r ac7999229ac6 chicPlotViewpoint.xml
--- a/chicPlotViewpoint.xml	Tue Mar 24 14:12:09 2020 -0400
+++ b/chicPlotViewpoint.xml	Fri Aug 14 06:02:35 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>creates plots for viewpoints</description>
     <macros>
         <token name="@BINARY@">chicPlotViewpoint</token>
@@ -13,41 +13,51 @@
         mkdir significantFolder &&
         mkdir plots &&
 
+        #if $tar_input_conditional.tar_input_selector == 'tar_input':
+            ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 
+            tar -C interactionFiles -xvf viewpoints.tar &&
 
-        #for $file in $interactionFiles:
-            #set identifier = @ESCAPE_IDENTIFIER_FILE@
-            ln -s '$file' 'interactionFiles/$identifier' &&
-        #end for
+            #if $differentialFiles:
+                ln -s '$tar_input_conditional.differentialFiles' differential.tar && 
+                tar -C differentialFolder -xvf differential.tar &&
+            #end if
+            #if $significantFiles:
+                ln -s '$tar_input_conditional.significantFiles' significantFiles.tar && 
+                tar -C significantFolder -xvf significantFiles.tar &&
+            #end if
+        #else:
+            #for $file in $tar_input_conditional.interactionFiles:
+                #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                ln -s '$file' 'interactionFiles/$identifier' &&
+            #end for
 
-        #if $differentialFiles:
-            #for $file in $differentialFiles:
-                #set identifier = @ESCAPE_IDENTIFIER_FILE@
-                ln -s '$file' 'differentialFolder/$identifier' &&
+            #for $file in $tar_input_conditional.differentialFiles:
+                    #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                    ln -s '$file' 'differentialFolder/$identifier' &&
+            #end for
+
+            #for $file in $tar_input_conditional.significantFiles:
+                    #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                    ln -s '$file' 'significantFolder/$identifier' &&
             #end for
         #end if
 
-        #if $significantFiles:
-            #for $file in $significantFiles:
-                #set identifier = @ESCAPE_IDENTIFIER_FILE@
-                ln -s '$file' 'significantFolder/$identifier' &&
-            #end for
-        #end if
 
         #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
-            #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
-            #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ])
-            #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ])
+            #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ])
+            #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ])
+            #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ])
 
         #end if
 
         @BINARY@
             #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
                 --interactionFile $interactonfileslist
-                #if $differentialFiles:
+                #if $tar_input_conditional.differentialFiles:
                     --differentialTestResult $differentialfileslist
                 #end if
 
-                #if $significantFiles:
+                #if $tar_input_conditional.significantFiles:
                     --significantInteractions $significantfileslist
                 #end if
 
@@ -104,14 +114,34 @@
             #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
                 && mv out_plot.$image_file_format plots/out_plot.$image_file_format
             #end if
+
+            #if $tar:
+                && cd plots
+                && tar -cvf ../plots.tar *
+                && cd ..
+                && rm -rf plots
+            #end if
     ]]></command>
     <inputs>
-        <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
-        <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
-        <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='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='differentialFiles' type="data" format="tar" label="Rejected H0 files" multiple="true" optional='false'/>
+                <param name='significantFiles' type="data" format="tar" label="Significant interaction files" multiple="true" optional='false'/>
+            </when>
+            <when value="interval_input">
+                <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
+                <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
+                <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/>
+            </when>
+        </conditional>
 
-        <param name="rangeUpstream" type="integer" value="500000"  label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
-        <param name="rangeDownstream" type="integer" value="500000"  label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
+        <param name="rangeUpstream" type="integer" value="100000"  label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
+        <param name="rangeDownstream" type="integer" value="100000"  label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
         <param argument="--backgroundModelFile" type="data" format='tabular'
                         label="Background model"
                         help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
@@ -151,19 +181,26 @@
         <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 disturbing the presenation of small p-values."/>
   
-
+        <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="plotsCollection" type="list" label="cHi-C viewpoint plots">
             <discover_datasets pattern="__name_and_ext__" directory="plots" />
         </collection>
-
+        <data name="plotsTar" from_work_dir="plots.tar" format="tar" label="cHi-C viewpoint plots tar">
+            <filter>tar</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_4487435_4487435_Sox17.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_19093103_19093103_Tfap2d.txt"/>
-            <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
-            <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.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/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_4487435_4487435_Sox17.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_19093103_19093103_Tfap2d.txt"/>
+                <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
+                <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/>
+            </conditional>
 
 
             <conditional name="batchmode_conditional">
@@ -176,7 +213,6 @@
             <param name="pvalue" value='True'/>
             <param name="truncateZeroPvalues" value='True'/>
 
-            <!-- <param name="alpha" value='0.5'/> -->
             <param name='backgroundModelFile' value='cHi-C/background.txt'/>
             <param name='xFold' value='1.5'/>
             <output_collection name="plotsCollection" type="list" count="3">
@@ -187,7 +223,26 @@
 
         </test>
         <test>
-            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_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"/>
+            </conditional>
+
+            <conditional name="batchmode_conditional">
+                <param name="batchmode_selector" value='optionSinglemode'/>
+            </conditional>
+
+            <output_collection name="plotsCollection" type="list" count="1">
+                <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
+
+            </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"/>
+            </conditional>
 
             <conditional name="batchmode_conditional">
                 <param name="batchmode_selector" value='optionSinglemode'/>
@@ -200,16 +255,51 @@
         </test>
 
         <test>
-            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_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/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_4487435_4487435_Sox17.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_19093103_19093103_Tfap2d.txt"/>
+                <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
+                <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/>
+            </conditional>
 
             <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionSinglemode'/>
+                <param name="batchmode_selector" value='optionBatchmode'/>
+                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
+                <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
+                <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
+                <param name='computeSampleNumber' value='2'/>
+            </conditional>
+            <param name="pvalue" value='True'/>
+            <param name="truncateZeroPvalues" value='True'/>
+
+            <param name='backgroundModelFile' value='cHi-C/background.txt'/>
+            <param name='xFold' value='1.5'/>
+            <param name='tar' value='True'/>
+            <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' 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="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar"/>
+                <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar"/>
             </conditional>
 
-            <output_collection name="plotsCollection" type="list" count="1">
-                <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
+            <conditional name="batchmode_conditional">
+                <param name="batchmode_selector" value='optionBatchmode'/>
+                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
+                <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
+                <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
+                <param name='computeSampleNumber' value='2'/>
+            </conditional>
+            <param name="pvalue" value='True'/>
+            <param name="truncateZeroPvalues" value='True'/>
 
-            </output_collection>
+            <param name='backgroundModelFile' value='cHi-C/background.txt'/>
+            <param name='xFold' value='1.5'/>
+            <param name='tar' value='True'/>
+            <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' />
         </test>
     </tests>
     <help><![CDATA[
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