# HG changeset patch
# User iuc
# Date 1524814357 14400
# Node ID ec59bf4c3d06ef27c5c0d2525a834e911806e33f
# Parent  ccd1d30138274f0b9e872a02edd8ce505ace1f51
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
diff -r ccd1d3013827 -r ec59bf4c3d06 hicAggregateContacts.xml
--- a/hicAggregateContacts.xml	Wed Mar 07 03:37:18 2018 -0500
+++ b/hicAggregateContacts.xml	Fri Apr 27 03:32:37 2018 -0400
@@ -1,5 +1,6 @@
+
 
-    Takes a list of positions in the hic-matrix and makes a pooled image
+    allow plotting of aggregated Hi-C contacts between regions specified in a file
     
         hicAggregateContacts
         macros.xml
@@ -64,21 +65,21 @@
     
     
         
-        
+        
         
+            label="Interactions between regions in first and second BED file are plotted"/>
 
         
 
         
-            
+            
                 
             
         
 
         
+            help="The bed regions will be centered between -half number of bins
+            and +half number of bins indicated." />
 
         
-            
+                  cases, you might prefer kmeans.">
+            
             
         
 
@@ -111,15 +112,18 @@
             help="Clustering is by default carried out on the whole
                   submatrices. If this parameter is given, the
                   clustering is only carried out based on the submatrix
-                  diagonal (representing values at the same distance to each other)" />
+                  diagonal (representing values at the same distance to each other)." />
 
         
             
             
         
         
-        
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+        
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+        
 
         
             
@@ -134,7 +138,7 @@
 
     
     
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@@ -161,34 +165,50 @@
         
     
     
     
 
diff -r ccd1d3013827 -r ec59bf4c3d06 involucro
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diff -r ccd1d3013827 -r ec59bf4c3d06 macros.xml
--- a/macros.xml	Wed Mar 07 03:37:18 2018 -0500
+++ b/macros.xml	Fri Apr 27 03:32:37 2018 -0400
@@ -1,7 +1,6 @@
 
     \${GALAXY_SLOTS:-4}
-    2.1
-
+    2.1.2
     
         #if $use_range.select_use_range == "yes_use_range":
             --range $range_min:$range_max
@@ -28,7 +27,7 @@
     
     
          
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-    \${GALAXY_SLOTS:-4}
-<<<<<<< HEAD
-    2.0
-
-    
-        #if $use_range.select_use_range == "yes_use_range":
-            --range $range_min:$range_max
-        #end if
-    
-
-=======
-    2.1alpha1
->>>>>>> joachimwolff-master
-    
-        
-            hicexplorer
-            
-        
-        @BINARY@ --version
-    
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-    
-        
-            10.5281/zenodo.1133705
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-        #set $matrices = []
-        #set $mlabels = []
-        #for $counter, $i in enumerate($input_files):
-            ln -s $i.matrix #echo str($counter)+'_matrix'#;
-            #silent $matrices.append( '%s_matrix' % $counter )
-
-            #if str($i.mlabel.value) != "":
-                #set $mlabels += ['"%s"' % ($i.mlabel.value)]
-            #else
-                #set $mlabels += ['"%s"' % ($i.matrix.name)]
-            #end if
-        #end for
-        #set $mlabels = ' '.join($mlabels)
-        #set $matrices = ' '.join($matrices)
-    
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-        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
-            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
-                #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
-                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
-                #end if
-            #end if
-        #end if
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-.. class:: infomark
-
-For more information on the tools, please visit our `help site`_.
-
-If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
-
-This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
-
-.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
-.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-.. _help site: https://hicexplorer.readthedocs.org
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-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
-        #set files=[]
-        #set labels=[]
-        #for $i in $input_files:
-            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
-            #set $temp_input_path = $temp_input_handle.name
-            #silent $temp_input_handle.close()
-            #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
-            #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
-            #silent $files.append('%s.bam' % $temp_input_path)
-
-            ##set $files += [str($i.bamfile)]
-            #if str($i.label.value) != "":
-                #set $labels += ["\"%s\"" % ($i.label.value)]
-            #else
-                #set $labels += ["\"%s\"" % ($i.bamfile.name)]
-            #end if
-        #end for
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-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
-        #set files=[]
-        #set labels=[]
-        #for $i in $input_files:
-            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
-            #set $temp_input_path = $temp_input_handle.name
-            #silent $temp_input_handle.close()
-            #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
-            #silent $files.append('%s.bw' % $temp_input_path)
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-            ##set $files += [str($i.bigwigfile)]
-            #if str($i.label.value) != "":
-                #set $labels += ["\"%s\"" % ($i.label.value)]
-            #else
-                #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
-            #end if
-        #end for
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-    #if $source.ref_source=="history":
-        --genome $source.input1
-    #else:
-        --genome "${source.input1_2bit.fields.path}"
-    #end if
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-                output['saveMatrix'] is True
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-            ((
-                output['showOutputSettings'] == 'yes' and
-                output['saveData'] is True
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diff -r ccd1d3013827 -r ec59bf4c3d06 static/images/hicAggregateContacts.png
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diff -r ccd1d3013827 -r ec59bf4c3d06 static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png
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diff -r ccd1d3013827 -r ec59bf4c3d06 static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot (1).png
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diff -r ccd1d3013827 -r ec59bf4c3d06 test-data/small_matrix_50kb_pearson_pca1_plot.svg
--- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg	Wed Mar 07 03:37:18 2018 -0500
+++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg	Fri Apr 27 03:32:37 2018 -0400
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