# HG changeset patch
# User bgruening
# Date 1580950559 18000
# Node ID 3f529510975e98dd8f845c3a895e42c6a538f862
# Parent  ae9cc6dbfaca17ffc2db9372fb3561dd31dc07a4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
diff -r ae9cc6dbfaca -r 3f529510975e hicTransform.xml
--- a/hicTransform.xml	Mon Dec 16 15:41:36 2019 -0500
+++ b/hicTransform.xml	Wed Feb 05 19:55:59 2020 -0500
@@ -10,7 +10,16 @@
         ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
         @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'
         --method $method_selector
+        #if $ligation_factor:
+            $ligation_factor
+        #end if
+        $perChromosome
+        #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
+        #if chroms:
+            --chromosomes $chroms
+        #end if
         --outFileName 'matrix.$matrix_h5_cooler.ext'
+
         && mv 'matrix.$matrix_h5_cooler.ext' matrix
 ]]>
     
@@ -18,12 +27,19 @@
         
         
                 
-                
+                
                 
                 
                 
         
-
+        
+        
+        
+            
+                
+            
+        
     
     
         
@@ -35,7 +51,18 @@
     
         
             
-            
+            
+            
+        
+        
+            
+            
+            
+