--- a/hicConvertFormat.xml	Wed Feb 05 19:46:37 2020 -0500
+++ b/hicConvertFormat.xml	Wed Mar 11 16:59:15 2020 -0400
@@ -28,17 +28,17 @@
                 --matrices "matrix.h5"
                 --inputFormat h5
 
-            #end if 
+            #end if
             #if $xml_path.inputFormat_selector == 'optionHomer':
                 --matrices "matrix.homer"
                 --inputFormat homer
 
-            #end if 
+            #end if
             #if $xml_path.inputFormat_selector == 'optionHicpro':
                 --matrices "matrix.hicpro"
                 --bedFileHicpro "matrix.bed"
                 --inputFormat hicpro
-            #end if 
+            #end if
             #if $xml_path.inputFormat_selector == 'optionHic':
                 --matrices "matrix.hic"
                 #if $xml_path.resolutions:
@@ -47,7 +47,7 @@
                     --resolutions $resolutions
                 #end if
                 --inputFormat hic
-            #end if 
+            #end if
         </token>
         <import>macros.xml</import>
     </macros>
@@ -57,11 +57,11 @@
 
 
         ## single to single case
-        
+
 
         #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
             #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional
-        
+
             #if $xml_path.inputFormat_selector == 'optionCool':
                 ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" &&
 
@@ -71,12 +71,12 @@
 
             #end if
             #if $xml_path.inputFormat_selector == 'optionHomer':
-               ln -s "$xml_path.matrixHomer" "matrix.homer" && 
+               ln -s "$xml_path.matrixHomer" "matrix.homer" &&
 
             #end if
 
             #if $xml_path.inputFormat_selector == 'optionHicpro':
-                ln -s "$xml_path.matrixHicpro" "matrix.hicpro" && 
+                ln -s "$xml_path.matrixHicpro" "matrix.hicpro" &&
                 ln -s "$xml_path.bedHicpro" "matrix.bed" &&
             #end if
 
@@ -86,10 +86,10 @@
 
 
 
-            @BINARY@ 
+            @BINARY@
             @SINGLE_INPUT@
-            
-            
+
+
             --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
             --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
 
@@ -101,7 +101,7 @@
             #end if
         #end if
 
-        
+
         ### Set up links to matrices to have correct ending
         #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
             #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
@@ -155,7 +155,7 @@
                         ln -s '$m' "${counter}_matrix.hicpro" &&
                     #end for
                     #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ])
-                    
+
                     #for $counter, $bed in enumerate($xml_manyToOne.bedHicpro):
                         ln -s '$bed' "${counter}_matrix.bed" &&
                     #end for
@@ -165,7 +165,7 @@
             #end if
 
 
-        @BINARY@ 
+        @BINARY@
             --outputFormat mcool
 
             #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
@@ -180,21 +180,21 @@
                     --matrices "matrix.h5"
                     --inputFormat h5
 
-                #end if 
+                #end if
                 #if $xml_path.inputFormat_selector == 'optionHomer':
                     --matrices "matrix.homer"
                     --inputFormat homer
 
-                #end if 
+                #end if
                 #if $xml_path.inputFormat_selector == 'optionHicpro':
                     --matrices "matrix.hicpro"
                     --bedFileHicpro "matrix.bed"
                     --inputFormat hicpro
-                #end if 
+                #end if
                 #if $xml_path.inputFormat_selector == 'optionHic':
                     --matrices "matrix.hic"
                     --inputFormat hic
-                #end if 
+                #end if
             #end if
 
             #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'manyToOne_option':
@@ -232,7 +232,7 @@
             <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type">
                 <option value="singleMatrix" selected="True">single matrix</option>
                 <option value="multipleMatrix">multiple matrix</option>
-            </param>            
+            </param>
             <when value='singleMatrix'>
                 <expand macro='convertFormat_single_macro' />
                 <expand macro='convertFormat_single_output_macro' />
@@ -278,7 +278,7 @@
                     <param name='inputFormat_selector' value='optionCool'/>
                     <param name='matrix_h5_cooler' value='small_test_matrix.cool'/>
                 </conditional>
-                
+
                 <conditional name='outputFormat_conditional'>
                     <param name='outputFormat_selector' value='h5'/>
                 </conditional>
@@ -296,7 +296,7 @@
                     <param name='inputFormat_selector' value='optionH5'/>
                     <param name='matrix_h5_cooler' value='small_test_matrix.h5'/>
                 </conditional>
-                
+
                 <conditional name='outputFormat_conditional'>
                     <param name='outputFormat_selector' value='cool'/>
                 </conditional>
@@ -314,7 +314,7 @@
                     <param name='inputFormat_selector' value='optionCool'/>
                     <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
                 </conditional>
-                
+
                 <conditional name='outputFormat_conditional'>
                     <param name='outputFormat_selector' value='homer'/>
                 </conditional>
@@ -328,13 +328,13 @@
                     <param name='inputFormat_selector' value='optionCool'/>
                     <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
                 </conditional>
-                
+
                 <conditional name='outputFormat_conditional'>
                     <param name='outputFormat_selector' value='ginteractions'/>
                 </conditional>
             </conditional>
             <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tsv" compare="sim_size" delta="40000"/>
-            
+
         </test>
         <test>
             <conditional name='outputSingleMultiple_conditional'>
@@ -361,10 +361,10 @@
 
 Conversion of Hi-C matrices of different file formats. We support the conversion of hic to cool format via hic2cool,
 and homer, HicPro, h5 and cool format to h5, cool, homer or ginteractions format. Moreover, hicConvertFormat accepts multiple input files
-from one format with different resolutions and creates a mcool file. Each original file is stored under the path e.g. ::/resolutions/10000.
+from one format with different resolutions and creates a mcool file. Each original file is stored under a path, e.g. matrix.mcool::/resolutions/10000.
 A batch computation is possible, the number of input files and output files needs to match, all input files need to be of the same format type and
 all output files too.
-For input and output of cooler files special options are available, for all other formats they will be ignored.
+For input and output of cooler files, special options are available, for all other formats they will be ignored.
 HiCPro file format needs an additional bed file as input.
 
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_