--- a/chicViewpoint.xml	Wed Feb 05 19:38:12 2020 -0500
+++ b/chicViewpoint.xml	Wed Mar 11 17:23:23 2020 -0400
@@ -14,7 +14,7 @@
             ln -s '$m' '$identifier' &&
         #end for
         #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
-       
+
         @BINARY@
 
             --matrices $m
@@ -35,13 +35,13 @@
                         label="Reference points"
                         help="Bed file contains all reference points which should be used to create viewpoints." />
         <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="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 argument="--backgroundModelFile" type="data" format='tabular'
                         label="Background model"
                         help="The background file computed by chicViewpointBackgroundModel" />
-        <param argument="--averageContactBin" type="integer" value="5"  label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>    
-        <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 argument="--averageContactBin" type="integer" value="5"  label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
+        <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='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt'  falsevalue="" checked="false" label="Save interaction file names (batch processing)"
                     help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
     </inputs>
@@ -56,49 +56,49 @@
     <tests>
         <test>
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
-            
+
             <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
-            <param name="backgroundModelFile" value="cHi-C/background.bed"/>
+            <param name="backgroundModelFile" value="cHi-C/background.txt"/>
             <param name="fixateRange" value="500000"/>
             <param name="rangeUpstream" value="200000"/>
             <param name="rangeDownstream" value="200000"/>
             <param name="writeFileNamesToFile" value="True"/>
 
-           
+
             <output_collection name="interactionFilesCollection" type="list" count="6">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/>
-                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/>
-                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
 
-                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/>
-                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
             </output_collection>
             <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
-            
+
         </test>
         <test>
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
-            
+
             <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
-            <param name="backgroundModelFile" value="cHi-C/background.bed"/>
+            <param name="backgroundModelFile" value="cHi-C/background.txt"/>
             <param name="fixateRange" value="500000"/>
             <param name="rangeUpstream" value="200000"/>
             <param name="rangeDownstream" value="200000"/>
             <param name="writeFileNamesToFile" value="False"/>
 
-           
+
             <output_collection name="interactionFilesCollection" type="list" count="6">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/>
-                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/>
-                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
 
-                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/>
-                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
             </output_collection>
             <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
-            
+
         </test>
     </tests>
     <help><![CDATA[
@@ -109,10 +109,10 @@
 Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files
 are named by the name of the reference point, the sample name and  the location of the reference point:
 
-gene_matrix_name_chr_start_end.bed
+gene_matrix_name_chr_start_end.txt
 
 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
-file all the file names will be written to; in the case of multiple samples two consecutive lines are consideres as treatment vs control in the differential analysis.
+file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis.
 
 For more information about HiCExplorer please consider our documentation on readthedocs.io_