--- a/hicBuildMatrix.xml	Thu Nov 02 11:11:01 2017 -0400
+++ b/hicBuildMatrix.xml	Mon Nov 27 11:15:32 2017 -0500
@@ -21,7 +21,7 @@
             #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
                 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
                 --minDistance $restrictionCutFileBinSize_conditional.minDistance
-                --maxDistance $restrictionCutFileBinSize_conditional.maxDistance          
+                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize          
             #end if
 
             #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
@@ -71,45 +71,45 @@
                 <option value="optionBinSize" selected="True">Bin size</option>
             </param>
             <when value="optionRestrictionCutFile">
-                <param argument="--restrictionCutFile" type="data" format="bed" optional="True"
-                        help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
-                            bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>
-                <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
+                <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
                         help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments
-                        (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/>
-                <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
+                        (i.e. the region between one restriction site and the next)." />
+                <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
                         help="Restriction sites that are closer that this distance are merged into one.
-                        This option only applies if --restrictionCutFile is given." argument="--minDistance"/>
-
-                <param name="maxDistance" type="integer" value="" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one"
-                        help="This option only applies if --restrictionCutFile is given."  argument="--maxDistance"/>
+                        This option only applies if --restrictionCutFile is given."/>
+                <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true"
+                        label="Maximum library insert size defines different cut offs based on the maximum expected library size"
+                        help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
+                              which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
+                              belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
+                              is too far away from the nearest restriction site." />
             </when>
             <when value="optionBinSize">
-                <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp"
-                        help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
-                        Otherwise all reads in the interval are considered. " argument="--binSize"/>
+                <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"
+                    help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
+                    Otherwise all reads in the interval are considered. "/>
             </when>
         </conditional>
 
-        <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
+        <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
             help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
-            &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/>
+            &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
 
         <expand macro="region" />
 
         <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue=""
-            label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. '
- +                             'They will be counted and shown in the QC plots." />
+            label="Keep self circles"
+            help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
 
         <expand macro="minMappingQuality" />
 
-        <param name="danglingSequence" type="text" optional="true" label="The dangling sequence"
+        <param argument="--danglingSequence" type="text" optional="true" label="The dangling sequence"
             help="Dangling end sequence left by the restriction enzyme. For DpnII for example, 
                     the dangling end is the same restriction sequence. This is used
                     to discard reads that end/start with such sequence 
                     and that are considered un-ligated fragments or 
                     'dangling-ends'. If not given, such statistics will 
-                    not be available." argument="--danglingSequence"/>
+                    not be available."/>
     </inputs>
     <outputs>
         <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>