--- a/multiqc.xml	Tue Dec 05 05:24:03 2017 -0500
+++ b/multiqc.xml	Sat Dec 23 15:57:55 2017 -0500
@@ -1,7 +1,7 @@
 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">1.2</token>
+        <token name="@WRAPPER_VERSION@">1.3</token>
         <token name="@LN_FILES@">
 <![CDATA[
 #for $file in $repeat.software_cond.input
@@ -134,6 +134,9 @@
     #elif str($repeat.software_cond.software) == "hisat2"
         #set $pattern = "HISAT2 summary stats:"
         @LN_FILES@
+    #elif str($repeat.software_cond.software) == "hicexplorer"
+        #set $pattern = "Min rest. site distance"
+        @LN_FILES@
     #elif str($repeat.software_cond.software) == "htseq"
         #set $pattern = "__too_low_aQual"
         @LN_FILES@
@@ -382,6 +385,7 @@
                     <option value="flexbar">Flexbar</option>
                     <option value="gatk">GATK (BaseRecalibrator or VariantEval output)</option>
                     <!--<option value="goleft_indexcov">goleft indexcov</option>-->
+                    <option value="hicexplorer">HiCExplorer</option>
                     <!--<option value="hicup">HiCUP</option>-->
                     <option value="hisat2">HISAT2</option>
                     <!--<option value="homer">HOMER</option>-->
@@ -467,6 +471,9 @@
                         <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
                     </repeat>
                 </when>
+                <when value="hicexplorer">
+                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/>
+                </when>
                 <when value="hisat2">
                     <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/>
                 </when>
@@ -727,6 +734,12 @@
             </repeat>
             <repeat name="results">
                 <conditional name="software_cond">
+                    <param name="software" value="hicexplorer" />
+                    <param name="input" value="hicexplorer1.log,hicexplorer2.log" />
+                </conditional>
+            </repeat>
+            <repeat name="results">
+                <conditional name="software_cond">
                     <param name="software" value="kallisto" />
                     <param name="input" value="kallisto_1.txt,kallisto_2.txt" />
                 </conditional>
@@ -763,6 +776,8 @@
                     <has_text text="kallisto_alignment" />
                     <has_text text="star_alignment_plot" />
                     <has_text text="tophat_alignment" />
+                    <has_text text="hicexplorer" />
+                    
                 </assert_contents>
             </output>
             <output_collection name="stats" type="list">
@@ -770,6 +785,7 @@
                 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="0"/>
                 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
                 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="0"/>
+                <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
                 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>