--- a/multiqc.xml	Sun Aug 05 18:26:28 2018 -0400
+++ b/multiqc.xml	Mon Aug 06 10:42:11 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
         <token name="@WRAPPER_VERSION@">1.5</token>
@@ -216,6 +216,14 @@
     #elif str($repeat.software_cond.software) == "kallisto"
         #set $pattern = "finding pseudoalignments for the reads"
         @LN_FILES@
+    #elif str($repeat.software_cond.software) == "macs2"
+        #set $pattern = "# This file is generated by MACS"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls')
+            grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
+            ln -s '$file' '$file_path' &&
+        #end for
     #elif str($repeat.software_cond.software) == "picard"
         #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
             #if str($repeat2.type) == "alignment_metrics"
@@ -505,7 +513,7 @@
                     <!--<option value="jellyfish">Jellyfish</option>-->
                     <option value="kallisto">Kallisto</option>
                     <!--<option value="leehom">leeHom</option>-->
-                    <!--<option value="macs2">MACS2</option>-->
+                    <option value="macs2">MACS2</option>
                     <!--<option value="methylQA">methylQA</option>-->
                     <!--<option value="peddy">Peddy</option>-->
                     <option value="picard">Picard</option>
@@ -614,6 +622,9 @@
                 <when value="kallisto">
                     <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/>
                 </when>
+                <when value="macs2">
+                    <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/>
+                </when>
                 <when value="picard">
                     <repeat name="output" title="Picard output" min="1">
                         <param name="type" type="select" label="Type of Picard output?">
@@ -887,6 +898,12 @@
             </repeat>
             <repeat name="results">
                 <conditional name="software_cond">
+                    <param name="software" value="macs2" />
+                    <param name="input" value="macs_1.txt,macs_2.txt" />
+                </conditional>
+            </repeat>
+            <repeat name="results">
+                <conditional name="software_cond">
                     <param name="software" value="star" />
                     <repeat name="output">
                         <conditional name="type">
@@ -915,6 +932,7 @@
                     <has_text text="bowtie2_se_plot" />
                     <has_text text="hisat2_se_plot" />
                     <has_text text="kallisto_alignment" />
+                    <has_text text="MACS2" />
                     <has_text text="star_alignment_plot" />
                     <has_text text="tophat_alignment" />
                     <has_text text="hicexplorer" />
@@ -928,6 +946,7 @@
                 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/>
                 <!-- <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="macs" file="macs_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"/>
             </output_collection>