--- a/multiqc.xml	Sat Apr 13 08:30:21 2019 -0400
+++ b/multiqc.xml	Sat Jan 18 03:08:54 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
+<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@">1.7</token>
@@ -456,6 +456,8 @@
     --comment "$comment"
 #end if
 
+$flat
+
 #if $configfile == "T"
     --config '$multiqc_config'
 #end if
@@ -809,7 +811,7 @@
         </repeat>
         <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/>
         <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>
-        <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
+        <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="False" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
         <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
     </inputs>
     <outputs>
@@ -820,6 +822,9 @@
         <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
             <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
         </collection>
+        <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
+            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+_plot_.+)\.txt" format="tabular" directory="report_data" />
+        </collection>
     </outputs>
     <tests>
         <test>
@@ -1221,6 +1226,30 @@
             </repeat>
             <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>
         </test>
+        <test>
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="fastqc" />
+                    <repeat name="output">
+                        <param name="type" value="data"/>
+                        <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
+                    </repeat>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="True"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report" />
+                    <has_text text="Commment for the report" />
+                    <has_text text="fastqc_seq_heatmap_key_t" />
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list">
+                <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**