--- 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**

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt	Sat Jan 18 03:08:54 2020 -0500
@@ -0,0 +1,3 @@
+Sample	1	2	3	4	5	6	7	8	9	10	12	14	16	18	20	22	24	26	28	30	32	34	36	38	40	42	44	46	48	50	52	54	56	58	60	62	64	66	68	70	72	74	76	78	80	82	84	86	88	90	92	94	96	98	100
+poulet5_1	20.91988023102569	20.71684045861661	20.351574954545285	22.531542025544244	24.673566076408722	25.813099918237516	27.587864804423386	27.598941941168345	27.07115949658203	27.129873548155864	27.009298149330405	27.123565889736383	27.086309823818645	27.07924614241606	27.082520375286073	27.054301117420636	27.06350966402712	27.082996389756914	27.065495857740743	27.09608772106672	27.087097581099798	27.098251253504774	27.05184077595959	27.06521958267531	27.072148859992012	27.065725464720796	27.07168031241483	27.048083061725073	27.04642354460909	27.062865644448927	27.01859629866081	26.994157155710866	27.110127347871376	26.995846540401494	27.00461640700544	26.981614641085088	26.98900313236189	27.001189102815392	26.917739099268616	26.98481793846533	26.89518908041471	26.93677034448514	26.87640237596556	26.906094478605482	26.80463992772047	26.717012197170796	26.46960974280285	26.442842795754324	26.34282375517549	26.03493946215965	25.833215729758187	25.503102494315826	24.52807178671565	23.202399486277717	23.72906749698524
+poulet5_2	20.590586487162543	20.458478471078855	20.178608096352797	22.495204387546714	24.59397272343746	25.77560491172265	26.651378201897337	27.54968284369178	27.089005372429988	27.058984726469017	26.954911162632676	27.066410552214123	27.04552938409328	27.025118630273028	27.019042445557012	27.010315513591614	27.03931879529138	26.978450544896567	27.003714779595967	27.025971722873706	27.017791740868923	27.00628899118533	27.00906294218011	27.034922661648913	27.005346295860726	27.000909094303132	27.004913216028434	26.979999925331065	26.941037674211962	26.99995146519121	26.95084543903468	26.97609847339359	26.99262270906369	26.942271578389317	26.88024222603034	26.866450873439888	26.947610407356386	26.975012040366025	26.966286975124042	26.917634562757375	26.885127441207544	26.846286527110426	26.769134848366058	26.709703975000842	26.551336760637525	26.42626069165836	26.309463541024982	26.127226534353312	25.91885539987082	25.674260497519125	25.371903572535274	24.758753999454918	23.84710415196622	22.40618968149965	23.009550156991438