--- a/multiqc.xml	Thu Nov 19 21:54:37 2020 +0000
+++ b/multiqc.xml	Sat Nov 21 12:54:24 2020 +0000
@@ -1,7 +1,7 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy2">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">1.8</token>
+        <token name="@WRAPPER_VERSION@">1.9</token>
         <token name="@ESCAPE_IDENTIFIER@">
 <![CDATA[
 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
@@ -479,6 +479,7 @@
 #end if
 
 $flat
+$export
 
 #if $configfile == "T"
     --config '$multiqc_config'
@@ -843,6 +844,7 @@
         <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 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 argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
         <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>
@@ -855,7 +857,7 @@
         </collection>
         <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
             <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
-            <filter>flat</filter>
+            <filter>export</filter>
         </collection>
     </outputs>
     <tests>
@@ -908,12 +910,13 @@
             <param name="title" value="Title of the report"/>
             <param name="comment" value="Commment for the report"/>
             <param name="flat" value="true"/>
+            <param name="export" value="true"/>
             <param name="saveLog" 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="cutadapt_plot" />
+                    <has_text text="cutadapt_trimmed_sequences_plot" />
                     <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
                     <has_text text="fastqc_seq_heatmap_key_t" />
                     <has_text text="flexbar_plot" />
@@ -927,7 +930,7 @@
                     <has_text_matching expression="\[INFO   \]  MultiQC complete$"/>
                 </assert_contents>
             </output>
-            <output_collection name="stats" type="list" count="11">
+            <output_collection name="stats" type="list" count="10">
                 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
@@ -1286,6 +1289,7 @@
             <param name="title" value="Title of the report"/>
             <param name="comment" value="Commment for the report"/>
             <param name="flat" value="true"/>
+            <param name="export" value="true"/>
             <output name="html_report">
                 <assert_contents>
                     <has_text text="Title of the report" />