--- a/multiqc.xml	Fri Oct 09 14:56:59 2020 +0000
+++ b/multiqc.xml	Thu Nov 19 21:54:37 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy2">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
         <token name="@WRAPPER_VERSION@">1.8</token>
@@ -842,8 +842,8 @@
         </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 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"/>
+        <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>
         <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
@@ -854,11 +854,12 @@
             <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
         </collection>
         <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
-            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+_plot_.+)\.txt" format="tabular" directory="report_data" />
+            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
+            <filter>flat</filter>
         </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="cutadapt" />
@@ -906,7 +907,8 @@
             </repeat>
             <param name="title" value="Title of the report"/>
             <param name="comment" value="Commment for the report"/>
-            <param name="saveLog" value="True"/>
+            <param name="flat" value="true"/>
+            <param name="saveLog" value="true"/>
             <output name="html_report">
                 <assert_contents>
                     <has_text text="Title of the report" />
@@ -920,8 +922,12 @@
                     <has_text text="trimmomatic_plot" />
                 </assert_contents>
             </output>
-            <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>
-            <output_collection name="stats" type="list">
+            <output name="log">
+                <assert_contents>
+                    <has_text_matching expression="\[INFO   \]  MultiQC complete$"/>
+                </assert_contents>
+            </output>
+            <output_collection name="stats" type="list" count="11">
                 <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"/>
@@ -931,8 +937,9 @@
                 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
                 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
             </output_collection>
+            <output_collection name="plots" type="list" count="29"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="bismark" />
@@ -995,7 +1002,7 @@
                     <param name="input" value="tophat.txt" />
                 </conditional>
             </repeat>
-            <param name="saveLog" value="False"/>
+            <param name="saveLog" value="false"/>
             <output name="html_report">
                 <assert_contents>
                     <has_text text="bismark-alignment" />
@@ -1009,7 +1016,7 @@
                     <has_text text="hicexplorer1_log_1" />
                 </assert_contents>
             </output>
-            <output_collection name="stats" type="list">
+            <output_collection name="stats" type="list" count="8">
                 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>
                 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
@@ -1021,7 +1028,7 @@
                 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="bamtools" />
@@ -1221,7 +1228,7 @@
                     <has_text text="snpeff" />
                 </assert_contents>
             </output>
-            <output_collection name="stats" type="list">
+            <output_collection name="stats" type="list" count="19">
                 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/>
                 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/>
@@ -1249,7 +1256,7 @@
                 <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="custom_content" />
@@ -1264,8 +1271,9 @@
                 </conditional>
             </repeat>
             <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>
+	    <output_collection name="stats" type="list" count="1"/>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="fastqc" />
@@ -1277,7 +1285,7 @@
             </repeat>
             <param name="title" value="Title of the report"/>
             <param name="comment" value="Commment for the report"/>
-            <param name="flat" value="True"/>
+            <param name="flat" value="true"/>
             <output name="html_report">
                 <assert_contents>
                     <has_text text="Title of the report" />
@@ -1285,7 +1293,8 @@
                     <has_text text="fastqc_seq_heatmap_key_t" />
                 </assert_contents>
             </output>
-            <output_collection name="plots" type="list">
+	    <output_collection name="stats" type="list" count="1"/>
+            <output_collection name="plots" type="list" count="1">
                 <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>