MultiQC Update: Add functionality to retrieve PNG plots (#7358)

Author: SaimMomin12

tools/multiqc/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.27</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">multiqc</xref>
@@ -109,7 +109,7 @@ sp:
     </xml>
     <xml name="general_tests">
         <!--Test 01-->
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="cutadapt"/>
@@ -159,6 +159,7 @@ sp:
             <param name="comment" value="Commment for the report"/>
             <param name="flat" value="true"/>
             <param name="export" value="true"/>
+            <param name="png_plots" value="true"/>
             <output name="html_report">
                 <assert_contents>
                     <has_text text="Title of the report"/>
@@ -187,6 +188,7 @@ sp:
                 </assert_contents>
             </output>
             <output_collection name="plots" type="list" count="29"/>
+            <output_collection name="png_plot" type="list" count="38"/>
         </test>
         <!--Test 02-->
         <test expect_num_outputs="2">
@@ -537,7 +539,7 @@ sp:
             </output-->
         </test>
         <!--Test 05-->
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="fastqc"/>
@@ -551,6 +553,7 @@ sp:
             <param name="comment" value="Commment for the report"/>
             <param name="flat" value="true"/>
             <param name="export" value="true"/>
+            <param name="png_plots" value="true"/>
             <output name="html_report">
                 <assert_contents>
                     <has_text text="Title of the report"/>
@@ -573,6 +576,8 @@ sp:
                     </assert_contents>
                 </element>
             </output_collection>
+            <output_collection name="png_plot" type="list" count="11"/>
+            
         </test>
         <!--Test 06-->
         <test expect_num_outputs="2">

tools/multiqc/multiqc.xml

@@ -212,7 +212,7 @@ multiqc multiqc_WDir
 
 $flat
 $export
-
+ 
 #if $configfile == "T"
     --config '$multiqc_config'
 #end if
@@ -223,6 +223,11 @@ ls -l ./report_data/ &&
 ##cat ./report_data/multiqc_busco.txt &&
 cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated
 
+#if $png_plots == "true"
+    && mkdir -p ./png_plots
+    && cp ./report_plots/png/*.png ./png_plots/ | true ## don't fail if no png plots are generated
+#end if
+
     ]]></command>
     <expand macro="configfile"/>
     <inputs>
@@ -498,6 +503,7 @@ cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are g
         </param>
         <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
         <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
+        <param name="png_plots" type="boolean" truevalue="true" falsevalue="false" label="Output PNG plots?" help="Choose if you want PNG plots in an output collection"/>
     </inputs>
     <outputs>
         <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage"/>
@@ -506,14 +512,18 @@ cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are g
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="plots"/>
             <filter>export</filter>
         </collection>
+        <collection name="png_plot" type="list" label="${tool.name} on ${on_string}: PNG Plots">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="png_plots"/>
+            <filter>png_plots</filter>
+        </collection>
     </outputs>
     <tests>
         <expand macro="general_tests"/>
         <expand macro="bcftools_test"/>
         <expand macro="bowtie2_test"/>
         <expand macro="fastqc_test"/>
         <expand macro="trimmomatic_test"/>
-        <!-- Test 10 -->
+                <!-- Test 10 -->
         <expand macro="flexbar_test"/>
         <expand macro="fastp_test"/>
         <expand macro="bismark_test"/>
@@ -544,7 +554,7 @@ cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are g
         <expand macro="gtdbtk_test"/>
         <expand macro="sambamba_test"/>
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
-
+ 
     </tests>
     <help><![CDATA[
 **What it does**