--- a/multiqc.xml	Tue Mar 02 08:02:36 2021 +0000
+++ b/multiqc.xml	Tue Mar 02 21:08:49 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
         <token name="@WRAPPER_VERSION@">1.9</token>
@@ -12,7 +12,7 @@
     #set $file_path += '_' + str($file_paths.count($file_path))
 #end if
 #set $file_paths += [$file_path]
-grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
+grep -q '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
 ln -s '$file' '$file_path'  &&
         ]]></token>
         <token name="@CREATE_REPEAT_DIR_1@">
@@ -282,6 +282,9 @@
     #elif str($repeat.software_cond.software) == "prokka"
         #set $pattern = "contigs:"
         @LN_FILES@
+    #elif str($repeat.software_cond.software) == "pycoqc"
+        #set $pattern = "\"pycoqc\":"
+        @LN_FILES@
     #elif str($repeat.software_cond.software) == "qualimap"
         #for $file in $repeat.software_cond.input
             #if re.search("genome_results", str($file.element_identifier))
@@ -570,6 +573,7 @@
                     <option value="picard">Picard</option>
                     <!--<option value="preseq">Preseq</option>-->
                     <option value="prokka">Prokka</option>
+                    <option value="pycoqc">PycoQC</option>
                     <!--<option value="qorts">QoRTs</option>-->
                     <option value="qualimap">Qualimap (BamQC or RNASeq output)</option>
                     <option value="quast">QUAST</option>
@@ -702,6 +706,9 @@
                 <when value="prokka">
                     <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/>
                 </when>
+                <when value="pycoqc">
+                    <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/>
+                </when>
                 <when value="qualimap">
                     <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" />
                 </when>
@@ -1320,6 +1327,28 @@
                 <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>
+        <test expect_num_outputs="2">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="pycoqc" />
+                    <param name="input" value="pycoqc.json"/>
+                </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="General Statistics" />
+                    <has_text text="pycoqc_count_plot" />
+                    <has_text text="pycoqc_read_len_plot" />
+                    <has_text text="pycoqc_read_qual_plot" />
+                </assert_contents>
+            </output>
+	    <output_collection name="stats" type="list" count="2"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**