Adds wrapper features for Multiqc to support mosdepth

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>

tools/multiqc/mosdepth_plugin.xml

@@ -0,0 +1,67 @@
+<macros>
+    <token name="@MOSDEPTH_COMMAND@"><![CDATA[
+        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+            @CREATE_REPEAT_DIR_1@
+            #if str($repeat2.type) == "dist"
+                #for $file in $repeat2.input
+                    @ESCAPE_IDENTIFIER@
+                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.mosdepth.*.dist.txt')
+                    ln -s '$file' '$file_path' &&
+                #end for
+            #elif str($repeat2.type) == "summary"
+                #for $file in $repeat2.input
+                    @ESCAPE_IDENTIFIER@
+                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.mosdepth.summary.txt')
+                    ln -s '$file' '$file_path' &&
+                #end for
+            #end if
+        #end for
+    ]]></token>
+
+    <xml name="mosdepth_form">
+        <repeat name="output" title="Mosdepth output" min="1">
+            <param name="type" type="select" label="Type of Mosdepth output?">
+                <option value="dist">Global or Region Coverage Distribution</option>
+                <option value="summary">Coverage Summary</option>
+            </param>
+            <param name="input" type="data" format="tabular" label="summary, global, or region coverage output of mosdepth"/>
+        </repeat>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="mosdepth_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="mosdepth"/>
+                    <repeat name="output">
+                        <param name="type" value="dist"/>
+                        <param name="input" value="test.mosdepth.global.dist.txt"/>
+                    </repeat>
+                    <repeat name="output">
+                        <param name="type" value="summary"/>
+                        <param name="input" value="test.mosdepth.summary.txt"/>
+                    </repeat>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Comment 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"/>
+                    <has_text text="Comment for the report"/>
+                    <has_text text="Cumulative coverage distribution"/>
+                    <has_text text="Average coverage per contig"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="mosdepth-1_x_pc"/>
+                    <has_text text="mosdepth-length"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="3"/>
+        </test>
+    </xml>
+</macros>

tools/multiqc/multiqc.xml

@@ -14,6 +14,7 @@
         <import>featurecounts_plugin.xml</import>
         <import>flexbar_plugin.xml</import>
         <import>gatk_plugin.xml</import>
+        <import>mosdepth_plugin.xml</import>
         <import>picard_plugin.xml</import>
         <import>pycoqc_plugin.xml</import>
         <import>qualimap_plugin.xml</import>
@@ -106,6 +107,8 @@ mkdir multiqc_WDir &&
             grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
             ln -s '$file' '$file_path' &&
         #end for
+    #elif str($repeat.software_cond.software) == "mosdepth"
+        @MOSDEPTH_COMMAND@
     #elif str($repeat.software_cond.software) == "picard"
         @PICARD_COMMAND@
     #elif str($repeat.software_cond.software) == "prokka"
@@ -267,7 +270,7 @@ cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are g
                     <!--<option value="leehom">leeHom</option>-->
                     <option value="macs2">MACS2</option>
                     <!--<option value="methylQA">methylQA</option>-->
-                    <!--<option value="mosdepth">mostdepth</option>-->
+                    <option value="mosdepth">mosdepth</option>
                     <!--<option value="mtnucratio">mtnucratio</option>-->
                     <!--<option value="peddy">Peddy</option>-->
                     <option value="picard">Picard</option>
@@ -365,6 +368,9 @@ cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are g
                 <when value="macs2">
                     <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/>
                 </when>
+                <when value="mosdepth">
+                    <expand macro="mosdepth_form"/>
+                </when>
                 <when value="picard">
                     <expand macro="picard_form"/>
                 </when>
@@ -523,6 +529,7 @@ cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are g
         <expand macro="samtools_test"/>
         <expand macro="busco_test"/>
         <expand macro="featurecounts_test"/>
+        <expand macro="mosdepth_test"/>
         <expand macro="picard_test"/>
         <!-- Test 20 -->
         <expand macro="qualimap_test"/>