--- a/merqury.xml	Sun Apr 18 23:47:56 2021 +0000
+++ b/merqury.xml	Thu Nov 11 16:38:42 2021 +0000
@@ -1,9 +1,9 @@
-<tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01">
+<tool id="merqury" name="Merqury" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>evaluate the assembly quality</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="edam_ontology"/>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <version_command>merqury --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -137,29 +137,44 @@
                 </valid>
             </sanitizer>
         </param>
+        <param name="output_selector" type="select" display="checkboxes" multiple="true" optional="true" label="Output options">
+            <option value="qv" selected="true">QV stats</option>
+            <option value="plots" selected="true">Plots</option>
+            <option value="sizes">Size files</option>
+            <option value="stats" selected="true">Stats file</option>
+            <option value="bed">BED: hap-mer tracks</option>
+            <option value="wig">WIG: hap-mer tracks</option>
+        </param>
     </inputs>
     <outputs>
-        <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: bed">
+        <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
+            <filter>"bed" in output_selector</filter>
         </collection>
-        <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: wig">
+        <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: WIG files">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
+            <filter>"wig" in output_selector</filter>
         </collection>
-        <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: qv">
+        <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: QV stats">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
+            <filter>"qv" in output_selector</filter>
         </collection>
-        <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png">
+        <collection name="png_files" type="list" label="${tool.name} on ${on_string}: plots">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
+            <filter>"plots" in output_selector</filter>
         </collection>
         <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
+            <filter>"sizes" in output_selector</filter>
         </collection>
         <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
+            <filter>"stats" in output_selector</filter>
         </collection>
     </outputs>
     <tests>
-        <test>
+        <!--Test 01: trio mode-->
+        <test  expect_num_outputs="2">
             <conditional name="mode">
                 <param name="options" value="trio"/>
                 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
@@ -171,42 +186,14 @@
                 </conditional>
             </conditional>
             <param name="label" value="output_01"/>
-            <output_collection name="png_files" type="list" count="3">
-                <element name="output_01.assembly.mat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="2733" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_01.assembly.pat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="2733" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_01.hapmers.blob" file="output_01.hapmers.blob.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="10764" delta="100"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
-            <output_collection name="stats_files" type="list" count="2">
-                <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
-                <element name="output_01.completeness" ftype="tabular"/>
-            </output_collection>
-            <output_collection name="wig_files" type="list" count="2">
-                <element name="output_01.assembly.pat" ftype="wig"/>
-                <element name="output_01.assembly.mat" file="output_01.assembly.mat.wig" ftype="wig"/>
-            </output_collection>
+            <param name="output_selector" value="sizes"/>
             <output_collection name="sizes_files" type="list" count="2">
                 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
                 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
             </output_collection>
-            <output_collection name="bed_files" type="list" count="3">
-                <element name="output_01.assembly.100_20000.phased_block" ftype="bed"/>
-                <element name="output_01.assembly.100_20000.switch" ftype="bed"/>
-                <element name="output_01.assembly.sort"/>
-            </output_collection>
         </test>
-        <test>
+        <!--Test 02: standard mode-->
+        <test  expect_num_outputs="11">
             <conditional name="mode">
                 <param name="options" value="default"/>
                 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
@@ -216,35 +203,37 @@
                 </conditional>
             </conditional>
             <param name="label" value="output_02"/>
+            <param name="output_selector" value="qv,png,bed,wig,sizes,stats"/>
+            <param name="output_selector" value="plots,stats,wig,sizes,bed"/>
             <output_collection name="png_files" type="list" count="6">
                 <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png">
                     <assert_contents>
-                        <has_size value="58059" delta="100"/>
+                        <has_size value="71874" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png">
                     <assert_contents>
-                        <has_size value="57763" delta="100"/>
+                        <has_size value="71888" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png">
                     <assert_contents>
-                        <has_size value="61814" delta="100"/>
+                        <has_size value="71123" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png">
                     <assert_contents>
-                        <has_size value="64445" delta="100"/>
+                        <has_size value="47245" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png">
                     <assert_contents>
-                        <has_size value="64795" delta="100"/>
+                        <has_size value="46896" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png">
                     <assert_contents>
-                        <has_size value="66317" delta="100"/>
+                        <has_size value="45945" delta="100"/>
                     </assert_contents>
                 </element>
             </output_collection>
@@ -258,19 +247,20 @@
             <output_collection name="wig_files" type="list" count="1">
                 <element name="assembly_only" ftype="wig">
                     <assert_contents>
-                        <has_size value="29909811" delta="100"/>
+                        <has_size value="0"/>
                     </assert_contents>
                 </element>
             </output_collection>
             <output_collection name="bed_files" type="list" count="1">
                 <element name="assembly_only" ftype="bed">
                     <assert_contents>
-                        <has_size value="73516121" delta="100"/>
+                        <has_size value="0"/>
                     </assert_contents>
                 </element>
             </output_collection>
         </test>
-        <test>
+        <!--Test 03: Standard mode two assemblies-->
+        <test  expect_num_outputs="4">
             <conditional name="mode">
                 <param name="options" value="default"/>
                 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
@@ -281,58 +271,7 @@
                 </conditional>
             </conditional>
             <param name="label" value="output_03"/>
-            <output_collection name="png_files" type="list" count="10">
-                <element name="output_03.assembly_01.spectra-cn.fl" file="output_03.assembly_01.spectra-cn.fl.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="58059" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.assembly_01.spectra-cn.ln" file="output_03.assembly_01.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="57763" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.assembly_01.spectra-cn.st" file="output_03.assembly_01.spectra-cn.st.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="61814" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.assembly_02.spectra-cn.fl" file="output_03.assembly_02.spectra-cn.fl.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="61579" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.assembly_02.spectra-cn.ln" file="output_03.assembly_02.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="61538" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.assembly_02.spectra-cn.st" file="output_03.assembly_02.spectra-cn.st.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="67297" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.spectra-asm.ln" file="output_03.spectra-asm.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="2733" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.spectra-cn.fl" file="output_03.spectra-cn.fl.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="61397" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.spectra-cn.ln" file="output_03.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="61050" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_03.spectra-cn.st" file="output_03.spectra-cn.st.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="65243" delta="100"/>
-                    </assert_contents>
-                </element>
-            </output_collection>    
+            <param name="output_selector" value="qv,stats"/>
             <output_collection name="stats_files" type="list" count="1">
                 <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>
             </output_collection>
@@ -342,7 +281,8 @@
                 <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>
             </output_collection>
         </test>
-        <test>
+        <!--Test 04: trio mode two assemblies-->
+        <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="options" value="trio"/>
                 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
@@ -355,61 +295,10 @@
                 </conditional>
             </conditional>
             <param name="label" value="output_04"/>
-            <output_collection name="png_files" type="list" count="5">
-                <element name="output_04.assembly_01.mat.spectra-cn.ln" file="output_04.assembly_01.mat.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="2733" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_04.assembly_01.pat.spectra-cn.ln" file="output_04.assembly_01.pat.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="2733" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_04.assembly_02.mat.spectra-cn.ln" file="output_04.assembly_02.mat.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="2733" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_04.assembly_02.pat.spectra-cn.ln" file="output_04.assembly_02.pat.spectra-cn.ln.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="2733" delta="100"/>
-                    </assert_contents>
-                </element>
-                <element name="output_04.hapmers.blob" file="output_04.hapmers.blob.png" ftype="png">
-                    <assert_contents>
-                        <has_size value="10764" delta="100"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
-            <output_collection name="stats_files" type="list" count="3">
-                <element name="output_04.assembly_01.100_20000.phased_block" ftype="tabular"/>
-                <element name="output_04.assembly_02.100_20000.phased_block" file="output_04.assembly_02.100_20000.phased_block.stats.tabular" ftype="tabular"/>
-                <element name="output_04.completeness"/>
-            </output_collection>
+            <param name="output_selector" value="qv"/>
             <output_collection name="qv_files" type="list" count="1">
                 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>
             </output_collection>
-            <output_collection name="wig_files" type="list" count="4">
-                <element name="output_04.assembly_01.pat" ftype="wig"/>
-                <element name="output_04.assembly_01.mat" ftype="wig"/>
-                <element name="output_04.assembly_02.pat" ftype="wig"/>
-                <element name="output_04.assembly_02.mat" ftype="wig"/>
-            </output_collection>
-            <output_collection name="sizes_files" type="list" count="4">
-                <element name="output_04.assembly_01.100_20000.phased_block"/>
-                <element name="output_04.assembly_01.contig" file="output_04.assembly_01.contig.tabular" ftype="tabular"/>
-                <element name="output_04.assembly_02.100_20000.phased_block"/>
-                <element name="output_04.assembly_02.contig" file="output_04.assembly_02.contig.tabular" ftype="tabular"/>
-            </output_collection>
-            <output_collection name="bed_files" type="list" count="6">
-                <element name="output_04.assembly_01.100_20000.phased_block" ftype="bed"/>
-                <element name="output_04.assembly_01.100_20000.switch" file="output_04.assembly_01.100_20000.switch.bed" ftype="bed"/>
-                <element name="output_04.assembly_01.sort" file="output_04.assembly_01.sort.bed" ftype="bed"/>
-                <element name="output_04.assembly_02.100_20000.phased_block" ftype="bed"/>
-                <element name="output_04.assembly_02.100_20000.switch" ftype="bed"/>
-                <element name="output_04.assembly_02.sort" ftype="bed"/>
-            </output_collection>
         </test>
     </tests>
     <help><![CDATA[