# HG changeset patch
# User iuc
# Date 1636648722 0
# Node ID 39edec572baebb3b7dd173de23f27d8942e25d58
# Parent  9d79beb19ac3ea2821f848c665187f9c212de5f7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"

diff -r 9d79beb19ac3 -r 39edec572bae macros.xml
--- a/macros.xml	Sun Apr 18 23:47:56 2021 +0000
+++ b/macros.xml	Thu Nov 11 16:38:42 2021 +0000
@@ -1,12 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
-    <xml name="edam_ontology">
-        <edam_topics>                                                                                  
-            <edam_topic>topic_0196</edam_topic>
-        </edam_topics>
-        <edam_operations>
-            <edam_operation>operation_0525</edam_operation>
-        </edam_operations>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">merqury</xref>
+        </xrefs>
     </xml>
     <xml name="requirements">
         <requirements>
diff -r 9d79beb19ac3 -r 39edec572bae merqury.xml
--- 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[
diff -r 9d79beb19ac3 -r 39edec572bae test-data/assembly.fasta.gz
Binary file test-data/assembly.fasta.gz has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.100_20000.phased_block.blob.png
Binary file test-data/output_01.assembly.100_20000.phased_block.blob.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.bed
--- a/test-data/output_01.assembly.bed	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-tig00000005	227845	227853	pat
-tig00000005	426764	426772	pat
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.block.N.png
Binary file test-data/output_01.assembly.block.N.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.contig.tabular
--- a/test-data/output_01.assembly.contig.tabular	Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_01.assembly.contig.tabular	Thu Nov 11 16:38:42 2021 +0000
@@ -1,8 +1,2 @@
 contig	assembly	732575
-contig	assembly	684532
-contig	assembly	512140
-contig	assembly	437616
-contig	assembly	367569
-contig	assembly	295265
-contig	assembly	56868
-contig	assembly	27107
+contig	assembly	305392
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.continuity.N.png
Binary file test-data/output_01.assembly.continuity.N.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.mat.spectra-cn.ln.png
Binary file test-data/output_01.assembly.mat.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.pat.bed
--- a/test-data/output_01.assembly.pat.bed	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-tig00000005	227825	227850	0.2
-tig00000005	227850	227875	0.12
-tig00000005	426750	426775	0.32
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.pat.spectra-cn.ln.png
Binary file test-data/output_01.assembly.pat.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.spectra-cn.ln.png
Binary file test-data/output_01.assembly.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.hapmers.blob.png
Binary file test-data/output_01.hapmers.blob.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.switches.txt
--- a/test-data/output_01.switches.txt	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-output_01.assembly.100_20000 switch error rate (%) (Num. switches / Total markers found): 0	2	0%
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.assembly.spectra-cn.fl.png
Binary file test-data/output_02.assembly.spectra-cn.fl.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.assembly.spectra-cn.ln.png
Binary file test-data/output_02.assembly.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.assembly.spectra-cn.st.png
Binary file test-data/output_02.assembly.spectra-cn.st.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.completeness.stats.tabular
--- a/test-data/output_02.completeness.stats.tabular	Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_02.completeness.stats.tabular	Thu Nov 11 16:38:42 2021 +0000
@@ -1,1 +1,1 @@
-assembly	all	193949	279149	69.4787
+assembly	all	32353	32353	100
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.spectra-asm.fl.png
Binary file test-data/output_02.spectra-asm.fl.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.spectra-asm.ln.png
Binary file test-data/output_02.spectra-asm.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.spectra-asm.st.png
Binary file test-data/output_02.spectra-asm.st.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02_qv.tabular
--- a/test-data/output_02_qv.tabular	Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_02_qv.tabular	Thu Nov 11 16:38:42 2021 +0000
@@ -1,1 +1,1 @@
-assembly	2882439	3113584		
+assembly	0	1037953		
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_01.spectra-cn.fl.png
Binary file test-data/output_03.assembly_01.spectra-cn.fl.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_01.spectra-cn.ln.png
Binary file test-data/output_03.assembly_01.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_01.spectra-cn.st.png
Binary file test-data/output_03.assembly_01.spectra-cn.st.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_02.spectra-cn.fl.png
Binary file test-data/output_03.assembly_02.spectra-cn.fl.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_02.spectra-cn.ln.png
Binary file test-data/output_03.assembly_02.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_02.spectra-cn.st.png
Binary file test-data/output_03.assembly_02.spectra-cn.st.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.completeness.stats.tabular
--- a/test-data/output_03.completeness.stats.tabular	Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_03.completeness.stats.tabular	Thu Nov 11 16:38:42 2021 +0000
@@ -1,3 +1,3 @@
-assembly_01	all	193949	279149	69.4787
-assembly_02	all	64441	279149	23.0848
-both	all	193949	279149	69.4787
+assembly_01	all	32353	32353	100
+assembly_02	all	32353	32353	100
+both	all	32353	32353	100
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-asm.ln.png
Binary file test-data/output_03.spectra-asm.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-cn.fl.png
Binary file test-data/output_03.spectra-cn.fl.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-cn.ln.png
Binary file test-data/output_03.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-cn.st.png
Binary file test-data/output_03.spectra-cn.st.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03_qv.tabular
--- a/test-data/output_03_qv.tabular	Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_03_qv.tabular	Thu Nov 11 16:38:42 2021 +0000
@@ -1,3 +1,3 @@
-assembly_01	2882439	3113584		
-assembly_02	964973	1037945		
-Both	3847412	4151529		
+assembly_01	0	1037953		
+assembly_02	0	1037953		
+Both	0	2075906		
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.100_20000.phased_block.blob.png
Binary file test-data/output_04.assembly_01.100_20000.phased_block.blob.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.100_20000.switch.bed
--- a/test-data/output_04.assembly_01.100_20000.switch.bed	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-tig00000005	227845	227853	pat	Same	pat
-tig00000005	426764	426772	pat	Same	pat
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.bed
--- a/test-data/output_04.assembly_01.bed	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-tig00000005	227845	227853	pat
-tig00000005	426764	426772	pat
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.block.N.png
Binary file test-data/output_04.assembly_01.block.N.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.contig.tabular
--- a/test-data/output_04.assembly_01.contig.tabular	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-contig	assembly_01	732575
-contig	assembly_01	684532
-contig	assembly_01	512140
-contig	assembly_01	437616
-contig	assembly_01	367569
-contig	assembly_01	295265
-contig	assembly_01	56868
-contig	assembly_01	27107
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.continuity.N.png
Binary file test-data/output_04.assembly_01.continuity.N.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.mat.spectra-cn.ln.png
Binary file test-data/output_04.assembly_01.mat.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.pat.bed
--- a/test-data/output_04.assembly_01.pat.bed	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-tig00000005	227825	227850	0.2
-tig00000005	227850	227875	0.12
-tig00000005	426750	426775	0.32
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.pat.spectra-cn.ln.png
Binary file test-data/output_04.assembly_01.pat.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.sort.bed
--- a/test-data/output_04.assembly_01.sort.bed	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-tig00000005	227845	227853	pat
-tig00000005	426764	426772	pat
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_02.contig.tabular
--- a/test-data/output_04.assembly_02.contig.tabular	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-contig	assembly_02	732575
-contig	assembly_02	305392
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_02.mat.spectra-cn.ln.png
Binary file test-data/output_04.assembly_02.mat.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_02.pat.spectra-cn.ln.png
Binary file test-data/output_04.assembly_02.pat.spectra-cn.ln.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.hapmers.blob.png
Binary file test-data/output_04.hapmers.blob.png has changed
diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.switches.txt
--- a/test-data/output_04.switches.txt	Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-output_04.assembly_02.100_20000 switch error rate (%) (Num. switches / Total markers found): 
diff -r 9d79beb19ac3 -r 39edec572bae test-data/read-db.meryldb
Binary file test-data/read-db.meryldb has changed