# HG changeset patch
# User iuc
# Date 1618789676 0
# Node ID 9d79beb19ac3ea2821f848c665187f9c212de5f7

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

diff -r 000000000000 -r 9d79beb19ac3 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,33 @@
+<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>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">merqury</requirement>
+            <requirement type="package" version="1.34">tar</requirement>
+            <requirement type="package" version="4.6.0">findutils</requirement>
+            <requirement type="package" version="8.32">coreutils</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">                                                                   
+                @misc{githubMerqury,                                                                 
+                author = {Arang Rhie, Brian P. Walez, Sergey Koren, Adam M. Phillippy},
+                year = {2020},                                                                 
+                title = {Merqury},                                                        
+                publisher = {GitHub},
+                journal = {GitHub repository},                                               
+                url = {https://github.com/marbl/merqury},                        
+                }                                                                    
+            </citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 9d79beb19ac3 merqury.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merqury.xml	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,444 @@
+<tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01">
+    <description>evaluate the assembly quality</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <version_command>merqury --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p output_files
+        #if $mode.options == 'default'
+            && mkdir -p read-db.meryl
+            && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1
+            #if $mode.assembly_options.number_assemblies == 'one'
+                #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
+                    && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
+                #else
+                    && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
+                #end if 
+                && merqury.sh read-db.meryl assembly.fasta ${label}
+                && mv ${label}* output_files
+                && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
+            #else
+                #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
+                    && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
+                #else
+                    && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
+                #end if 
+                #if $mode.assembly_options.assembly_02.ext.endswith(".gz")
+                    && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
+                #else
+                    && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta
+                #end if 
+                && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label}
+                && mv ${label}* output_files
+                && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
+            #end if
+        #else
+            && mkdir -p read-db.meryl pat.meryl mat.meryl
+            && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1
+            && tar -zxf ${mode.meryldb_PAT} -C pat.meryl --strip-components=1
+            && tar -zxf ${mode.meryldb_MAT} -C mat.meryl --strip-components=1
+            #if $mode.assembly_options.number_assemblies == 'one'
+                #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
+                    && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
+                #else
+                    && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
+                #end if 
+                && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label}
+                && mv ${label}* output_files
+                && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
+            #else
+                #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
+                    && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
+                #else
+                    && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
+                #end if 
+                #if $mode.assembly_options.assembly_02.ext.endswith(".gz")
+                    && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
+                #else
+                    && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta
+                #end if
+                && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label}
+                && mv ${label}* output_files
+                && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
+            #end if
+        #end if
+    ]]>    </command>
+    <inputs>
+        <conditional name="mode">
+            <param name="options" type="select" 
+                label="Evaluation mode" help="Merqury allows two operational modes: default and trio mode.">
+                <option value="default">Default mode</option>
+                <option value="trio">Trio mode</option>
+            </param>
+            <when value="default">
+                <param name="meryldb_F1" type="data" format="meryldb"
+                            label="K-mer counts database" 
+                            help="Select the k-mer counts of the read set."/>
+                <conditional name="assembly_options">
+                    <param name="number_assemblies" type="select"
+                        label="Number of assemblies" help="Select the number of assemblies.">
+                        <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>
+                        <option value="two">Two assemblies (diploid)</option>
+                    </param>
+                    <when value="one">
+                        <param name="assembly_01" type="data" format="fasta,fasta.gz" 
+                            label="Genome assembly" 
+                            help="Select the assembled genome (FASTA)."/>
+                    </when>
+                    <when value="two">
+                        <param name="assembly_01" type="data" format="fasta,fasta.gz" 
+                            label="First genome assembly" 
+                            help="Select the first assembled genome (FASTA)."/>
+                        <param name="assembly_02" type="data" format="fasta,fasta.gz" 
+                            label="Second genome assembly" 
+                            help="Select the second assembled genome (FASTA)."/>
+                    </when>
+                </conditional>
+            </when>
+            <when value='trio'>
+                <param name="meryldb_F1" type="data" format="meryldb"
+                    label="F1 k-mer counts" 
+                    help="Select the k-mer counts of the read set (meryldb )."/>
+                <param name="meryldb_PAT" type="data" format="meryldb"
+                    label="Paternal hap-mer database" 
+                    help="K-mer counts of the paternal haplotype (meryldb)."/> 
+                <param name="meryldb_MAT" type="data" format="meryldb"
+                    label="Maternal hap-mer database" 
+                    help="K-mer counts of the maternal haplotype (meryldb)."/>
+                <conditional name="assembly_options">
+                    <param name="number_assemblies" type="select"
+                        label="Number of assemblies" help="Select the number of assemblies.">
+                        <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>
+                        <option value="two">Two assemblies (diploid)</option>
+                    </param>
+                    <when value="one">
+                        <param name="assembly_01" type="data" format="fasta,fasta.gz" 
+                            label="Genome assembly" 
+                            help="Select the assembled genome (FASTA)."/>
+                    </when>
+                    <when value="two">
+                        <param name="assembly_01" type="data" format="fasta,fasta.gz" 
+                            label="First genome assembly" 
+                            help="Select the first assembled genome (FASTA)."/>
+                        <param name="assembly_02" type="data" format="fasta,fasta.gz" 
+                            label="Second genome assembly" 
+                            help="Select the second assembled genome (FASTA)."/>
+                    </when>
+                </conditional>       
+            </when>
+        </conditional>
+        <param name='label' type="text" value="output_merqury" label="Identification label" help="Assign an identification label.">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: bed">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
+        </collection>
+        <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: wig">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
+        </collection>
+        <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: qv">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
+        </collection>
+        <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
+        </collection>
+        <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
+        </collection>
+        <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="mode">
+                <param name="options" value="trio"/>
+                <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
+                <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
+                <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
+                <conditional name="assembly_options">
+                    <param name="number_assemblies" value="one"/>
+                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
+                </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>
+            <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>
+            <conditional name="mode">
+                <param name="options" value="default"/>
+                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
+                <conditional name="assembly_options">
+                    <param name="number_assemblies" value="one"/>
+                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
+                </conditional>
+            </conditional>
+            <param name="label" value="output_02"/>
+            <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"/>
+                    </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"/>
+                    </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"/>
+                    </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"/>
+                    </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"/>
+                    </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"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="stats_files" type="list" count="1">
+                <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/>
+            </output_collection>
+            <output_collection name="qv_files" type="list" count="2">
+                <element name="output_02.assembly" ftype="tabular"/>
+                <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/>
+            </output_collection>
+            <output_collection name="wig_files" type="list" count="1">
+                <element name="assembly_only" ftype="wig">
+                    <assert_contents>
+                        <has_size value="29909811" delta="100"/>
+                    </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"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <conditional name="mode">
+                <param name="options" value="default"/>
+                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
+                <conditional name="assembly_options">
+                    <param name="number_assemblies" value="two"/>
+                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
+                    <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
+                </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>    
+            <output_collection name="stats_files" type="list" count="1">
+                <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>
+            </output_collection>
+            <output_collection name="qv_files" type="list" count="3">
+                <element name="output_03.assembly_01" ftype="tabular"/>
+                <element name="output_03.assembly_02" ftype="tabular"/>
+                <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>
+            </output_collection>
+        </test>
+        <test>
+            <conditional name="mode">
+                <param name="options" value="trio"/>
+                <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
+                <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
+                <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
+                <conditional name="assembly_options">
+                    <param name="number_assemblies" value="two"/>
+                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
+                    <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
+                </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>
+            <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[
+.. class:: infomark
+
+**Purpose**
+
+Merqury allows a reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo
+assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. 
+
+For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors.                    
+
+----
+                    
+.. class:: infomark
+                    
+**Input**
+
+Merqury requires two types of inputs: meryldbs and the genome assemblies.
+There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.
+
+----
+                    
+.. class:: infomark
+                    
+**Output**
+
+The generated metrics include consensus quality and k-mer completeness, and when parental genomic sequences are available (either assembled or unassembled), Merqury can output haplotype completeness, phase block statistics, switch error rates, and visual representations of phase consistency for the child’s genome. This includes TDF (or BED) features that can be displayed in a genome browser for visualizing the presence of k-mer classes across a genome (e.g., the k-mers inherited from a parental genome).                    
+
+    ]]>    </help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 9d79beb19ac3 test-data/assembly.fasta.gz
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diff -r 000000000000 -r 9d79beb19ac3 test-data/child.meryldb
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diff -r 000000000000 -r 9d79beb19ac3 test-data/mat.meryldb
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.100_20000.phased_block.blob.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_01.assembly.bed	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,2 @@
+tig00000005	227845	227853	pat
+tig00000005	426764	426772	pat
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.block.N.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.contig.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_01.assembly.contig.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,8 @@
+contig	assembly	732575
+contig	assembly	684532
+contig	assembly	512140
+contig	assembly	437616
+contig	assembly	367569
+contig	assembly	295265
+contig	assembly	56868
+contig	assembly	27107
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.continuity.N.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.mat.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.pat.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_01.assembly.pat.bed	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,3 @@
+tig00000005	227825	227850	0.2
+tig00000005	227850	227875	0.12
+tig00000005	426750	426775	0.32
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.pat.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.assembly.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.hapmers.blob.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_01.switches.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_01.switches.txt	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,1 @@
+output_01.assembly.100_20000 switch error rate (%) (Num. switches / Total markers found): 0	2	0%
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02.assembly.spectra-cn.fl.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02.assembly.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02.assembly.spectra-cn.st.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02.completeness.stats.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_02.completeness.stats.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,1 @@
+assembly	all	193949	279149	69.4787
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02.spectra-asm.fl.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02.spectra-asm.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02.spectra-asm.st.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_02_qv.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_02_qv.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,1 @@
+assembly	2882439	3113584		
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.assembly_01.spectra-cn.fl.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.assembly_01.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.assembly_02.spectra-cn.fl.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.assembly_02.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.assembly_02.spectra-cn.st.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.completeness.stats.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_03.completeness.stats.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,3 @@
+assembly_01	all	193949	279149	69.4787
+assembly_02	all	64441	279149	23.0848
+both	all	193949	279149	69.4787
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.spectra-asm.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_03_qv.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_03_qv.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,3 @@
+assembly_01	2882439	3113584		
+assembly_02	964973	1037945		
+Both	3847412	4151529		
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.100_20000.phased_block.blob.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.100_20000.switch.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04.assembly_01.100_20000.switch.bed	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,2 @@
+tig00000005	227845	227853	pat	Same	pat
+tig00000005	426764	426772	pat	Same	pat
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04.assembly_01.bed	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,2 @@
+tig00000005	227845	227853	pat
+tig00000005	426764	426772	pat
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.block.N.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.contig.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04.assembly_01.contig.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,8 @@
+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 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.continuity.N.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.pat.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04.assembly_01.pat.bed	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,3 @@
+tig00000005	227825	227850	0.2
+tig00000005	227850	227875	0.12
+tig00000005	426750	426775	0.32
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.pat.spectra-cn.ln.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_01.sort.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04.assembly_01.sort.bed	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,2 @@
+tig00000005	227845	227853	pat
+tig00000005	426764	426772	pat
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.assembly_02.contig.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04.assembly_02.contig.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,2 @@
+contig	assembly_02	732575
+contig	assembly_02	305392
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.hapmers.blob.png
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diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04.switches.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04.switches.txt	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,1 @@
+output_04.assembly_02.100_20000 switch error rate (%) (Num. switches / Total markers found): 
diff -r 000000000000 -r 9d79beb19ac3 test-data/output_04_qv.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_04_qv.tabular	Sun Apr 18 23:47:56 2021 +0000
@@ -0,0 +1,1 @@
+Both				
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