| Next changeset 1:39edec572bae (2021-11-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" |
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added:
macros.xml merqury.xml test-data/assembly.fasta.gz test-data/assembly_02.fasta.gz test-data/child.meryldb test-data/mat.meryldb test-data/output_01.assembly.100_20000.phased_block.blob.png test-data/output_01.assembly.bed test-data/output_01.assembly.block.N.png test-data/output_01.assembly.contig.tabular test-data/output_01.assembly.continuity.N.png test-data/output_01.assembly.mat.spectra-cn.ln.png test-data/output_01.assembly.pat.bed test-data/output_01.assembly.pat.spectra-cn.ln.png test-data/output_01.assembly.spectra-cn.ln.png test-data/output_01.hapmers.blob.png test-data/output_01.switches.txt test-data/output_02.assembly.spectra-cn.fl.png test-data/output_02.assembly.spectra-cn.ln.png test-data/output_02.assembly.spectra-cn.st.png test-data/output_02.completeness.stats.tabular test-data/output_02.spectra-asm.fl.png test-data/output_02.spectra-asm.ln.png test-data/output_02.spectra-asm.st.png test-data/output_02_qv.tabular test-data/output_03.assembly_01.spectra-cn.fl.png test-data/output_03.assembly_01.spectra-cn.ln.png test-data/output_03.assembly_01.spectra-cn.st.png test-data/output_03.assembly_02.spectra-cn.fl.png test-data/output_03.assembly_02.spectra-cn.ln.png test-data/output_03.assembly_02.spectra-cn.st.png test-data/output_03.completeness.stats.tabular test-data/output_03.spectra-asm.ln.png test-data/output_03.spectra-cn.fl.png test-data/output_03.spectra-cn.ln.png test-data/output_03.spectra-cn.st.png test-data/output_03_qv.tabular test-data/output_04.assembly_01.100_20000.phased_block.blob.png test-data/output_04.assembly_01.100_20000.switch.bed test-data/output_04.assembly_01.bed test-data/output_04.assembly_01.block.N.png test-data/output_04.assembly_01.contig.tabular test-data/output_04.assembly_01.continuity.N.png test-data/output_04.assembly_01.mat.spectra-cn.ln.png test-data/output_04.assembly_01.pat.bed test-data/output_04.assembly_01.pat.spectra-cn.ln.png test-data/output_04.assembly_01.sort.bed test-data/output_04.assembly_02.contig.tabular test-data/output_04.assembly_02.mat.spectra-cn.ln.png test-data/output_04.assembly_02.pat.spectra-cn.ln.png test-data/output_04.hapmers.blob.png test-data/output_04.switches.txt test-data/output_04_qv.tabular test-data/pat.meryldb test-data/read-db.meryldb |
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| 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 |
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| @@ -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> |
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| 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 |
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| b'@@ -0,0 +1,444 @@\n+<tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01">\n+ <description>evaluate the assembly quality</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements"/>\n+ <version_command>merqury --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir -p output_files\n+ #if $mode.options == \'default\'\n+ && mkdir -p read-db.meryl\n+ && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1\n+ #if $mode.assembly_options.number_assemblies == \'one\'\n+ #if $mode.assembly_options.assembly_01.ext.endswith(".gz")\n+ && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta\n+ #else\n+ && ln -s \'$mode.assembly_options.assembly_01\' assembly.fasta\n+ #end if \n+ && merqury.sh read-db.meryl assembly.fasta ${label}\n+ && mv ${label}* output_files\n+ && find . -maxdepth 1 -name \'assembly_only*\' -type f -print0 | xargs -0r mv -t output_files\n+ #else\n+ #if $mode.assembly_options.assembly_01.ext.endswith(".gz")\n+ && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta\n+ #else\n+ && ln -s \'$mode.assembly_options.assembly_01\' assembly_01.fasta\n+ #end if \n+ #if $mode.assembly_options.assembly_02.ext.endswith(".gz")\n+ && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta\n+ #else\n+ && ln -s \'$mode.assembly_options.assembly_02\' assembly_02.fasta\n+ #end if \n+ && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label}\n+ && mv ${label}* output_files\n+ && find . -maxdepth 1 -name \'assembly_only*\' -type f -print0 | xargs -0r mv -t output_files\n+ #end if\n+ #else\n+ && mkdir -p read-db.meryl pat.meryl mat.meryl\n+ && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1\n+ && tar -zxf ${mode.meryldb_PAT} -C pat.meryl --strip-components=1\n+ && tar -zxf ${mode.meryldb_MAT} -C mat.meryl --strip-components=1\n+ #if $mode.assembly_options.number_assemblies == \'one\'\n+ #if $mode.assembly_options.assembly_01.ext.endswith(".gz")\n+ && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta\n+ #else\n+ && ln -s \'$mode.assembly_options.assembly_01\' assembly.fasta\n+ #end if \n+ && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label}\n+ && mv ${label}* output_files\n+ && find . -maxdepth 1 -name \'assembly_only*\' -type f -print0 | xargs -0r mv -t output_files\n+ #else\n+ #if $mode.assembly_options.assembly_01.ext.endswith(".gz")\n+ && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta\n+ #else\n+ && ln -s \'$mode.assembly_options.assembly_01\' assembly_01.fasta\n+ #end if \n+ #if $mode.assembly_options.assembly_02.ext.endswith(".gz")\n+ && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta\n+ #else\n+ && ln -s \'$mode.assembly_options.assembly_02\' assembly_02.fasta\n+ #end if\n+ && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label}\n+ && mv ${label}* output_files\n+ && find . -maxdepth 1 -name \'assembly_only*\' -type f -print0 | xargs -0r mv -t output_files\n+ #end if\n+ #end if\n+ ]]> </command>\n+ <inputs>\n+ <conditional name="mode">\n+ <param name="o'..b'/element>\n+ <element name="output_04.hapmers.blob" file="output_04.hapmers.blob.png" ftype="png">\n+ <assert_contents>\n+ <has_size value="10764" delta="100"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="stats_files" type="list" count="3">\n+ <element name="output_04.assembly_01.100_20000.phased_block" ftype="tabular"/>\n+ <element name="output_04.assembly_02.100_20000.phased_block" file="output_04.assembly_02.100_20000.phased_block.stats.tabular" ftype="tabular"/>\n+ <element name="output_04.completeness"/>\n+ </output_collection>\n+ <output_collection name="qv_files" type="list" count="1">\n+ <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>\n+ </output_collection>\n+ <output_collection name="wig_files" type="list" count="4">\n+ <element name="output_04.assembly_01.pat" ftype="wig"/>\n+ <element name="output_04.assembly_01.mat" ftype="wig"/>\n+ <element name="output_04.assembly_02.pat" ftype="wig"/>\n+ <element name="output_04.assembly_02.mat" ftype="wig"/>\n+ </output_collection>\n+ <output_collection name="sizes_files" type="list" count="4">\n+ <element name="output_04.assembly_01.100_20000.phased_block"/>\n+ <element name="output_04.assembly_01.contig" file="output_04.assembly_01.contig.tabular" ftype="tabular"/>\n+ <element name="output_04.assembly_02.100_20000.phased_block"/>\n+ <element name="output_04.assembly_02.contig" file="output_04.assembly_02.contig.tabular" ftype="tabular"/>\n+ </output_collection>\n+ <output_collection name="bed_files" type="list" count="6">\n+ <element name="output_04.assembly_01.100_20000.phased_block" ftype="bed"/>\n+ <element name="output_04.assembly_01.100_20000.switch" file="output_04.assembly_01.100_20000.switch.bed" ftype="bed"/>\n+ <element name="output_04.assembly_01.sort" file="output_04.assembly_01.sort.bed" ftype="bed"/>\n+ <element name="output_04.assembly_02.100_20000.phased_block" ftype="bed"/>\n+ <element name="output_04.assembly_02.100_20000.switch" ftype="bed"/>\n+ <element name="output_04.assembly_02.sort" ftype="bed"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**Purpose**\n+\n+Merqury allows a reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo\n+assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. \n+\n+For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. \n+\n+----\n+ \n+.. class:: infomark\n+ \n+**Input**\n+\n+Merqury requires two types of inputs: meryldbs and the genome assemblies.\n+There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.\n+\n+----\n+ \n+.. class:: infomark\n+ \n+**Output**\n+\n+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\xe2\x80\x99s 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). \n+\n+ ]]> </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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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 |
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| @@ -0,0 +1,2 @@ +tig00000005 227845 227853 pat +tig00000005 426764 426772 pat |
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| @@ -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 |
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| @@ -0,0 +1,3 @@ +tig00000005 227825 227850 0.2 +tig00000005 227850 227875 0.12 +tig00000005 426750 426775 0.32 |
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| @@ -0,0 +1,1 @@ +output_01.assembly.100_20000 switch error rate (%) (Num. switches / Total markers found): 0 2 0% |
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| @@ -0,0 +1,1 @@ +assembly all 193949 279149 69.4787 |
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| @@ -0,0 +1,1 @@ +assembly 2882439 3113584 |
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| @@ -0,0 +1,3 @@ +assembly_01 all 193949 279149 69.4787 +assembly_02 all 64441 279149 23.0848 +both all 193949 279149 69.4787 |
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| @@ -0,0 +1,3 @@ +assembly_01 2882439 3113584 +assembly_02 964973 1037945 +Both 3847412 4151529 |
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| @@ -0,0 +1,2 @@ +tig00000005 227845 227853 pat Same pat +tig00000005 426764 426772 pat Same pat |
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| @@ -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 |
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| @@ -0,0 +1,3 @@ +tig00000005 227825 227850 0.2 +tig00000005 227850 227875 0.12 +tig00000005 426750 426775 0.32 |
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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 |
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| @@ -0,0 +1,1 @@ +output_04.assembly_02.100_20000 switch error rate (%) (Num. switches / Total markers found): |
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| 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 |
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| @@ -0,0 +1,1 @@ +Both |
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| diff -r 000000000000 -r 9d79beb19ac3 test-data/read-db.meryldb |
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| Binary file test-data/read-db.meryldb has changed |
