| Previous changeset 2:589078edd230 (2022-04-25) Next changeset 4:09c589057ee8 (2023-08-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f |
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modified:
merqury.xml test-data/output_05_log.txt |
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added:
test-data/output_06.completeness.stats.tabular test-data/output_06_qv.tabular |
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| diff -r 589078edd230 -r f8113c25bc6b merqury.xml --- a/merqury.xml Mon Apr 25 11:20:41 2022 +0000 +++ b/merqury.xml Tue Jul 12 15:23:31 2022 +0000 |
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| b'@@ -16,8 +16,8 @@\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+ #end if\n+ && merqury.sh read-db.meryl assembly.fasta ${label}\n #if \'log\' in $output_selector\n &> $log_file\n #end if\n@@ -28,12 +28,12 @@\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+ #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+ #end if\n && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label}\n #if \'log\' in $output_selector\n &> $log_file\n@@ -51,7 +51,7 @@\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+ #end if\n && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label}\n #if \'log\' in $output_selector\n &> $log_file\n@@ -63,7 +63,7 @@\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+ #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@@ -77,18 +77,25 @@\n && find . -maxdepth 1 -name \'assembly_only*\' -type f -print0 | xargs -0r mv -t output_files\n #end if\n #end if\n- \n+\n+ #if $output_add_headers:\n+ && sed -i \'1s/^/assembly\\tk-mer set\\tsolid k-mers in assembly\\tsolid k-mers in reads\\tcompleteness %\\n/\'\n+ \'output_files/${label}.completeness.stats\'\n+ && sed -i \'1s/^/assembly\\tunique k-mers\\tcommon k-mers\\tQV\\terror rate\\n/\'\n+ \'output_files/${label}.qv\'\n+ #end if\n+\n ]]> </command>\n <inputs>\n <conditional name="mode">\n- <param name="options" type="select" \n+ <param name="options" type="select"\n label="Evaluation mode" help="Merqury allows two operational modes: default and trio mode.">\n <option value="default">Default mode</option>\n <option value="trio">Trio mode</option>\n </param>\n <when value="default">\n <param name="meryldb_F1" type="data" format="meryldb"\n- label="K-mer counts database" \n+ label="K-mer counts database"\n help="Select the k-mer counts of the read set."/>\n <conditional name="assembly_options">\n <param name="number_assemblies" type="select"\n@@ -97,29 +104,29 @@\n <option value="two">Two assemblies (diploid)</option>\n </param>\n <when value="one">\n- <param name="assembly_01" type="data" format="fasta,fasta.gz" \n- label="Genome assembly" \n+ <param name="assembly_01" type="data" format="fasta,fasta.gz"\n+ label="Genome assembly"\n '..b'o file to compare"\n <element name="output_03.assembly_01" ftype="tabular"/>\n <element name="output_03.assembly_02" ftype="tabular"/>\n+ -->\n <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>\n </output_collection>\n </test>\n@@ -337,6 +348,26 @@\n </output_collection>\n <output name="log_file" file="output_05_log.txt" ftype="txt" lines_diff=\'4\'/>\n </test>\n+ <!--Test 06: standard mode with tabular headers -->\n+ <test expect_num_outputs="2">\n+ <conditional name="mode">\n+ <param name="options" value="default"/>\n+ <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>\n+ <conditional name="assembly_options">\n+ <param name="number_assemblies" value="one"/>\n+ <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>\n+ </conditional>\n+ </conditional>\n+ <param name="label" value="output_06"/>\n+ <param name="output_selector" value="stats,qv"/>\n+ <param name="output_add_headers" value="true"/>\n+ <output_collection name="stats_files" type="list" count="1">\n+ <element name="output_06.completeness" file="output_06.completeness.stats.tabular" ftype="tabular"/>\n+ </output_collection>\n+ <output_collection name="qv_files" type="list" count="2">\n+ <element name="output_06" file="output_06_qv.tabular" ftype="tabular"/>\n+ </output_collection>\n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n@@ -344,26 +375,28 @@\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+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+For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors.\n \n ----\n- \n+\n .. class:: infomark\n- \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+\n .. class:: infomark\n- \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+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+You can add column headers to the ``completeness`` and ``qv`` outputs by checking the option "Add column header on tabular outputs".\n \n ]]> </help>\n <expand macro="citations"/>\n' |
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| diff -r 589078edd230 -r f8113c25bc6b test-data/output_05_log.txt --- a/test-data/output_05_log.txt Mon Apr 25 11:20:41 2022 +0000 +++ b/test-data/output_05_log.txt Tue Jul 12 15:23:31 2022 +0000 |
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| @@ -37,7 +37,7 @@ Result saved as output_05.assembly_01.100_20000.phased_block.sizes # Plot output_05.assembly_01.100_20000.phased_block.bed -Rscript /home/laptop/miniconda3/envs/mulled-v1-df114ce4641e6c1c408ddc8230d91a93fc95c8ba1dfeff221f556e667abb43c0/share/merqury/plot/plot_block_N.R -b output_05.assembly_01.100_20000.phased_block.sizes -c output_05.assembly_01.contig.sizes -o output_05.assembly_01 +Rscript /usr/local/share/merqury/plot/plot_block_N.R -b output_05.assembly_01.100_20000.phased_block.sizes -c output_05.assembly_01.contig.sizes -o output_05.assembly_01 Loading required package: argparse Loading required package: ggplot2 Loading required package: scales @@ -49,7 +49,7 @@ Result saved as output_05.assembly_02.100_20000.phased_block.sizes # Plot output_05.assembly_02.100_20000.phased_block.bed -Rscript /home/laptop/miniconda3/envs/mulled-v1-df114ce4641e6c1c408ddc8230d91a93fc95c8ba1dfeff221f556e667abb43c0/share/merqury/plot/plot_block_N.R -b output_05.assembly_02.100_20000.phased_block.sizes -c output_05.assembly_02.contig.sizes -o output_05.assembly_02 +Rscript /usr/local/share/merqury/plot/plot_block_N.R -b output_05.assembly_02.100_20000.phased_block.sizes -c output_05.assembly_02.contig.sizes -o output_05.assembly_02 Loading required package: argparse Loading required package: ggplot2 Loading required package: scales |
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| diff -r 589078edd230 -r f8113c25bc6b test-data/output_06.completeness.stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_06.completeness.stats.tabular Tue Jul 12 15:23:31 2022 +0000 |
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| @@ -0,0 +1,2 @@ +assembly k-mer set solid k-mers in assembly solid k-mers in reads completeness % +assembly all 32353 32353 100 |
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| diff -r 589078edd230 -r f8113c25bc6b test-data/output_06_qv.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_06_qv.tabular Tue Jul 12 15:23:31 2022 +0000 |
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| @@ -0,0 +1,2 @@ +assembly unique k-mers common k-mers QV error rate +assembly 0 1037953 |