| Previous changeset 4:cdd90678004a (2018-12-14) Next changeset 6:73b103195e2a (2020-01-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 |
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modified:
gemini_macros.xml gemini_stats.xml repository_dependencies.xml test-data/gemini_amend_input.db test-data/gemini_annotate_result.db test-data/gemini_auto_dom_input.db test-data/gemini_auto_rec_input.db test-data/gemini_comphets_input.db test-data/gemini_de_novo_input.db test-data/gemini_is_somatic_result.db test-data/gemini_load_result1.db test-data/gemini_load_result2.db test-data/gemini_versioned_databases.loc test-data/test-cache/gemini-config.yaml |
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added:
test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi |
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removed:
test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi |
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| diff -r cdd90678004a -r 86d4303cc3ca gemini_macros.xml --- a/gemini_macros.xml Fri Dec 14 12:47:19 2018 -0500 +++ b/gemini_macros.xml Fri Jan 11 17:43:48 2019 -0500 |
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| b'@@ -1,15 +1,12 @@\n <macros>\n <!-- gemini version to be used -->\n- <token name="@VERSION@">0.18.1</token>\n+ <token name="@VERSION@">0.20.1</token>\n <!-- minimal annotation files version required by this version of gemini -->\n- <token name="@DB_VERSION@">181</token>\n+ <token name="@DB_VERSION@">200</token>\n \n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@VERSION@">gemini</requirement>\n- <requirement type="package" version="0.2.6">tabix</requirement>\n- <!-- for conda useage -->\n- <!--requirement type="package" version="1.3.1">htslib</requirement-->\n <yield />\n </requirements>\n </xml>\n@@ -24,9 +21,17 @@\n <exit_code range=":-1" />\n <regex match="Error:" />\n <regex match="Exception:" />\n+ <yield />\n </stdio>\n </xml>\n \n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n <xml name="annotation_dir">\n <param name="annotation_databases" type="select" label="Choose a gemini annotation source">\n <options from_data_table="gemini_versioned_databases">\n@@ -36,31 +41,36 @@\n </param>\n </xml>\n \n- <xml name="add_header_column">\n- <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" \n- label="Add a header of column names to the output" help="(--header)"/>\n- </xml>\n-\n- <xml name="radius">\n- <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >\n- <validator type="in_range" min="0"/>\n+ <xml name="infile">\n+ <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n+ <options options_filter_attribute="metadata.gemini_version" >\n+ <filter type="add_value" value="@VERSION@" />\n+ </options>\n </param>\n </xml>\n- <xml name="variant_mode">\n- <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" \n- label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>\n+\n+ <xml name="add_header_column">\n+ <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True" \n+ label="Add a header of column names to the output" />\n </xml>\n \n- <xml name="column_filter">\n+ <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">\n <conditional name="report">\n- <param name="report_selector" type="select" label="Columns to include in the report"\n- help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">\n- <option value="all" selected="True">all</option>\n- <option value="column_filter">User given columns</option>\n+ <param name="report_selector" type="select"\n+ label="Set of columns to include in the variant report table"\n+ help="@HELP@">\n+ <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>\n+ <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>\n+ <option value="custom">Custom (report user-specified columns)</option>\n </param>\n- <when value="all"/>\n- <when value="column_filter">\n- <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">\n+ <when value="full" />\n+ <when value="minimal">\n+ '..b'r($report.extra_cols).strip():\n+ #if $cols:\n+ #set $cols = $cols + \', \' + str($report.extra_cols)\n+ #else:\n+ #set $cols = str($report.extra_cols)\n+ #end if\n+ #end if\n+ #if not $cols:\n+ #set $cols = "variant_id, gene"\n+ #end if\n #end if\n </token>\n \n <token name="@COLUMN_SELECT@">\n- #if $report.report_selector != \'all\':\n- --columns "${report.columns}\n- #if str($report.extra_cols).strip()\n- #echo \',\'+\',\'.join(str($report.extra_cols).split()) \n- #end if\n- "\n+ @SET_COLS@\n+ #if $cols != "*"\n+ --columns \'$cols\'\n #end if\n </token>\n \n- <xml name="family">\n- <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>\n- </xml>\n-\n- <xml name="lenient">\n- <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>\n- </xml>\n-\n- <xml name="unaffected">\n- <param name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" label="Report candidates that also impact samples labeled as unaffected." help="(--allow-unaffected)"/>\n- </xml>\n-\n- <xml name="min_kindreds">\n- <param name="min_kindreds" type="integer" value="1" label="The min. number of kindreds that must have a candidate variant in a gene" help="default: 1 (--min-kindreds)" />\n- </xml>\n-\n- <xml name="min_sequence_depth">\n- <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"\n- help="default: 0 (-d)" />\n- </xml>\n-\n- <xml name="min_gq">\n- <param name="min_gq" type="integer" value="0" label="the minimum genotype quality required for each sample in a family" help="default: 0 (--min-gq)">\n- <validator type="in_range" min="0"/>\n- </param>\n- </xml>\n-\n- <xml name="gt_pl_max">\n- <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n- <yield />\n- </citations>\n- </xml>\n-\n- <xml name="infile">\n- <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n- <options options_filter_attribute="metadata.gemini_version" >\n- <filter type="add_value" value="@VERSION@" />\n- </options>\n- <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator>\n- </param>\n- </xml>\n-\n+ <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[\n+ #set $region_elements = []\n+ #for $r in $regions:\n+ ## The actual chromosome name needs to be single-quoted\n+ ## in SQL, so we need to quote the single quotes like the\n+ ## sanitize_query macro would if the whole was a parameter.\n+ #set $r_elements = ["chrom = \'\\"\'\\"\'%s\'\\"\'\\"\'" % str($r.chrom).strip()]\n+ #if str($r.start).strip():\n+ #silent $r_elements.append("start >= %d" % int($r.start))\n+ #end if\n+ #if str($r.stop).strip():\n+ #silent $r_elements.append("end <= %d" % int($r.stop))\n+ #end if\n+ #silent $region_elements.append("(%s)" % " AND ".join($r_elements))\n+ #end for\n+ ]]>\n+ </token>\n </macros>\n' |
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| diff -r cdd90678004a -r 86d4303cc3ca gemini_stats.xml --- a/gemini_stats.xml Fri Dec 14 12:47:19 2018 -0500 +++ b/gemini_stats.xml Fri Jan 11 17:43:48 2019 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">\n+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">\n <description>Compute useful variant statistics</description>\n <macros>\n <import>gemini_macros.xml</import>\n@@ -10,41 +10,83 @@\n <command>\n <![CDATA[\n gemini @BINARY@\n- $stats_type\n-\n- #set $multiline_sql_expr = $gt_filter\n- #set $cmdln_param = "--gt-filter"\n- @MULTILN_SQL_EXPR_TO_CMDLN@\n+ #if str($stats.type) == "gts-stats":\n+ #set $multiline_sql_expr = $stats.variants.gt_filter\n+ #set $cmdln_param = "--gt-filter"\n+ @MULTILN_SQL_EXPR_TO_CMDLN@\n \n- #set $multiline_sql_expr = $summarize\n- #set $cmdln_param = "--summarize"\n- @MULTILN_SQL_EXPR_TO_CMDLN@\n-\n- "${ infile }"\n- > "${ outfile }"\n+ #if str($stats.variants.constraint).strip():\n+ #set $multiline_sql_expr = "select * from variants WHERE " + str($stats.variants.constraint)\n+ #else:\n+ #set $multiline_sql_expr = "select * from variants"\n+ #end if\n+ #set $cmdln_param = "--summarize"\n+ @MULTILN_SQL_EXPR_TO_CMDLN@\n+ #else:\n+ ${stats.stats_option}\n+ #end if\n+ \'$infile\'\n+ > \'$outfile\'\n ]]>\n </command>\n <inputs>\n <expand macro="infile" />\n \n- <param name="stats_type" type="select" label="Studying ..." help="">\n- <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option>\n- <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option>\n- <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option>\n- <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option>\n- <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option>\n- <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option>\n- <option value="--vars-by-sample">Return the total variants per sample, sum of homozygous and heterozygous variants (--vars-by-sample)</option>\n- <option value="--gts-by-sample">Return the count of each genotype class observed per sample (--gts-by-sample)</option>\n- </param>\n-\n- <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">\n- <expand macro="sanitize_query" />\n- </param>\n-\n- <param name="summarize" type="text" area="True" size="5x50" label="The query to be issued to the database to summarize" help="(--summarize)">\n- <expand macro="sanitize_query" />\n- </param>\n+ <conditional name="stats">\n+ <param name="type" type="select"\n+ label="Select the type of statistics you are interested in" help="">\n+ <option value="gts-stats">Genotype counts tabulated by sample (--summarize)</option>\n+ <option value="snp-counts">Counts of SNPs by nucleotide change (--snp-counts)</option>\n+ <option value="tstv-stats">Transition / transversion statistics for the SNPs in the dataset</option>\n+ <option value="aaf">Alternate allele frequency spectrum of all variants (--sfs)</option>\n+ <option value="sample-distance">Pair-wise genetic distances between for all samples (--mds)</option>\n+ </param>\n+ <when value="snp-counts">\n+ <param name="stats_option" type="hidden" value="--snp-counts" />\n+ </when>\n+ <when value="aaf">\n+ '..b'	num_het	num_hom_alt	num_unknown	total" />\n+ <has_line_matching expression="sample	total	num_het	num_hom_alt	num_hom_ref" />\n </assert_contents>\n </output>\n </test>\n@@ -74,31 +127,60 @@\n <help><![CDATA[\n **What it does**\n \n-The stats tool computes some useful variant statistics for a GEMINI database.\n-Like computing the transition and transversion ratios for the snps.\n+The stats tool computes one of the following useful variant statistics for a GEMINI database:\n+\n+**Genotype counts tabulated by sample**:\n \n-**Settings and examples**\n+This mode uses the ``gemini stats --summarize`` option to produce a table with\n+one row per sample, which tabulates the numbers of sites, for which a given\n+sample shows a:\n \n---tstv-coding:\n- Compute the transition/transversion ratios for the snps in the coding regions.\n+- non-reference genotype (*total* column; the sum of the *num_het* and *num_hom_alt* columns next to it)\n+- heterozygous genotype (*num_het* column)\n+- homozygous variant genotype (*num_hom_alt* column)\n+- homozygous reference genotype (*num_hom_ref* column)\n \n---tstv-noncoding:\n- Compute the transition/transversion ratios for the snps in the non-coding regions.\n+You can choose to calculate the table based on all variants in your database,\n+or to filter the variants before the calculation using GEMINI genotype filter\n+expressions and/or WHERE clauses of GEMINI queries.\n \n-EXAMPLE Compute the type and count of the snps; --snp-counts::\n+**Counts of SNPs by nucleotide change**:\n+\n+This runs ``gemini stats`` with the ``--snp-count`` option. The result is a\n+simple table listing the number of occurences of each observed REF->ALT change\n+in your database, e.g.::\n \n type count\n A->G 2\n C->T 1\n G->A 1\n \n-EXAMPLE Calculate the site frequency spectrum of the variants; --sfs::\n+**Transition / transversion statistics**\n+\n+This mode uses ``gemini stats`` with the ``--tstv``, ``--tstv-coding``, or\n+``--tstv-noncoding`` option to compute the transition/transversion ratios for\n+all SNPs, for SNPs in coding, or SNPs in non-coding regions, respectively.\n+\n+The result is presented in a 1x3 table listing the number of\n+transitions (*ts* column), transversions (*tv* column) and the ratio of the two\n+(*ts/tv* column), e.g.::\n+\n+ ts tv ts/tv\n+ 126 39 3.2307\n+\n+**Alternate allele frequency spectrum**\n+\n+Runs ``gemini stats --sfs`` to produce binned alternate allele frequency counts\n+in a table like::\n \n aaf count\n 0.125 2\n 0.375 1\n \n-EXAMPLE Compute the pair-wise genetic distance between each sample; --mds::\n+**Pairwise genetic distances**\n+\n+Runs ``gemini stats --mds`` and tabulates all pairwise genetic distance for the\n+samples in your database. An example could look like this::\n \n sample1 sample2 distance\n M10500 M10500 0.0\n@@ -106,34 +188,6 @@\n M10500 M10475 2.0\n M10500 M10478 0.5714\n \n-EXAMPLE Return a count of the types of genotypes per sample; --gts-by-sample::\n-\n- sample num_hom_ref num_het num_hom_alt num_unknown total\n- M10475 4 1 3 1 9\n- M10478 2 2 4 1 9\n-\n-\n-\n-EXAMPLE Return the total variants per sample (sum of homozygous and heterozygous variants); --vars-by-sample::\n-\n- sample total\n- M10475 4\n- M10478 6\n-\n-**Final solution**\n-\n---summarize:\n- If none of these tools are exactly what you want, you can summarize the variants per sample of an arbitrary query using the \xe2\x80\x93summarize flag. \n-\n-EXAMPLE If you wanted to know, for each sample, how many variants are on chromosome 1 that are also in dbSNP;--summarize "select * from variants where in_dbsnp=1 and chrom=\'chr1\'":: \n-\n- sample total num_het num_hom_alt\n- M10475 1 1 0\n- M128215 1 1 0\n- M10478 2 2 0\n- M10500 2 1 1\n-\n-\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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| diff -r cdd90678004a -r 86d4303cc3ca repository_dependencies.xml --- a/repository_dependencies.xml Fri Dec 14 12:47:19 2018 -0500 +++ b/repository_dependencies.xml Fri Jan 11 17:43:48 2019 -0500 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0" ?> <repositories description="This requires the GEMINI data manager definition to install all required annotation databases."> - <repository changeset_revision="fe5a9a7d95b0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository changeset_revision="f57426daa04d" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> </repositories> \ No newline at end of file |
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| diff -r cdd90678004a -r 86d4303cc3ca test-data/gemini_versioned_databases.loc --- a/test-data/gemini_versioned_databases.loc Fri Dec 14 12:47:19 2018 -0500 +++ b/test-data/gemini_versioned_databases.loc Fri Jan 11 17:43:48 2019 -0500 |
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| @@ -1,3 +1,3 @@ ## GEMINI versioned databases #DownloadDate dbkey DBversion Description Path -1999-01-01 hg19 181 GEMINI annotations (test snapshot) ${__HERE__}/test-cache +1999-01-01 hg19 200 GEMINI annotations (test snapshot) ${__HERE__}/test-cache |
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| diff -r cdd90678004a -r 86d4303cc3ca test-data/test-cache/gemini-config.yaml --- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 12:47:19 2018 -0500 +++ b/test-data/test-cache/gemini-config.yaml Fri Jan 11 17:43:48 2019 -0500 |
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| @@ -2,12 +2,14 @@ versions: ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4 ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2 - ExAC.r0.3.sites.vep.tidy.vcf.gz: 3 + ExAC.r0.3.sites.vep.tidy.vcf.gz: 4 GRCh37-gms-mappability.vcf.gz: 2 - clinvar_20160203.tidy.vcf.gz: 5 + clinvar_20170130.tidy.vcf.gz: 5 cosmic-v68-GRCh37.tidy.vcf.gz: 3 - dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4 + dbsnp.b147.20160601.tidy.vcf.gz: 1 detailed_gene_table_v75: 2 geno2mp.variants.tidy.vcf.gz: 1 + gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2 hg19.rmsk.bed.gz: 2 summary_gene_table_v75: 2 + whole_genome_SNVs.tsv.compressed.gz: 2 |
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