| Previous changeset 4:7ca6716748c2 (2018-12-14) Next changeset 6:840fb4850be3 (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_query.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 7ca6716748c2 -r cd00221d67cb gemini_macros.xml --- a/gemini_macros.xml Fri Dec 14 12:51:59 2018 -0500 +++ b/gemini_macros.xml Fri Jan 11 17:47:02 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 7ca6716748c2 -r cd00221d67cb gemini_query.xml --- a/gemini_query.xml Fri Dec 14 12:51:59 2018 -0500 +++ b/gemini_query.xml Fri Jan 11 17:47:02 2019 -0500 |
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| b'@@ -1,8 +1,32 @@\n-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">\n+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">\n <description>Querying the GEMINI database</description>\n <macros>\n <import>gemini_macros.xml</import>\n <token name="@BINARY@">query</token>\n+\n+ <xml name="sorting">\n+ <param name="order_by" type="text"\n+ label="Sort the output by the following column(s)"\n+ help="" />\n+ <param name="sort_order" type="select" label="Sort order">\n+ <option value=" ASC">Ascending</option>\n+ <option value=" DESC">Descending</option>\n+ </param>\n+ </xml>\n+ <xml name="pheno_strat">\n+ <param name="phenotype" type="text"\n+ label="Phenotype to stratify samples across"\n+ help="Leave blank to stratify across the default phenotype column" />\n+ </xml>\n+ <xml name="sample_delimiter" token_applied_to="samples">\n+ <param argument="--sample-delim" name="sample_delim" type="text" value=","\n+ label="Delimiter to use in the list of affected @APPLIED_TO@"\n+ help="" />\n+ </xml>\n+ <xml name="dgidb_query">\n+ <param argument="--dgidb" name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"\n+ label="Request drug-gene interaction info from DGIdb" help="" />\n+ </xml>\n </macros>\n <expand macro="requirements" />\n <expand macro="stdio" />\n@@ -10,91 +34,251 @@\n <command>\n <![CDATA[\n gemini @BINARY@\n+ ${query.oformat.report.header}\n+ ${query.oformat.report.dgidb}\n \n- --in "${in}"\n+ #for $i in $query.filter_by_genotype:\n+ #set $multiline_sql_expr = str($i.gt_filter)\n+ #set $cmdln_param = "--gt-filter"\n+ @MULTILN_SQL_EXPR_TO_CMDLN@\n+ #end for\n \n- #set $multiline_sql_expr = $gt_filter\n- #set $cmdln_param = "--gt-filter"\n- @MULTILN_SQL_EXPR_TO_CMDLN@\n-\n- #set $multiline_sql_expr = $sample_filter\n- #set $cmdln_param = "--sample-filter"\n- @MULTILN_SQL_EXPR_TO_CMDLN@\n+ #for $i in $query.filter_by_sample:\n+ $i.family_wise\n+ #if int($i.min_kindreds) > 0:\n+ --min-kindreds ${i.min_kindreds}\n+ #end if\n+ ${i.in}\n+ #set $multiline_sql_expr = str($i.sample_filter)\n+ #set $cmdln_param = "--sample-filter"\n+ @MULTILN_SQL_EXPR_TO_CMDLN@\n+ #end for\n \n- $show_samples\n- $show_families\n- $family_wise\n- $header\n- $dgidb\n- #if $region.strip():\n- --region "${region}"\n+ #if str($query.oformat.report.format) == \'with_samples\':\n+ #set $sample_delim = str($query.oformat.report.sample_delim) or \',\'\n+ --show-samples --sample-delim \'$sample_delim\'\n+ #elif str($query.oformat.report.format) == \'with_samples_flattened\':\n+ --show-samples --format sampledetail\n+ #elif str($query.oformat.report.format) == \'with_families\':\n+ #set $sample_delim = str($query.oformat.report.sample_delim) or \',\'\n+ --show-families --sample-delim \'$sample_delim\'\n+ #elif str($query.oformat.report.format) == \'carrier_summary\':\n+ --carrier-summary-by-phenotype\n+ #if str($query.oformat.report.phenotype).strip():\n+ \'${query.oformat.report.phenotype}\'\n+ #else:\n+ affected\n+ #end if\n+ #else:\n+ --format ${query.oformat.report.format}\n #end if\n- #if int($min_kindreds) > 0:\n- --min-kindreds $min_kindreds\n+\n+ #if str($query.'..b' for which sample 1 is a heterozygous carrier\n+and if the genomic position in sample1 is covered by at least 15 sequencing\n+reads, as well as GEMINI wildcard filters of the general form\n+*(COLUMN).(SAMPLE_FILTER).(RULE).(RULE_ENFORCEMENT)* like::\n+\n+ (gt_types).(phenotype==2).(!=HOM_REF).(all)\n+\n+, which keeps only variants for which all phenotypic samples are homozygous.\n+\n+*Sample filters*\n+\n+Sample filters have the same format as the second component of the genotype\n+wildcard filters above, so::\n+\n+ phenotype == 2\n+\n+would filter for phenotypically affected samples. In this case, however, the\n+filter determines, from which samples variants should be reported, i.e., here,\n+only variants found in phenotypically affected samples become analyzed. You can\n+use the ``--in`` filter to adjust the exact meaning of the sample filter.\n+\n+*Region filters*\n+\n+They let you restrict your analysis to parts of the genome, which can be useful\n+if you have prior knowledge of the approximate location of a variant of\n+interest.\n+\n+If you specify more then one region filter, they get combined with a logical\n+*OR*, meaning variants and genes falling in *any* of the regions are reported.\n \n-http://gemini.readthedocs.org/en/latest/content/querying.html\n+*Additional constraints on variants*\n+\n+These get translated directly into the WHERE clause of an SQL query and, thus,\n+have to be expressed in valid SQL syntax. As an example you could use::\n+\n+ is_exonic = 1 and impact_severity != \'LOW\'\n+\n+to indicate that you are only interested in exonic variants that are not of\n+*LOW* impact severity, *i.e.*, not silent mutations.\n+\n+Note that in SQL syntax tests for equality use a single ``=``, while genotype\n+filters (discussed above) are following Python syntax and use ``==`` for the\n+same purpose. Also note that non-numerical values need to be enclosed in\n+single-quotes, *e.g.* ``\'LOW\'``, but numerical values must *NOT* be.\n+\n+-----\n+\n+*Building your query with the Advanced query constructor*\n+\n+For the sake of simplicity, the basic mode of the tool limits your queries to\n+the variants table of the underlying database. While this still allows many\n+useful queries to be formulated, it prevents you from joining information from\n+other tables (in particular, the gene_detailed table) or to query a different\n+table directly.\n+\n+In advanced mode, you take responsibility for formulating the complete SQL\n+query in correct syntax, which allows you to do anything you could do with the\n+command line tool. Beyond querying other tables, this includes changing output\n+column names, deriving simple statistics on columns using the SQL Min, Max,\n+Count, Avg and Sum functions, and more.\n+\n+The price you pay for this extra flexibility is that you will have to make sure\n+that any other tool options you set are compatible with the result of your\n+particular query. For example, most output formats except the tabular default\n+output of GEMINI are incompatible with non-standard queries. Choosing\n+non-compatible options can result in them getting ignored silently, but also\n+in tool errors, or in problems with downstream tools.\n+\n+The chapter `Querying the GEMINI database\n+<http://gemini.readthedocs.org/en/latest/content/querying.html>`__ of the\n+GEMINI documentation can get you started with formulating your own queries.\n+\n+Note that genotype filters and sample filters cannot be expressed as genuine\n+SQL queries, so even the Advanced query constructor is offering them. Region\n+filters and sort order of rows and columns on the other hand can be controlled\n+through SQL queries, like in this example::\n+\n+ SELECT gene, chrom, start, end, ref, alt FROM variants WHERE chrom = \'chr1\'\n+ AND start >= 10000000 and stop <= 20000000 and is_lof = 1 ORDER BY chrom,\n+ start\n+\n+, which would report all loss-of-function variants between 10,000,000 and\n+20,000,000 on chr1 and report the selected columns sorted on chromosome, then\n+position.\n+\n ]]>\n </help>\n <expand macro="citations"/>\n' |
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| diff -r 7ca6716748c2 -r cd00221d67cb repository_dependencies.xml --- a/repository_dependencies.xml Fri Dec 14 12:51:59 2018 -0500 +++ b/repository_dependencies.xml Fri Jan 11 17:47:02 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 7ca6716748c2 -r cd00221d67cb test-data/gemini_versioned_databases.loc --- a/test-data/gemini_versioned_databases.loc Fri Dec 14 12:51:59 2018 -0500 +++ b/test-data/gemini_versioned_databases.loc Fri Jan 11 17:47:02 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 7ca6716748c2 -r cd00221d67cb test-data/test-cache/gemini-config.yaml --- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 12:51:59 2018 -0500 +++ b/test-data/test-cache/gemini-config.yaml Fri Jan 11 17:47:02 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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