Mercurial > repos > iuc > gemini_db_info
changeset 5:bc8b01d1b496 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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--- a/gemini_db_info.xml Fri Dec 14 12:41:01 2018 -0500 +++ b/gemini_db_info.xml Fri Jan 11 17:37:04 2019 -0500 @@ -1,21 +1,47 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> - <description>List the gemini database tables and columns</description> +<tool id="gemini_db_info" name="GEMINI database info" version="@VERSION@"> + <description>Retrieve information about tables, columns and annotation data stored in a GEMINI database</description> <macros> <import>gemini_macros.xml</import> - <token name="@BINARY@">db_info</token> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ - gemini @BINARY@ - "${ infile }" | tr -s ' ' '\t' - > "${ outfile }" + #if str($select.info_type) == 'scheme': + gemini db_info '$infile' | tr -s ' ' '\t' + #elif str($select.info_type) == 'resources': + gemini query --header -q "SELECT name as data_source, resource as resource_file from resources" '$infile' + #elif str($select.info_type) == 'gene_detailed': + gemini query --header -q "SELECT gene, synonym as synonyms, transcript FROM gene_detailed WHERE gene is not NULL GROUP BY transcript ORDER BY gene" '$infile' + #else: + gemini query --header -q "SELECT * FROM samples" "$infile" | cut -f 2-${select.format} + #end if + + > '$outfile' ]]> </command> <inputs> <expand macro="infile" /> + <conditional name="select"> + <param name="info_type" type="select" + label="Information to retrieve from the database"> + <option value="scheme">Names of database tables and their columns</option> + <option value="resources">List of annotation data sources</option> + <option value="gene_detailed">List of genes and their transcripts</option> + <option value="samples">Write out sample information in PED format</option> + </param> + <when value="scheme" /> + <when value="resources" /> + <when value="gene_detailed" /> + <when value="samples"> + <param name="format" type="select" display="radio" + label="Format of the pedigree file"> + <option value="">Allow extra columns to accomodate custom sample info</option> + <option value="7">Restrict to 6 PED standard columns and drop additional info</option> + </param> + </when> + </conditional> </inputs> <outputs> <data name="outfile" format="tabular" /> @@ -23,67 +49,71 @@ <tests> <test> <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> + <conditional name="select"> + <param name="info_type" value="scheme" /> + </conditional> <output name="outfile"> <assert_contents> <has_line_matching expression="table_name	column_name	type.*" /> </assert_contents> </output> </test> + <test> + <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> + <conditional name="select"> + <param name="info_type" value="resources" /> + </conditional> + <output name="outfile"> + <assert_contents> + <has_line line="data_source	resource_file" /> + <has_n_columns n="2" /> + </assert_contents> + </output> + </test> + <test> + <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> + <conditional name="select"> + <param name="info_type" value="gene_detailed" /> + </conditional> + <output name="outfile"> + <assert_contents> + <has_line line="gene	synonyms	transcript" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + </test> + <test> + <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" /> + <conditional name="select"> + <param name="info_type" value="samples" /> + </conditional> + <output name="outfile"> + <assert_contents> + <has_line_matching expression="family_id	name	paternal_id	maternal_id	sex	phenotype	.+" /> + </assert_contents> + </output> + </test> + <test> + <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" /> + <conditional name="select"> + <param name="info_type" value="samples" /> + <param name="format" value="7" /> + </conditional> + <output name="outfile"> + <assert_contents> + <has_line line="family_id	name	paternal_id	maternal_id	sex	phenotype" /> + <has_n_columns n="6" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ **What it does** -Because of the sheer number of annotations that are stored in gemini, there are admittedly too many columns to remember by rote. -If you can’t recall the name of particular column, just use the db_info tool. -It will report all of the tables and all of the columns / types in each table:: +Because of the sheer number of annotations that are stored in gemini, it is easy to lose the overview of what is actually available through database queries. - table_name column_name type - variants chrom text - variants start integer - variants end integer - variants variant_id integer - variants anno_id integer - variants ref text - variants alt text - variants qual float - variants filter text - variants type text - variants sub_type text - variants gts blob - variants gt_types blob - variants gt_phases blob - variants gt_depths blob - variants call_rate float - variants in_dbsnp bool - variants rs_ids text - variants in_omim bool - variants clin_sigs text - variants cyto_band text - variants rmsk text - variants in_cpg_island bool - variants in_segdup bool - variants is_conserved bool - variants num_hom_ref integer - variants num_het integer - variants num_hom_alt integer - variants num_unknown integer - variants aaf float - variants hwe float - variants inbreeding_coeff float - variants pi float - variants recomb_rate float - variants gene text - variants transcript text - variants is_exonic bool - variants is_coding bool - variants is_lof bool - variants exon text - variants codon_change text - variants aa_change text - ... ... ... - -For more columns see https://gemini.readthedocs.org/en/latest/content/tools.html#db-info-list-the-gemini-database-tables-and-columns - +This tool offers a simple way to inspect the structure, the origin of the +annotations and some of the actual annotation content quickly. ]]></help> <expand macro="citations"/> </tool>
--- a/gemini_macros.xml Fri Dec 14 12:41:01 2018 -0500 +++ b/gemini_macros.xml Fri Jan 11 17:37:04 2019 -0500 @@ -1,15 +1,12 @@ <macros> <!-- gemini version to be used --> - <token name="@VERSION@">0.18.1</token> + <token name="@VERSION@">0.20.1</token> <!-- minimal annotation files version required by this version of gemini --> - <token name="@DB_VERSION@">181</token> + <token name="@DB_VERSION@">200</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">gemini</requirement> - <requirement type="package" version="0.2.6">tabix</requirement> - <!-- for conda useage --> - <!--requirement type="package" version="1.3.1">htslib</requirement--> <yield /> </requirements> </xml> @@ -24,9 +21,17 @@ <exit_code range=":-1" /> <regex match="Error:" /> <regex match="Exception:" /> + <yield /> </stdio> </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003153</citation> + <yield /> + </citations> + </xml> + <xml name="annotation_dir"> <param name="annotation_databases" type="select" label="Choose a gemini annotation source"> <options from_data_table="gemini_versioned_databases"> @@ -36,31 +41,36 @@ </param> </xml> - <xml name="add_header_column"> - <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" - label="Add a header of column names to the output" help="(--header)"/> - </xml> - - <xml name="radius"> - <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" > - <validator type="in_range" min="0"/> + <xml name="infile"> + <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." > + <options options_filter_attribute="metadata.gemini_version" > + <filter type="add_value" value="@VERSION@" /> + </options> </param> </xml> - <xml name="variant_mode"> - <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" - label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/> + + <xml name="add_header_column"> + <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True" + label="Add a header of column names to the output" /> </xml> - <xml name="column_filter"> + <xml name="column_filter" token_help="" token_minimalset="variant_id, gene"> <conditional name="report"> - <param name="report_selector" type="select" label="Columns to include in the report" - help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns."> - <option value="all" selected="True">all</option> - <option value="column_filter">User given columns</option> + <param name="report_selector" type="select" + label="Set of columns to include in the variant report table" + help="@HELP@"> + <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option> + <option value="full">Full (report all columns defined in the GEMINI database variants table)</option> + <option value="custom">Custom (report user-specified columns)</option> </param> - <when value="all"/> - <when value="column_filter"> - <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)"> + <when value="full" /> + <when value="minimal"> + <param name="columns" type="hidden" value="@MINIMALSET@" /> + <param name="extra_cols" type="hidden" value="" /> + </when> + <when value="custom"> + <param name="columns" type="select" display="checkboxes" multiple="true" optional="true" + label="Choose columns to include in the report" help="(--columns)"> <option value="gene">gene</option> <option value="chrom">chrom</option> <option value="start">start</option> @@ -69,27 +79,23 @@ <option value="alt">alt</option> <option value="impact">impact</option> <option value="impact_severity">impact_severity</option> - <option value="max_aaf_all">alternative allele frequency</option> + <option value="max_aaf_all">alternative allele frequency (max_aaf_all)</option> </param> - <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/> + <param name="extra_cols" type="text" + label="Additional columns (comma-separated)" + help="Column must be specified by the exact name they have in the GEMINI database, e.g., is_exonic or num_hom_alt, but, for genotype columns, GEMINI wildcard syntax is supported. The order of columns in the list is maintained in the output."> + <expand macro="sanitize_query" /> + </param> </when> </conditional> </xml> - <xml name="filter"> - <conditional name="filter"> - <param name="filter_selector" type="select" label="Apply additional constraints" - help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter."> - <option value="no">No additional constraints</option> - <option value="yes">Apply additional constraints</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="filter" type="text" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)"> - <expand macro="sanitize_query" /> - </param> - </when> - </conditional> + <xml name="filter" token_argument="--filter"> + <param argument="@ARGUMENT@" name="filter" type="text" + label="Additional constraints expressed in SQL syntax" + help="Constraints defined here will become the WHERE clause of the SQL query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'."> + <expand macro="sanitize_query" /> + </param> </xml> <xml name="sanitize_query"> @@ -103,10 +109,90 @@ </sanitizer> </xml> + <xml name="lenient" token_argument="--lenient" token_truevalue="--lenient" token_help="The exact consequence of this setting depends on the type of inheritance pattern you are looking for (see the tool help below)."> + <param argument="@ARGUMENT@" name="lenient" type="boolean" truevalue="@TRUEVALUE@" falsevalue="" checked="False" + label="Include hits with less convincing inheritance patterns" + help= "@HELP@" /> + </xml> + + <xml name="unaffected"> + <param argument="--allow-unaffected" name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" + label="Report candidates shared by unaffected samples" + help="Activating this option will enable the reporting of variants as candidate causative even if they are shared by unaffected samples in the family tree. The default will only report variants that are unique to affected samples."/> + </xml> + + <xml name="min_kindreds" token_label="Minimum number of families with a candidate variant for a gene to be reported" token_help="This is the number of families required to have a variant fitting the inheritance model in the same gene in order for the gene and its variants to be reported. For example, we may only be interested in candidates where at least 4 families have a variant (with a fitting inheritance pattern) in that gene."> + <param argument="--min-kindreds" name="min_kindreds" type="integer" value="1" min="1" + label="@LABEL@" + help="@HELP@" /> + </xml> + + <xml name="insert_constraint" token_max_repeat="1"> + <repeat name="constraint" title="Additional constraints on variants" default="0" max="@MAX_REPEAT@"> + <expand macro="filter" /> + <yield /> + </repeat> + </xml> + + <xml name="overwritable_where_default" token_default_where=""> + <param name="overwrite_default_filter" type="boolean" checked="false" + label="Overwrite the default constraint of this tool" + help="By default, this tool restricts its analysis to @DEFAULT_WHERE@ and this constraint is applied on top of any constraint expressed above. With this option here selected, your custom constraint, if given, will overwrite the default instead." /> + </xml> + + <xml name="gt_filter" token_default_repeat="0" token_min_repeat="0" token_max_repeat="1"> + <repeat name="filter_by_genotype" title="Genotype filter expression" default="@DEFAULT_REPEAT@" min="@MIN_REPEAT@" max="@MAX_REPEAT@"> + <param argument="--gt-filter" name="gt_filter" type="text" value="" area="True" size="5x50" + label="Restrictions to apply to genotype values" help=""> + <expand macro="sanitize_query" /> + <validator type="expression" message="Genotype filter expression cannot be empty">value.strip()</validator> + </param> + <yield /> + </repeat> + </xml> + + <xml name="sample_filter"> + <repeat name="filter_by_sample" title="Sample filter expression" default="0" max="1"> + <param argument="--sample-filter" name="sample_filter" type="text" area="True" size="5x50" + label="SQL filter to use to filter the sample table" help=""> + <expand macro="sanitize_query" /> + <validator type="expression" message="Sample filter expression cannot be empty">value.strip()</validator> + </param> + <param argument="--in" name="in" type="select" + label="A variant must be in either all, none or any samples passing the sample-query filter" + help=""> + <option value="">Return a variant if it is found in any sample passing the sample filter. (default) </option> + <option value="--in all">Return a variant if it is found in ALL samples passing the sample filter. (all)</option> + <option value="--in none">Return a variant if it is found in NO sample passing the sample filter. (none)</option> + <option value="--in only">Return a variant if it is found in any sample passing the sample filter, and in NO sample NOT passing it. (only)</option> + <option value="--in only all">Return a variant if is found in ALL samples passing the sample filter, and in NO sample NOT passing it. (only all)</option> + </param> + <expand macro="min_kindreds" + label="Minimum number of families in which a variant must pass the sample filter" help=""/> + <param argument="--family-wise" name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False" + label="Apply the sample-filter on a family-wise basis" help="If a variant passes the sample filter in at least the minimum number of families specified above it is retained." /> + </repeat> + </xml> + + <xml name="region_filter"> + <repeat name="regions" title="Region Filter" default="0" min="0" + help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported."> + <param name="chrom" type="text" label="Chromosome"> + <validator type="expression" message="A chromosome identifier is required when specifying a region filter">value.strip()</validator> + </param> + <param name="start" type="text" label="Region Start"> + <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> + </param> + <param name="stop" type="text" label="Region End"> + <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> + </param> + </repeat> + </xml> + <token name="@PROVIDE_ANNO_DATA@"><![CDATA[ mkdir gemini && - ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data && - export GEMINI_CONFIG="${annotation_databases.fields.path}" && + ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data && + export GEMINI_CONFIG='${annotation_databases.fields.path}' && ]]></token> <token name="@MULTILN_SQL_EXPR_TO_CMDLN@"> @@ -119,67 +205,50 @@ #end if </token> - <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> - #if str($filter.filter_selector) == 'yes' and $filter.filter: - --filter '${ str( $filter.filter ) }' + <token name="@SET_COLS@"> + #if str($report.report_selector) == 'full': + #set cols = "*" + #else: + #if $report.columns and str($report.columns) != '': + #set $cols = str($report.columns) + #else + #set $cols = '' + #end if + #if str($report.extra_cols).strip(): + #if $cols: + #set $cols = $cols + ', ' + str($report.extra_cols) + #else: + #set $cols = str($report.extra_cols) + #end if + #end if + #if not $cols: + #set $cols = "variant_id, gene" + #end if #end if </token> <token name="@COLUMN_SELECT@"> - #if $report.report_selector != 'all': - --columns "${report.columns} - #if str($report.extra_cols).strip() - #echo ','+','.join(str($report.extra_cols).split()) - #end if - " + @SET_COLS@ + #if $cols != "*" + --columns '$cols' #end if </token> - <xml name="family"> - <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/> - </xml> - - <xml name="lenient"> - <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/> - </xml> - - <xml name="unaffected"> - <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)"/> - </xml> - - <xml name="min_kindreds"> - <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)" /> - </xml> - - <xml name="min_sequence_depth"> - <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample" - help="default: 0 (-d)" /> - </xml> - - <xml name="min_gq"> - <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)"> - <validator type="in_range" min="0"/> - </param> - </xml> - - <xml name="gt_pl_max"> - <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)" /> - </xml> - - <xml name="citations"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1003153</citation> - <yield /> - </citations> - </xml> - - <xml name="infile"> - <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." > - <options options_filter_attribute="metadata.gemini_version" > - <filter type="add_value" value="@VERSION@" /> - </options> - <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> - </param> - </xml> - + <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[ + #set $region_elements = [] + #for $r in $regions: + ## The actual chromosome name needs to be single-quoted + ## in SQL, so we need to quote the single quotes like the + ## sanitize_query macro would if the whole was a parameter. + #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()] + #if str($r.start).strip(): + #silent $r_elements.append("start >= %d" % int($r.start)) + #end if + #if str($r.stop).strip(): + #silent $r_elements.append("end <= %d" % int($r.stop)) + #end if + #silent $region_elements.append("(%s)" % " AND ".join($r_elements)) + #end for + ]]> + </token> </macros>
--- a/repository_dependencies.xml Fri Dec 14 12:41:01 2018 -0500 +++ b/repository_dependencies.xml Fri Jan 11 17:37:04 2019 -0500 @@ -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
--- a/test-data/gemini_versioned_databases.loc Fri Dec 14 12:41:01 2018 -0500 +++ b/test-data/gemini_versioned_databases.loc Fri Jan 11 17:37:04 2019 -0500 @@ -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
--- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 12:41:01 2018 -0500 +++ b/test-data/test-cache/gemini-config.yaml Fri Jan 11 17:37:04 2019 -0500 @@ -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