# HG changeset patch
# User iuc
# Date 1547245538 18000
# Node ID 1cdc7f1dd60521dc13d4701f5e113e6184618798
# Parent 3790ec5643b40fa93901718bd001cb2fb0a7afc7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
diff -r 3790ec5643b4 -r 1cdc7f1dd605 gemini_macros.xml
--- a/gemini_macros.xml Mon Dec 17 11:58:07 2018 -0500
+++ b/gemini_macros.xml Fri Jan 11 17:25:38 2019 -0500
@@ -21,9 +21,17 @@
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#end if
-
- #if str($filter.filter_selector) == 'yes' and $filter.filter:
- --filter '${ str( $filter.filter ) }'
+
+ #if str($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
- #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
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- value is not None and value.metadata.gemini_version == "@VERSION@"
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+ = %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
+ ]]>
+
diff -r 3790ec5643b4 -r 1cdc7f1dd605 gemini_query.xml
--- a/gemini_query.xml Mon Dec 17 11:58:07 2018 -0500
+++ b/gemini_query.xml Fri Jan 11 17:25:38 2019 -0500
@@ -3,6 +3,30 @@
gemini_macros.xml
query
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+ --min-kindreds ${i.min_kindreds}
+ #end if
+ ${i.in}
+ #set $multiline_sql_expr = str($i.sample_filter)
+ #set $cmdln_param = "--sample-filter"
+ @MULTILN_SQL_EXPR_TO_CMDLN@
+ #end for
- $show_samples
- $show_families
- $family_wise
- $header
- $dgidb
- #if $region.strip():
- --region "${region}"
+ #if str($query.oformat.report.format) == 'with_samples':
+ #set $sample_delim = str($query.oformat.report.sample_delim) or ','
+ --show-samples --sample-delim '$sample_delim'
+ #elif str($query.oformat.report.format) == 'with_samples_flattened':
+ --show-samples --format sampledetail
+ #elif str($query.oformat.report.format) == 'with_families':
+ #set $sample_delim = str($query.oformat.report.sample_delim) or ','
+ --show-families --sample-delim '$sample_delim'
+ #elif str($query.oformat.report.format) == 'carrier_summary':
+ --carrier-summary-by-phenotype
+ #if str($query.oformat.report.phenotype).strip():
+ '${query.oformat.report.phenotype}'
+ #else:
+ affected
+ #end if
+ #else:
+ --format ${query.oformat.report.format}
#end if
- #if int($min_kindreds) > 0:
- --min-kindreds $min_kindreds
+
+ #if str($query.interface) == 'basic':
+ ## build the SQL query string from its components
+ #if str($query.oformat.report.format) in ('vcf', 'tped'):
+ #set $cols = "*"
+ #else:
+ #set $report = $query.oformat.report.report
+ @SET_COLS@
+ #end if
+ #set $q = "SELECT %s FROM variants" % $cols
+ #set $where_clause_elements = []
+ #if str($query.filter).strip():
+ #silent $where_clause_elements.append(str($query.filter).strip())
+ #end if
+
+ #set $regions = $query.regions
+ @PARSE_REGION_ELEMENTS@
+ #if $region_elements:
+ #silent $where_clause_elements.append(" OR ".join($region_elements))
+ #end if
+ #if $where_clause_elements:
+ #set $q = $q + " WHERE " + " AND ".join($where_clause_elements)
+ #end if
+ #if str($query.oformat.report.order_by).strip():
+ #set $q = $q + " ORDER BY " + str($query.oformat.report.order_by).strip() + str($query.oformat.report.sort_order)
+ #end if
+ #else
+ ## The user entered the SQL query string directly.
+ #set $q = str($query.q)
#end if
- ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being
- ## --sample-delim STRING The delimiter to be used with the --show-samples option.
#set $multiline_sql_expr = $q
#set $cmdln_param = "-q"
@MULTILN_SQL_EXPR_TO_CMDLN@
- "${ infile }"
- > "${ outfile }"
+ '$infile'
+ > '$outfile'
]]>
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