Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_gene_wise/gemini_gene_wise/0.20.1+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_gene_wise/gemini_gene_wise/0.20.1 |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_gene_wise/gemini_gene_wise/0.18.1.1 |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_gene_wise/gemini_gene_wise/0.18.1.0 |
gemini_gene_wise |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
gemini | 0.20.1 | package |
Additional information about this tool |
gemini gene_wise #if int($min_filters) > 0: --min-filters $min_filters #end if #for $filter in $filter_by_genotype: #set $multiline_sql_expr = str($filter.gt_filter) #if $filter.is_required: #set $cmdln_param = "--gt-filter-required" #else: #set $cmdln_param = "--gt-filter" #end if #set $sql_expr = str($multiline_sql_expr).strip() #if str($sql_expr): #set $sql_expr = $sql_expr.replace('\r\n', '\n') #set $sql_expr = $sql_expr.replace('\r', '\n') #set $sql_expr = $sql_expr.replace('\\\n', ' ') $cmdln_param '$sql_expr' #end if #end for #set $report = $oformat.report #if str($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 $cols != "*" --columns '$cols' #end if #set $where_clause_elements = [] #set $filter_cmdln_param = '--filter' #for $cond in $constraint: #if str($cond.filter).strip(): #silent $where_clause_elements.append(str($cond.filter).strip()) #if $cond.overwrite_default_filter: #set $filter_cmdln_param = '--where' #end if #end if #end for #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 #if $region_elements: #silent $where_clause_elements.append(" OR ".join($region_elements)) #end if #set $filter = " AND ".join($where_clause_elements) #if str($filter): $filter_cmdln_param '$filter' #end if '$infile' > '$outfile'
Functional tests |
name | inputs | outputs | required files |
Test-1 |
infile: gemini_amend_input.db filter_by_genotype_0|gt_filter: ((gt_depths).(*).(>=1).(all)) |
name: value |
gemini_amend_input.db value |