| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 (this tool) |
| gemini_inheritance |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| gemini | 0.20.1 | package |
| Additional information about this tool |
gemini ${inheritance.pattern_type}
#for $cond in $inheritance.constraint:
#set $filter = str($cond.filter).strip()
#if str($filter):
#if str($inheritance.pattern_type) == "comp_hets" and $cond.overwrite_default_filter:
--gene-where '$filter'
#else:
--filter '$filter'
#end if
#end if
#end for
#if str($inheritance.pattern_type) in ("comp_hets", "mendel_errors"):
${inheritance.by_pattern_only}
#end if
${inheritance.lenient}
${inheritance.allow_unaffected}
#if str($inheritance.pattern_type).startswith('x_linked_') and str($inheritance.X).strip():
-X "${inheritance.X}"
#end if
#if int($family_wise.min_kindreds) > 0:
--min-kindreds ${family_wise.min_kindreds}
#end if
#if str($family_wise.families).strip():
#set $families = ','.join([f.strip() for f in $family_wise.families.split(',')])
--families "$families"
#end if
#if int($family_wise.per_variant_selection.min_dp) > 0:
-d ${family_wise.per_variant_selection.min_dp}
#end if
#if int($family_wise.per_variant_selection.min_gq) > 0:
--min-gq ${family_wise.per_variant_selection.min_gq}
#end if
#if int($family_wise.per_variant_selection.max_pl) > -1:
--gt-pl-max ${family_wise.per_variant_selection.max_pl}
#end if
#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
"${ infile }"
> "${ outfile }"
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
infile: gemini_auto_dom_input.db inheritance|lenient: True inheritance|pattern_type: autosomal_dominant oformat|report|report_selector: minimal |
name: value |
gemini_auto_dom_input.db value |
| Test-2 |
infile: gemini_auto_dom_input.db inheritance|lenient: True inheritance|pattern_type: autosomal_dominant oformat|report|columns: ['gene', 'chrom', 'impact'] oformat|report|report_selector: custom |
name: value |
gemini_auto_dom_input.db value |
| Test-3 |
infile: gemini_auto_dom_input.db inheritance|lenient: True inheritance|pattern_type: autosomal_dominant oformat|report|extra_cols: gene,chrom,impact oformat|report|report_selector: custom |
name: value |
gemini_auto_dom_input.db value |
| Test-4 |
infile: gemini_auto_rec_input.db inheritance|lenient: True inheritance|pattern_type: autosomal_recessive oformat|report|columns: ['gene', 'chrom', 'impact'] oformat|report|report_selector: custom |
name: value |
gemini_auto_rec_input.db value |
| Test-5 |
infile: gemini_de_novo_input.db inheritance|pattern_type: de_novo oformat|report|columns: ['gene', 'ref', 'alt', 'impact'] oformat|report|report_selector: custom |
name: value |
gemini_de_novo_input.db value |
| Test-6 |
infile: gemini_comphets_input.db inheritance|lenient: True inheritance|allow_unaffected: True inheritance|pattern_type: comp_hets oformat|report|columns: ['chrom', 'start', 'end', 'ref', 'alt', 'gene', 'impact'] oformat|report|report_selector: custom |
name: value |
gemini_comphets_input.db value |
| Test-7 |
infile: gemini_de_novo_input.db inheritance|pattern_type: mendel_errors oformat|report|columns: ['gene', 'ref', 'alt', 'impact'] oformat|report|report_selector: custom |
name: value |
gemini_de_novo_input.db value |