gemini_inheritance: gemini_inheritance.xml annotate

annotate gemini_inheritance.xml @ 4:ee21f3568be3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd

author	iuc
date	Wed, 13 Jul 2022 15:14:18 +0000
parents	7982b8deb171
children

rev	line source
0 541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	1 <tool id="gemini_inheritance" name="GEMINI inheritance pattern" version="@VERSION@">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	2 <description>based identification of candidate genes</description>
3 7982b8deb171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 0 diff changeset	3 <expand macro="bio_tools"/>
0 541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	4 <macros>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	5 <import>gemini_macros.xml</import>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	6 <xml name="name_X">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	7 <param name="X" type="text" value=""
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	8 label="Alias to use for X chromosome"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	9 help="The tool expects the X chromosome to be named 'X' or 'chrX'. If the reference genome used for variant calling had a different name for it, you will have to specify it here." />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	10 </xml>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	11 </macros>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	12 <expand macro="requirements" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	13 <expand macro="stdio" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	14 <expand macro="version_command" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	15 <command>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	16 <![CDATA[
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	17 gemini ${inheritance.pattern_type}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	18
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	19 #for $cond in $inheritance.constraint:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	20 #set $filter = str($cond.filter).strip()
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	21 #if str($filter):
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	22 #if str($inheritance.pattern_type) == "comp_hets" and $cond.overwrite_default_filter:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	23 --gene-where '$filter'
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	24 #else:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	25 --filter '$filter'
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	26 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	27 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	28 #end for
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	29
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	30 #if str($inheritance.pattern_type) in ("comp_hets", "mendel_errors"):
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	31 ${inheritance.by_pattern_only}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	32 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	33
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	34 ${inheritance.lenient}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	35 ${inheritance.allow_unaffected}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	36
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	37 #if str($inheritance.pattern_type).startswith('x_linked_') and str($inheritance.X).strip():
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	38 -X "${inheritance.X}"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	39 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	40
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	41 #if int($family_wise.min_kindreds) > 0:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	42 --min-kindreds ${family_wise.min_kindreds}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	43 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	44
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	45 #if str($family_wise.families).strip():
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	46 #set $families = ','.join([f.strip() for f in $family_wise.families.split(',')])
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	47 --families "$families"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	48 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	49
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	50 #if int($family_wise.per_variant_selection.min_dp) > 0:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	51 -d ${family_wise.per_variant_selection.min_dp}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	52 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	53
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	54 #if int($family_wise.per_variant_selection.min_gq) > 0:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	55 --min-gq ${family_wise.per_variant_selection.min_gq}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	56 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	57
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	58 #if int($family_wise.per_variant_selection.max_pl) > -1:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	59 --gt-pl-max ${family_wise.per_variant_selection.max_pl}
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	60 #end if
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	61
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	62 #set $report = $oformat.report
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	63 @COLUMN_SELECT@
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	64
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	65 "${ infile }"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	66 > "${ outfile }"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	67 ]]>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	68 </command>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	69 <inputs>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	70 <expand macro="infile" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	71 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	72 <param name="pattern_type" type="select"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	73 label="Your assumption about the inheritance pattern of the phenotype of interest">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	74 <option value="autosomal_recessive">Autosomal recessive</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	75 <option value="autosomal_dominant">Autosomal dominant</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	76 <option value="x_linked_recessive">X-linked recessive</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	77 <option value="x_linked_dominant">X-linked dominant</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	78 <option value="de_novo">Autosomal de-novo</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	79 <option value="x_linked_de_novo">X-linked de-novo</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	80 <option value="comp_hets">Compound heterozygous</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	81 <option value="mendel_errors">Violation of mendelian laws (LOH, plausible and implausible de-novo, uniparental disomy)</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	82 </param>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	83 <when value="comp_hets">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	84 <expand macro="insert_constraint">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	85 <expand macro="overwritable_where_default" default_where="exonic and high-impact variants (SQL clause: is_exonic = 1 or impact_severity != 'LOW')" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	86 </expand>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	87 <param argument="--pattern-only" name="by_pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="false"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	88 label="Ignore sample phenotypes during variant identification"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	89 help="When turned on, the identification of compound heterozygous variant pairs gets based on the family tree only, i.e., the tool looks for heterozygous allele pairs in any kid that weren't occuring together in the parents (see the tool help below for the exact criteria used to detect compound heterozygosity)." />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	90 <expand macro="lenient" argument="--max-priority" truevalue="--max-priority 3"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	91 help="When turned on, runs the tool with --max-priority 3 instead of the default value 1. This leads to inclusion of more ambiguous cases of compound heterozygosity." />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	92 <expand macro="unaffected" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	93 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	94 <when value="mendel_errors">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	95 <expand macro="insert_constraint" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	96 <param argument="--only-affected" name="by_pattern_only" type="boolean" truevalue="" falsevalue="--only-affected" checked="false"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	97 label="Ignore sample phenotypes during variant identification"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	98 help="When turned on, the identification of candidate variants gets based on the observed inheritance pattern only. The default is to report candidates only if there is evidence for them being phenotypically relevant, i.e., if they are observed in an affected sample." />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	99 <expand macro="lenient" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	100 <param name="allow_unaffected" type="hidden" value="" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	101 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	102 <when value="autosomal_recessive">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	103 <expand macro="insert_constraint" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	104 <expand macro="lenient" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	105 <expand macro="unaffected" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	106 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	107 <when value="autosomal_dominant">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	108 <expand macro="insert_constraint" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	109 <expand macro="lenient" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	110 <expand macro="unaffected" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	111 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	112 <when value="x_linked_recessive">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	113 <expand macro="insert_constraint" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	114 <param name="lenient" type="hidden" value="" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	115 <expand macro="unaffected" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	116 <expand macro="name_X" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	117 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	118 <when value="x_linked_dominant">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	119 <expand macro="insert_constraint" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	120 <param name="lenient" type="hidden" value="" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	121 <expand macro="unaffected" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	122 <expand macro="name_X" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	123 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	124 <when value="de_novo">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	125 <expand macro="insert_constraint" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	126 <expand macro="lenient" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	127 <expand macro="unaffected" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	128 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	129 <when value="x_linked_de_novo">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	130 <expand macro="insert_constraint" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	131 <param name="lenient" type="hidden" value="" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	132 <expand macro="unaffected" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	133 <expand macro="name_X" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	134 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	135 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	136 <section name="family_wise" title="Family-wise criteria for variant selection" expanded="true">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	137 <expand macro="min_kindreds" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	138 <param argument="--families" name="families" type="text" value=""
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	139 label="List of families to restrict the analysis to (comma-separated)"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	140 help="Leave empty for an analysis including all families"/>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	141 <conditional name="per_variant_selection">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	142 <param name="enabled" type="select"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	143 label="Specify additional criteria to exclude families on a per-variant basis">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	144 <option value="no">No, analyze all variants from all included families</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	145 <option value="yes">Yes, filter variants within families</option>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	146 </param>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	147 <when value="no">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	148 <param name="min_dp" type="hidden" value="0" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	149 <param name="min_gq" type="hidden" value="0" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	150 <param name="max_pl" type="hidden" value="-1" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	151 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	152 <when value="yes">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	153 <param argument="-d" name="min_dp" type="integer" value="0" min="0"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	154 label="Per-variant DP threshold for including a family"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	155 help="All samples from a family must have a sequencing depth of at least this value at a given variant site in order for the family to be included in the analysis of this particular variant. default: 0 (do not apply this filter)" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	156 <param argument="--min-gq" name="min_gq" type="integer" value="0" min="0"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	157 label="per-variant GQ threshold for including a family"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	158 help="The genotypes of all samples from a family must be called with at least this quality at a given variant site in order for the family to be included in the analysis of this particular variant. default: 0 (do not apply this filter)">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	159 </param>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	160 <param argument="--gt-pl-max" name="max_pl" type="integer" value="-1" min="-1"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	161 label="per-variant PL threshold for including a family"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	162 help="The genotypes at a given variant site of all samples from a family must not have a higher (phred-scaled) likelihood to be wrong than this value in order for the family to be included in the analysis of this particular variant. default: -1 (do not apply this filter); if used the GEMINI documentation suggests 10 as a reasonable value" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	163 </when>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	164 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	165 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	166 <section name="oformat" title="Output - included information" expanded="true">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	167 <expand macro="column_filter" help="The tool reports key information about the inheritance pattern detection for each candidate variant found. It can precede each such row with additional columns, listing information about the variant taken from the variants table of the GEMINI database. Here, you can control which subset of the variants table columns should be added to the output."/>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	168 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	169 </inputs>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	170 <outputs>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	171 <data name="outfile" format="tabular"
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	172 label="GEMINI ${inheritance.pattern_type} pattern on ${on_string}" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	173 </outputs>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	174 <tests>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	175 <test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	176 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	177 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	178 <param name="pattern_type" value="autosomal_dominant" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	179 <param name="lenient" value="true" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	180 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	181 <conditional name="report">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	182 <param name="report_selector" value="minimal" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	183 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	184 <output name="outfile">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	185 <assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	186 <has_line_matching expression="variant_id gene .*" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	187 </assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	188 </output>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	189 </test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	190 <test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	191 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	192 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	193 <param name="pattern_type" value="autosomal_dominant" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	194 <param name="lenient" value="true" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	195 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	196 <section name="oformat">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	197 <conditional name="report">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	198 <param name="report_selector" value="custom" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	199 <param name="columns" value="gene,chrom,impact" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	200 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	201 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	202 <output name="outfile">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	203 <assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	204 <has_line_matching expression="gene chrom impact.*" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	205 </assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	206 </output>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	207 </test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	208 <test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	209 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	210 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	211 <param name="pattern_type" value="autosomal_dominant" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	212 <param name="lenient" value="true" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	213 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	214 <section name="oformat">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	215 <conditional name="report">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	216 <param name="report_selector" value="custom" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	217 <!-- test with empty multiselect list and columns specified
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	218 via text field instead -->
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	219 <param name="extra_cols" value="gene,chrom,impact" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	220 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	221 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	222 <output name="outfile">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	223 <assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	224 <has_line_matching expression="gene chrom impact.*" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	225 </assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	226 </output>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	227 </test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	228 <test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	229 <param name="infile" value="gemini_auto_rec_input.db" ftype="gemini.sqlite" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	230 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	231 <param name="pattern_type" value="autosomal_recessive" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	232 <param name="lenient" value="true" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	233 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	234 <section name="oformat">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	235 <conditional name="report">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	236 <param name="report_selector" value="custom" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	237 <param name="columns" value="gene,chrom,impact" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	238 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	239 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	240 <output name="outfile">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	241 <assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	242 <has_line_matching expression="gene chrom impact.*" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	243 </assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	244 </output>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	245 </test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	246 <test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	247 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	248 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	249 <param name="pattern_type" value="de_novo" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	250 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	251 <section name="oformat">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	252 <conditional name="report">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	253 <param name="report_selector" value="custom" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	254 <param name="columns" value="gene,ref,alt,impact" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	255 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	256 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	257 <output name="outfile">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	258 <assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	259 <has_line_matching expression="gene ref alt impact.*" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	260 </assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	261 </output>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	262 </test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	263 <test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	264 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	265 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	266 <param name="pattern_type" value="comp_hets" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	267 <param name="lenient" value="true" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	268 <param name="allow_unaffected" value="true" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	269 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	270 <section name="oformat">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	271 <conditional name="report">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	272 <param name="report_selector" value="custom" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	273 <param name="columns" value="chrom,start,end,ref,alt,gene,impact" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	274 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	275 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	276 <output name="outfile">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	277 <assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	278 <has_line_matching expression="chrom start end .gene." />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	279 </assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	280 </output>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	281 </test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	282 <test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	283 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	284 <conditional name="inheritance">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	285 <param name="pattern_type" value="mendel_errors" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	286 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	287 <section name="oformat">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	288 <conditional name="report">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	289 <param name="report_selector" value="custom" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	290 <param name="columns" value="gene,ref,alt,impact" />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	291 </conditional>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	292 </section>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	293 <output name="outfile">
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	294 <assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	295 <has_line_matching expression="gene ref alt impact .violation." />
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	296 </assert_contents>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	297 </output>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	298 </test>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	299 </tests>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	300 <help>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	301 <![CDATA[
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	302
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	303 What it does
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	304
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	305 Assuming you have defined the familial relationships between samples when
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	306 loading your VCF into GEMINI, you can use this tool to identify candidate genes
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	307 and variants that explain the inheritance pattern of a phenotype of interest.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	308
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	309 Inheritance pattern detection rules
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	310
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	311 Autosomal recessive
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	312
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	313 Criteria:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	314
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	315 - all affected must be hom_alt
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	316 - [affected] no unaffected can be hom_alt (can be unknown)
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	317 - [default] if parents exist they must be unaffected and het for all affected kids
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	318 - [default] if there are no affecteds that have a parent, a warning is issued.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	319
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	320 If ``--lenient`` is specified, the 2 criteria prefixed with “[default]” are not
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	321 applied.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	322
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	323 If ``--allow-unaffected`` is specified, the criterion prefixed with
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	324 “[affected]” is not enforced.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	325
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	326 ----
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	327
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	328 Autosomal dominant
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	329
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	330 Criteria:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	331
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	332 - All affecteds must be het
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	333 - [affected] No unaffected can be het or homalt (can be unknown)
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	334 - de_novo mutations are not auto_dom (at least not in the first generation)
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	335 - At least 1 affected must have 1 affected parent (or have no parents).
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	336 - If no affected has a parent, a warning is issued.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	337 - [default] All affecteds must have parents with known phenotype.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	338 - [default] All affected kids must have at least 1 affected parent
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	339
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	340 If ``--lenient`` is specified, the criteria prefixed with “[default]” are not
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	341 enforced.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	342
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	343 If ``--allow-unaffected`` is specified, the criterion prefixed with
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	344 “[affected]” is not enforced.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	345
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	346 Note that, for autosomal dominant, ``--lenient`` allows singleton affecteds to
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	347 be used to meet the ``--min-kindreds`` requirement if they are HET.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	348
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	349 If there is incomplete penetrance in the kindred (unaffected obligate carriers),
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	350 these individuals currently must be coded as having unknown phenotype or as
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	351 being affected.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	352
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	353 ----
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	354
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	355 X-linked recessive
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	356
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	357 Criteria:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	358
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	359 - Affected females must be HOM_ALT
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	360 - Unaffected females are HET or HOM_REF
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	361 - Affected males are not HOM_REF
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	362 - Unaffected males are HOM_REF
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	363
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	364 Note: Pseudo-autosomal regions are not accounted for by the tool.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	365
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	366 ----
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	367
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	368 X-linked dominant
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	369
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	370 Criteria:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	371
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	372 - Affected males are HET or HOM_ALT
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	373 - Affected females must be HET
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	374 - Unaffecteds must be HOM_REF
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	375 - girls of affected dad must be affected
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	376 - boys of affected dad must be unaffected
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	377 - mothers of affected males must be het (and affected)
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	378 - at least 1 parent of affected females must be het (and affected).
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	379
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	380 Note: Pseudo-autosomal regions are not accounted for by the tool.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	381
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	382 ----
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	383
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	384 De-novo mutations
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	385
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	386 Criteria:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	387
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	388 - all affected must be het
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	389 - [affected] all unaffected must be homref or homalt
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	390 - at least 1 affected kid must have unaffected parents
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	391 - [default] if an affected has affected parents, it’s not de_novo
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	392 - [default] all affected kids must have unaffected (or no) parents
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	393 - [default] warning if none of the affected samples have parents.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	394
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	395 The last 3 items, prefixed with [default] can be turned off with ``--lenient``.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	396
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	397 If ``--allow-unaffected`` is specified, then the criterion prefixed [affected]
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	398 is not enforced.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	399
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	400 ----
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	401
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	402 X-linked de-novo mutations
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	403
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	404 Criteria:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	405
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	406 - affected female child must be het
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	407 - affected male child must be hom_alt (or het)
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	408 - parents should be unaffected and hom_ref
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	409
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	410 Note: Pseudo-autosomal regions are not accounted for by the tool.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	411
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	412 ----
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	413
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	414 Compound heterozygosity
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	415
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	416 Unlike canonical recessive sites where the same recessive allele is inherited
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	417 from both parents at the same site in the gene, compound heterozygosity
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	418 occurs when the individual’s phenotype is caused by two heterozygous recessive
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	419 alleles at different sites in a particular gene.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	420
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	421 To detect compound heterozygosity, the tool looks for two heterozygous variants
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	422 impacting the same gene at different loci. The complicating factor is that this
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	423 is a case of recessive inheritance and as such, we must also require that the
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	424 consequential alleles at each heterozygous site were inherited on different
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	425 chromosomes (one from each parent). Hence, where possible, the tool will phase
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	426 by transmission.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	427
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	428 Criteria (default):
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	429
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	430 - All affected individuals must be heterozygous at both sites.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	431 - No unaffected can be homozygous alterate at either site.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	432 - Neither parent of an affected sample can be homozygous reference at both
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	433 sites.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	434 - If any unphased-unaffected is het at both sites, the site will be given lower
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	435 priority.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	436 - No phased-unaffected can be heterozygous at both sites.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	437
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	438 a. ``--allow-unaffected`` keeps sites where a phased unaffected shares the
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	439 het-pair
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	440 b. unphased, unaffected that share the het pair are counted and reported for
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	441 each candidate pair.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	442 - Candidates where an affected from the same family does NOT share the same het
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	443 pair are removed.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	444 - Sites are automatically phased by transmission when parents are present in
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	445 order to remove false positive candidates.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	446
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	447 If data from one or both parents are unavailable and the child’s data was not
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	448 phased prior to loading into GEMINI, all comp_het variant pairs will
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	449 automatically be given at most priority == 2. If there’s only a single parent
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	450 and both the parent and the affected are HET at both sites, the candidate
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	451 will have priority 3.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	452
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	453 Criteria (``--pattern-only``):
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	454
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	455 - Kid must be HET at both sites.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	456 - Kid must have alts on different chromosomes.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	457 - Neither parent can be HOM_ALT at either site.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	458 - If either parent is phased at both sites and matches the kid, it’s excluded.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	459 - When the above criteria are met, and both parents and kid are phased or
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	460 parents are HET at different sites, the priority is 1.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	461 - If either parent is HET at both sites, priority is reduced.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	462 - If both parents are not phased, the priority is 2.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	463 - For every parent that’s a het at both sites, the priority is incremented by 1.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	464 - The priority in a family is the minimum found among all kids.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	465
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	466 ----
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	467
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	468 Violation of Mendelian laws
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	469
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	470 The tool can be used to detect the following kinds of non-Mendelian patterns:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	471
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	472 - loss of heterozygosity (LOH) events
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	473 - de-novo mutations
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	474 - implausible de-novo mutations
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	475 - potential cases of uniparental disomy
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	476
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	477 Criteria:
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	478
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	479 - LOH: child and one parent are opposite homozygotes; other parent is HET
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	480 - plausible de novo: kid is het. parents are same homozygotes
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	481 - implausible de novo: kid is homozygote. parents are same homozygotes and opposite to kid.
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	482 - uniparental disomy: parents are opposite homozygotes; kid is homozygote
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	483
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	484 ]]>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	485 </help>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	486 <expand macro="citations"/>
541cb8265fe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 iuc parents: diff changeset	487 </tool>

Mercurial > repos > iuc > gemini_inheritance

annotate gemini_inheritance.xml @ 4:ee21f3568be3 draft default tip