annotate gemini_inheritance.xml @ 0:3123ce7acd0e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:50:55 -0500
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1 <tool id="gemini_inheritance" name="GEMINI inheritance pattern" version="@VERSION@">
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2 <description>based identification of candidate genes</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <xml name="name_X">
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6 <param name="X" type="text" value=""
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7 label="Alias to use for X chromosome"
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8 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." />
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9 </xml>
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10 </macros>
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11 <expand macro="requirements" />
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12 <expand macro="stdio" />
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13 <expand macro="version_command" />
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14 <command>
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15 <![CDATA[
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16 gemini ${inheritance.pattern_type}
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17
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18 #for $cond in $inheritance.constraint:
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19 #set $filter = str($cond.filter).strip()
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20 #if str($filter):
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21 #if str($inheritance.pattern_type) == "comp_hets" and $cond.overwrite_default_filter:
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22 --gene-where '$filter'
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23 #else:
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24 --filter '$filter'
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25 #end if
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26 #end if
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27 #end for
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28
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29 #if str($inheritance.pattern_type) in ("comp_hets", "mendel_errors"):
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30 ${inheritance.by_pattern_only}
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31 #end if
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32
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33 ${inheritance.lenient}
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34 ${inheritance.allow_unaffected}
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35
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36 #if str($inheritance.pattern_type).startswith('x_linked_') and str($inheritance.X).strip():
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37 -X "${inheritance.X}"
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38 #end if
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39
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40 #if int($family_wise.min_kindreds) > 0:
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41 --min-kindreds ${family_wise.min_kindreds}
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42 #end if
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43
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44 #if str($family_wise.families).strip():
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45 #set $families = ','.join([f.strip() for f in $family_wise.families.split(',')])
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46 --families "$families"
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47 #end if
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48
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49 #if int($family_wise.per_variant_selection.min_dp) > 0:
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50 -d ${family_wise.per_variant_selection.min_dp}
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51 #end if
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52
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53 #if int($family_wise.per_variant_selection.min_gq) > 0:
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54 --min-gq ${family_wise.per_variant_selection.min_gq}
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55 #end if
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56
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57 #if int($family_wise.per_variant_selection.max_pl) > -1:
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58 --gt-pl-max ${family_wise.per_variant_selection.max_pl}
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59 #end if
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60
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61 #set $report = $oformat.report
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62 @COLUMN_SELECT@
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63
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64 "${ infile }"
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65 > "${ outfile }"
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66 ]]>
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67 </command>
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68 <inputs>
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69 <expand macro="infile" />
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70 <conditional name="inheritance">
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71 <param name="pattern_type" type="select"
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72 label="Your assumption about the inheritance pattern of the phenotype of interest">
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73 <option value="autosomal_recessive">Autosomal recessive</option>
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74 <option value="autosomal_dominant">Autosomal dominant</option>
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75 <option value="x_linked_recessive">X-linked recessive</option>
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76 <option value="x_linked_dominant">X-linked dominant</option>
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77 <option value="de_novo">Autosomal de-novo</option>
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78 <option value="x_linked_de_novo">X-linked de-novo</option>
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79 <option value="comp_hets">Compound heterozygous</option>
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80 <option value="mendel_errors">Violation of mendelian laws (LOH, plausible and implausible de-novo, uniparental disomy)</option>
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81 </param>
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82 <when value="comp_hets">
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83 <expand macro="insert_constraint">
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84 <expand macro="overwritable_where_default" default_where="exonic and high-impact variants (SQL clause: is_exonic = 1 or impact_severity != 'LOW')" />
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85 </expand>
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86 <param argument="--pattern-only" name="by_pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="false"
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87 label="Ignore sample phenotypes during variant identification"
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88 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)." />
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89 <expand macro="lenient" argument="--max-priority" truevalue="--max-priority 3"
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90 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." />
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91 <expand macro="unaffected" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
92 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
93 <when value="mendel_errors">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
94 <expand macro="insert_constraint" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
95 <param argument="--only-affected" name="by_pattern_only" type="boolean" truevalue="" falsevalue="--only-affected" checked="false"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
96 label="Ignore sample phenotypes during variant identification"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
97 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." />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
98 <expand macro="lenient" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
99 <param name="allow_unaffected" type="hidden" value="" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
100 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
101 <when value="autosomal_recessive">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
102 <expand macro="insert_constraint" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
103 <expand macro="lenient" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
104 <expand macro="unaffected" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
105 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
106 <when value="autosomal_dominant">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
107 <expand macro="insert_constraint" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
108 <expand macro="lenient" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
109 <expand macro="unaffected" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
110 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
111 <when value="x_linked_recessive">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
112 <expand macro="insert_constraint" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
113 <param name="lenient" type="hidden" value="" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
114 <expand macro="unaffected" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
115 <expand macro="name_X" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
116 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
117 <when value="x_linked_dominant">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
118 <expand macro="insert_constraint" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
119 <param name="lenient" type="hidden" value="" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
120 <expand macro="unaffected" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
121 <expand macro="name_X" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
122 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
123 <when value="de_novo">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
124 <expand macro="insert_constraint" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
125 <expand macro="lenient" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
126 <expand macro="unaffected" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
127 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
128 <when value="x_linked_de_novo">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
129 <expand macro="insert_constraint" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
130 <param name="lenient" type="hidden" value="" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
131 <expand macro="unaffected" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
132 <expand macro="name_X" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
133 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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134 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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135 <section name="family_wise" title="Family-wise criteria for variant selection" expanded="true">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
136 <expand macro="min_kindreds" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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137 <param argument="--families" name="families" type="text" value=""
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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138 label="List of families to restrict the analysis to (comma-separated)"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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139 help="Leave empty for an analysis including all families"/>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
140 <conditional name="per_variant_selection">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
141 <param name="enabled" type="select"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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142 label="Specify additional criteria to exclude families on a per-variant basis">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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143 <option value="no">No, analyze all variants from all included families</option>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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144 <option value="yes">Yes, filter variants within families</option>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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145 </param>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
146 <when value="no">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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147 <param name="min_dp" type="hidden" value="0" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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148 <param name="min_gq" type="hidden" value="0" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
149 <param name="max_pl" type="hidden" value="-1" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
150 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
151 <when value="yes">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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152 <param argument="-d" name="min_dp" type="integer" value="0" min="0"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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153 label="Per-variant DP threshold for including a family"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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154 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)" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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155 <param argument="--min-gq" name="min_gq" type="integer" value="0" min="0"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
156 label="per-variant GQ threshold for including a family"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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157 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)">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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158 </param>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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159 <param argument="--gt-pl-max" name="max_pl" type="integer" value="-1" min="-1"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
160 label="per-variant PL threshold for including a family"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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161 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" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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162 </when>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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163 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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164 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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165 <section name="oformat" title="Output - included information" expanded="true">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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166 <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."/>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
167 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
168 </inputs>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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169 <outputs>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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170 <data name="outfile" format="tabular"
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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171 label="GEMINI ${inheritance.pattern_type} pattern on ${on_string}" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
172 </outputs>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
173 <tests>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
174 <test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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175 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
176 <conditional name="inheritance">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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177 <param name="pattern_type" value="autosomal_dominant" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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178 <param name="lenient" value="true" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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179 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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180 <conditional name="report">
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diff changeset
181 <param name="report_selector" value="minimal" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
182 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
183 <output name="outfile">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
184 <assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
185 <has_line_matching expression="variant_id&#009;gene&#009;.*" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
186 </assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
187 </output>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
188 </test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
189 <test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
190 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
191 <conditional name="inheritance">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
192 <param name="pattern_type" value="autosomal_dominant" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
193 <param name="lenient" value="true" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
194 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
195 <section name="oformat">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
196 <conditional name="report">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
197 <param name="report_selector" value="custom" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
198 <param name="columns" value="gene,chrom,impact" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
199 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
200 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
201 <output name="outfile">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
202 <assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
203 <has_line_matching expression="gene&#009;chrom&#009;impact.*" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
204 </assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
205 </output>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
206 </test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
207 <test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
208 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
209 <conditional name="inheritance">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
210 <param name="pattern_type" value="autosomal_dominant" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
211 <param name="lenient" value="true" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
212 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
213 <section name="oformat">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
214 <conditional name="report">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
215 <param name="report_selector" value="custom" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
216 <!-- test with empty multiselect list and columns specified
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
217 via text field instead -->
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
218 <param name="extra_cols" value="gene,chrom,impact" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
219 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
220 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
221 <output name="outfile">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
222 <assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
223 <has_line_matching expression="gene&#009;chrom&#009;impact.*" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
224 </assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
225 </output>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
226 </test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
227 <test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
228 <param name="infile" value="gemini_auto_rec_input.db" ftype="gemini.sqlite" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
229 <conditional name="inheritance">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
230 <param name="pattern_type" value="autosomal_recessive" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
231 <param name="lenient" value="true" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
232 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
233 <section name="oformat">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
234 <conditional name="report">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
235 <param name="report_selector" value="custom" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
236 <param name="columns" value="gene,chrom,impact" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
237 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
238 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
239 <output name="outfile">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
240 <assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
241 <has_line_matching expression="gene&#009;chrom&#009;impact.*" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
242 </assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
243 </output>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
244 </test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
245 <test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
246 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
247 <conditional name="inheritance">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
248 <param name="pattern_type" value="de_novo" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
249 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
250 <section name="oformat">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
251 <conditional name="report">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
252 <param name="report_selector" value="custom" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
253 <param name="columns" value="gene,ref,alt,impact" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
254 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
255 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
256 <output name="outfile">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
257 <assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
258 <has_line_matching expression="gene&#009;ref&#009;alt&#009;impact.*" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
259 </assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
260 </output>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
261 </test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
262 <test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
263 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
264 <conditional name="inheritance">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
265 <param name="pattern_type" value="comp_hets" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
266 <param name="lenient" value="true" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
267 <param name="allow_unaffected" value="true" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
268 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
269 <section name="oformat">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
270 <conditional name="report">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
271 <param name="report_selector" value="custom" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
272 <param name="columns" value="chrom,start,end,ref,alt,gene,impact" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
273 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
274 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
275 <output name="outfile">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
276 <assert_contents>
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277 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*gene.*" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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278 </assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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279 </output>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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280 </test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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281 <test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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282 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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283 <conditional name="inheritance">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
284 <param name="pattern_type" value="mendel_errors" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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285 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
286 <section name="oformat">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
287 <conditional name="report">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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288 <param name="report_selector" value="custom" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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289 <param name="columns" value="gene,ref,alt,impact" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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290 </conditional>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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291 </section>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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292 <output name="outfile">
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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293 <assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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294 <has_line_matching expression="gene&#009;ref&#009;alt&#009;impact&#009;.*violation.*" />
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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295 </assert_contents>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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296 </output>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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297 </test>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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298 </tests>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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299 <help>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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300 <![CDATA[
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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301
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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302 **What it does**
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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303
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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304 Assuming you have defined the familial relationships between samples when
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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305 loading your VCF into GEMINI, you can use this tool to identify candidate genes
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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306 and variants that explain the inheritance pattern of a phenotype of interest.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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307
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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308 **Inheritance pattern detection rules**
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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309
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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310 *Autosomal recessive*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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311
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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312 Criteria:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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313
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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314 - all affected must be hom_alt
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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315 - [affected] no unaffected can be hom_alt (can be unknown)
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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316 - [default] if parents exist they must be unaffected and het for all affected kids
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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317 - [default] if there are no affecteds that have a parent, a warning is issued.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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318
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
319 If ``--lenient`` is specified, the 2 criteria prefixed with “[default]” are not
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
320 applied.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
321
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
322 If ``--allow-unaffected`` is specified, the criterion prefixed with
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
323 “[affected]” is not enforced.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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324
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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325 ----
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
326
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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327 *Autosomal dominant*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
328
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
329 Criteria:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
330
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
331 - All affecteds must be het
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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332 - [affected] No unaffected can be het or homalt (can be unknown)
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
333 - de_novo mutations are not auto_dom (at least not in the first generation)
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
334 - At least 1 affected must have 1 affected parent (or have no parents).
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
335 - If no affected has a parent, a warning is issued.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
336 - [default] All affecteds must have parents with known phenotype.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
337 - [default] All affected kids must have at least 1 affected parent
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
338
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
339 If ``--lenient`` is specified, the criteria prefixed with “[default]” are not
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
340 enforced.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
341
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
342 If ``--allow-unaffected`` is specified, the criterion prefixed with
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
343 “[affected]” is not enforced.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
344
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
345 Note that, for autosomal dominant, ``--lenient`` allows singleton affecteds to
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
346 be used to meet the ``--min-kindreds`` requirement if they are HET.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
347
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
348 If there is incomplete penetrance in the kindred (unaffected obligate carriers),
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
349 these individuals currently must be coded as having unknown phenotype or as
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
350 being affected.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
351
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
352 ----
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
353
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
354 *X-linked recessive*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
355
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
356 Criteria:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
357
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
358 - Affected females must be HOM_ALT
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
359 - Unaffected females are HET or HOM_REF
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
360 - Affected males are not HOM_REF
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
361 - Unaffected males are HOM_REF
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
362
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
363 Note: Pseudo-autosomal regions are not accounted for by the tool.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
364
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
365 ----
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
366
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
367 *X-linked dominant*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
368
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
369 Criteria:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
370
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
371 - Affected males are HET or HOM_ALT
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
372 - Affected females must be HET
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
373 - Unaffecteds must be HOM_REF
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
374 - girls of affected dad must be affected
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
375 - boys of affected dad must be unaffected
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
376 - mothers of affected males must be het (and affected)
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
377 - at least 1 parent of affected females must be het (and affected).
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
378
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
379 Note: Pseudo-autosomal regions are not accounted for by the tool.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
380
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
381 ----
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
382
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
383 *De-novo mutations*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
384
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
385 Criteria:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
386
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
387 - all affected must be het
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
388 - [affected] all unaffected must be homref or homalt
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
389 - at least 1 affected kid must have unaffected parents
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
390 - [default] if an affected has affected parents, it’s not de_novo
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
391 - [default] all affected kids must have unaffected (or no) parents
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
392 - [default] warning if none of the affected samples have parents.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
393
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
394 The last 3 items, prefixed with [default] can be turned off with ``--lenient``.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
395
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
396 If ``--allow-unaffected`` is specified, then the criterion prefixed [affected]
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
397 is not enforced.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
398
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
399 ----
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
400
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
401 *X-linked de-novo mutations*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
402
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
403 Criteria:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
404
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
405 - affected female child must be het
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
406 - affected male child must be hom_alt (or het)
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
407 - parents should be unaffected and hom_ref
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
408
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
409 Note: Pseudo-autosomal regions are not accounted for by the tool.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
410
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
411 ----
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
412
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
413 *Compound heterozygosity*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
414
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
415 Unlike canonical recessive sites where the same recessive allele is inherited
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
416 from both parents at the *same* site in the gene, compound heterozygosity
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
417 occurs when the individual’s phenotype is caused by two heterozygous recessive
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
418 alleles at *different* sites in a particular gene.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
419
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
420 To detect compound heterozygosity, the tool looks for two heterozygous variants
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
421 impacting the same gene at different loci. The complicating factor is that this
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
422 is a case of *recessive* inheritance and as such, we must also require that the
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
423 consequential alleles at each heterozygous site were inherited on different
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
424 chromosomes (one from each parent). Hence, where possible, the tool will phase
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
425 by transmission.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
426
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
427 Criteria (default):
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
428
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
429 - All affected individuals must be heterozygous at both sites.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
430 - No unaffected can be homozygous alterate at either site.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
431 - Neither parent of an affected sample can be homozygous reference at both
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
432 sites.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
433 - If any unphased-unaffected is het at both sites, the site will be given lower
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
434 priority.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
435 - No phased-unaffected can be heterozygous at both sites.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
436
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
437 a. ``--allow-unaffected`` keeps sites where a phased unaffected shares the
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
438 het-pair
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
439 b. unphased, unaffected that share the het pair are counted and reported for
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
440 each candidate pair.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
441 - Candidates where an affected from the same family does NOT share the same het
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
442 pair are removed.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
443 - Sites are automatically phased by transmission when parents are present in
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
444 order to remove false positive candidates.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
445
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
446 If data from one or both parents are unavailable and the child’s data was not
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
447 phased prior to loading into GEMINI, all comp_het variant pairs will
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
448 automatically be given at most priority == 2. If there’s only a single parent
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
449 and both the parent and the affected are HET at both sites, the candidate
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
450 will have priority 3.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
451
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
452 Criteria (``--pattern-only``):
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
453
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
454 - Kid must be HET at both sites.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
455 - Kid must have alts on different chromosomes.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
456 - Neither parent can be HOM_ALT at either site.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
457 - If either parent is phased at both sites and matches the kid, it’s excluded.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
458 - When the above criteria are met, and both parents and kid are phased or
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
459 parents are HET at different sites, the priority is 1.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
460 - If either parent is HET at both sites, priority is reduced.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
461 - If both parents are not phased, the priority is 2.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
462 - For every parent that’s a het at both sites, the priority is incremented by 1.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
463 - The priority in a family is the minimum found among all kids.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
464
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
465 ----
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
466
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
467 *Violation of Mendelian laws*
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff changeset
468
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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469 The tool can be used to detect the following kinds of non-Mendelian patterns:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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470
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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471 - loss of heterozygosity (LOH) events
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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472 - de-novo mutations
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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473 - implausible de-novo mutations
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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474 - potential cases of uniparental disomy
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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475
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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476 Criteria:
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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477
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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478 - LOH: child and one parent are opposite homozygotes; other parent is HET
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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479 - plausible de novo: kid is het. parents are same homozygotes
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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480 - implausible de novo: kid is homozygote. parents are same homozygotes and opposite to kid.
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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481 - uniparental disomy: parents are opposite homozygotes; kid is homozygote
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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482
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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483 ]]>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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484 </help>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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485 <expand macro="citations"/>
3123ce7acd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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486 </tool>