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comparison gemini_comp_hets.xml @ 0:a511fb5bd380 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:20:59 -0500
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-1:000000000000 0:a511fb5bd380
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identifying potential compound heterozygotes</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">comp_hets</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13
14 #if $report.report_selector != 'all':
15 --columns "${report.columns}"
16 #end if
17
18 @CMDLN_SQL_FILTER_FILTER_OPTION@
19
20 #if int($min_kindreds) > 0:
21 --min-kindreds $min_kindreds
22 #end if
23
24 #if str($families).strip():
25 --families $families
26 #end if
27
28 -d $d
29 $allow_unaffected
30
31 #if int($min_genotypequality) > 0:
32 --min-gq $min_genotypequality
33 #end if
34
35 #if int($gt_pl_max) != -1:
36 --gt_pl_max $gt_pl_max
37 #end if
38
39 $pattern_only
40 --max-priority $max_priority
41
42
43 "${ infile }"
44 > "${ outfile }"
45 ]]>
46 </command>
47 <inputs>
48 <expand macro="infile" />
49 <expand macro="column_filter" />
50 <expand macro="filter" />
51 <expand macro="min_kindreds" />
52 <expand macro="family" />
53 <expand macro="unaffected" />
54 <expand macro="min_sequence_depth" />
55 <param name="min_genotypequality" type="integer" value="0" label="The minimum genotype quality required for each sample in a family." help="default: 0 (--min-gq)">
56 <validator type="in_range" min="0"/>
57 </param>
58 <param name="gt_pl_max" type="integer" value="-1" label="The maximum phred-scaled genotype (PL) allowed for each sample in a family." help="default: -1 not set (--gt-pl-max)">
59 <validator type="in_range" min="-1"/>
60 </param>
61 <param name="pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="False"
62 label="Find compound hets by inheritance pattern, without regard to affection" help="(--pattern-only)"/>
63 <param name="max_priority" type="integer" value="1" label="Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets." help="default: 1 (--max-priority)">
64 <validator type="in_range" min="1"/>
65 </param>
66
67 </inputs>
68 <outputs>
69 <data name="outfile" format="tabular" />
70 </outputs>
71 <tests>
72 <test>
73 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
74 <param name="report_selector" value="column_filter" />
75 <param name="columns" value="chrom,start,end,ref,alt,gene,impact" />
76 <param name="allow_unaffected" value="True" />
77 <param name="max_priority" value="3" />
78 <output name="outfile" file="gemini_comphets_result.tabular" />
79 </test>
80 </tests>
81 <help>
82 **What it does**
83
84 Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is
85 inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused
86 by two heterozygous recessive alleles at _different_ sites in a particular gene.
87
88 So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci.
89 The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous
90 site were inherited on different chromosomes (one from each parent). As such, in order to use this tool, we require that all variants are phased.
91 Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene.
92
93
94 </help>
95 <expand macro="citations"/>
96 </tool>