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comparison gemini_comp_hets.xml @ 20:b5207530f991 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:19:47 -0500
parents 27ce3de83007
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19:27ce3de83007 20:b5207530f991
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 $only_affected
21 $ignore_phasing
22
23 "${ infile }"
24 > "${ outfile }"
25 ]]>
26 </command>
27 <inputs>
28 <expand macro="infile" />
29 <expand macro="add_header_column" />
30 <expand macro="column_filter" />
31 <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False"
32 label="Report solely those compund heterozygotes impacted a sample labeled as affected" help="(--only-affected)"/>
33 <param name="ignore_phasing" type="boolean" truevalue="--ignore-phasing" falsevalue="" checked="False"
34 label="Ignore phasing when screening for compound hets" help="Candidates are inherently putative. (--ignore-phasing)"/>
35 <expand macro="filter" />
36 </inputs>
37 <outputs>
38 <data name="outfile" format="tabular" />
39 </outputs>
40 <tests>
41 <test>
42 </test>
43 </tests>
44 <help>
45 **What it does**
46
47 Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is
48 inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused
49 by two heterozygous recessive alleles at _different_ sites in a particular gene.
50
51 So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci.
52 The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous
53 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.
54 Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene.
55
56
57 @CITATION@
58 </help>
59 <expand macro="citations"/>
60 </tool>