Mercurial > repos > iuc > gemini

comparison gemini_comp_hets.xml @ 17:65f742e605ec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:46:38 -0400
parents 53a5647e5271
children
comparison
equal deleted inserted replaced
16:ae03de7a9fee 17:65f742e605ec
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identifying potential compound heterozygotes</description> 2 <description>Identifying potential compound heterozygotes</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">comp_hets</token> 5 <token name="@BINARY@">comp_hets</token>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 gemini @BINARY@ 12 gemini @BINARY@
12 13
13 #if $report.report_selector != 'all': 14 #if $report.report_selector != 'all':
21 22
22 "${ infile }" 23 "${ infile }"
23 > "${ outfile }" 24 > "${ outfile }"
24 ]]> 25 ]]>
25 </command> 26 </command>
26 <expand macro="stdio" />
27 <inputs> 27 <inputs>
28 <expand macro="infile" /> 28 <expand macro="infile" />
29 <expand macro="add_header_column" /> 29 <expand macro="add_header_column" />
30 <expand macro="column_filter" /> 30 <expand macro="column_filter" />
31 <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" 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)"/> 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" 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)"/> 34 label="Ignore phasing when screening for compound hets" help="Candidates are inherently putative. (--ignore-phasing)"/>
35 <expand macro="filter" /> 35 <expand macro="filter" />
36 </inputs> 36 </inputs>
37 <outputs> 37 <outputs>
38 <data name="outfile" format="tabular" /> 38 <data name="outfile" format="tabular" />
42 </test> 42 </test>
43 </tests> 43 </tests>
44 <help> 44 <help>
45 **What it does** 45 **What it does**
46 46
47 Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is 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 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. 49 by two heterozygous recessive alleles at _different_ sites in a particular gene.
50 50
51 So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci. 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 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. 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. 54 Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene.
55 55
56 56
57 @CITATION@ 57 @CITATION@
58 </help> 58 </help>