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comparison gemini_roh.xml @ 5:d65ca2fa673b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:52:49 -0500
parents ce54eb6fd5f9
children e8349da26ed5
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4:ce54eb6fd5f9 5:d65ca2fa673b
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
2 <description>Identifying runs of homozygosity</description> 2 <description>Identifying runs of homozygosity</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">roh</token> 5 <token name="@BINARY@">roh</token>
6 </macros> 6 </macros>
15 --min-gt-depth $min_gt_depth 15 --min-gt-depth $min_gt_depth
16 --min-size $min_size 16 --min-size $min_size
17 --max-hets $max_hets 17 --max-hets $max_hets
18 --max-unknowns $max_unknowns 18 --max-unknowns $max_unknowns
19 #if $samples.strip(): 19 #if $samples.strip():
20 -s "${samples}" 20 #set $samples = ','.join([f.strip() for f in $samples.split(',')])
21 -s '$samples'
21 #end if 22 #end if
22 "${ infile }" 23 '$infile'
23 > "${ outfile }" 24 > '$outfile'
24 ]]> 25 ]]>
25 </command> 26 </command>
26 <inputs> 27 <inputs>
27 <expand macro="infile" /> 28 <expand macro="infile" />
28 29 <param argument="--min-snps" name="min_snps" type="integer" value="25" min="0"
29 <param name="min_snps" type="integer" value="25" label="Minimum number of expected homozygous SNPs" help="default: 25 (--min-snps)"> 30 label="Minimum number of expected homozygous SNPs"
30 <validator type="in_range" min="0"/> 31 help="default: 25" />
31 </param> 32 <param argument="--min-total-depth" name="min_total_depth" type="integer" value="20" min="0"
32 <param name="min_total_depth" type="integer" value="20" label="The minimum overall sequencing depth requiredfor a SNP to be considered" help="default: 20 (--min-total-depth)"> 33 label="The minimum overall sequencing depth required for a SNP to be considered"
33 <validator type="in_range" min="0"/> 34 help="default: 20" />
34 </param> 35 <param argument="--min-gt-depth" name="min_gt_depth" type="integer" value="0" min="0"
35 <param name="min_gt_depth" type="integer" value="0" label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered" 36 label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered"
36 help="default: 0 (--min-gt-depth)"> 37 help="default: 0" />
37 <validator type="in_range" min="0"/> 38 <param argument="--min-size" name="min_size" type="integer" value="100000" min="1"
38 </param> 39 label="Minimum run size in base pairs" help="default: 100000" />
39 <param name="min_size" type="integer" value="100000" label="Minimum run size in base pairs" help="default: 100000 (--min-size)"> 40 <param argument="--max-hets" name="max_hets" type="integer" value="1" min="0"
40 <validator type="in_range" min="1"/> 41 label="Maximum number of allowed hets in the run" help="default: 1" />
41 </param> 42 <param argument="--max-unknowns" name="max_unknowns" type="integer" value="3" min="0"
42 <param name="max_hets" type="integer" value="1" label="Maximum number of allowed hets in the run" help="default: 1 (--max-hets)"> 43 label="Maximum number of allowed unknowns in the run"
43 <validator type="in_range" min="1"/> 44 help="default: 3" />
44 </param> 45 <param argument="-s" name="samples" type="text" value=""
45 <param name="max_unknowns" type="integer" value="3" label="Maximum number of allowed unknowns in the run" help="default: 3 (-max-unknowns)"> 46 label="Comma separated list of samples to screen for ROHs" help="e.g. S120,S450"/>
46 <validator type="in_range" min="0"/>
47 </param>
48
49 <param name="samples" type="text" value="" label="Comma separated list of samples to screen for ROHs" help="e.g S120,S450 (-s)"/>
50
51 </inputs> 47 </inputs>
52
53 <outputs> 48 <outputs>
54 <data name="outfile" format="tabular" /> 49 <data name="outfile" format="tabular" />
55 </outputs> 50 </outputs>
56 <tests> 51 <tests>
57 <test> 52 <test>
68 </tests> 63 </tests>
69 <help><![CDATA[ 64 <help><![CDATA[
70 65
71 **What it does** 66 **What it does**
72 67
73 ===========================================================================
74 ``ROH``: Identifying runs of homozygosity
75 ===========================================================================
76 Runs of homozygosity are long stretches of homozygous genotypes that reflect 68 Runs of homozygosity are long stretches of homozygous genotypes that reflect
77 segments shared identically by descent and are a result of consanguinity or 69 segments shared identically by descent and are a result of consanguinity or
78 natural selection. Consanguinity elevates the occurrence of rare recessive 70 natural selection. Consanguinity elevates the occurrence of rare recessive
79 diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious 71 diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious
80 mutations. Hence, the identification of these runs holds medical value. 72 mutations. Hence, the identification of these runs holds medical value.