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comparison gemini_burden.xml @ 0:e799c1a6854b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:51:59 -0500
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>perform sample-wise gene-level burden calculations</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">burden</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13 --cases $cases
14 --controls $controls
15 $save_tscores
16 $nonsynonymous
17 $calpha
18 --permutations $permutations
19 #if float( str($min_aaf) ) >= 0.0:
20 --min-aaf $min_aaf
21 #end if
22 #if float( str($max_aaf) ) >= 0.0:
23 --max-aaf $max_aaf
24 #end if
25 "${ infile }"
26 > "${ outfile }"
27 ]]>
28
29 </command>
30 <inputs>
31 <expand macro="infile" />
32
33 <param name="cases" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
34 <param name="controls" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
35
36 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False"
37 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
38
39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False"
40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False"
42 label="Run the C-alpha association test" help="(--calpha)"/>
43 <param name="min_aaf" type="float" value="-1" label="The min. alt. allele frequency for a variant to be included"
44 help="(--min-aaf)">
45 <!--validator type="in_range" min="0.0"/-->
46 </param>
47 <param name="max_aaf" type="float" value="-1" label="The max. alt. allele frequency for a variant to be included"
48 help="(--max-aaf)">
49 <!--validator type="in_range" min="0.0"/-->
50 </param>
51
52 <param name="permutations" type="integer" value="1000" label="Number of permutations to run for the C-alpha test"
53 help="(--permutations)">
54 <validator type="in_range" min="0"/>
55 </param>
56
57 </inputs>
58 <outputs>
59 <data name="outfile" format="tabular" />
60 </outputs>
61 <tests>
62 <test>
63 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
64 <param name="controls" value="M10475 M10478" />
65 <param name="cases" value="M10500 M128215" />
66 <param name="calpha" value="True" />
67 <output name="outfile" file="gemini_burden_result.tabular" />
68 </test>
69 </tests>
70 <help><![CDATA[
71 **What it does**
72
73 Burden performs sample-wise gene-level burden calculations.
74
75 The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample:
76
77 GEMINI burden example::
78
79 gene M10475 M10478 M10500 M128215
80 WDR37 2 2 2 2
81 CTBP2 0 0 0 1
82 DHODH 1 0 0 0
83
84 **Setting examples**
85
86 **--nonsynonymous**
87
88 If you want to be a little bit less restrictive, you can include all non-synonymous variants instead.
89
90 GEMINI output with setting --nonsynonymous::
91
92 gene M10475 M10478 M10500 M128215
93 SYCE1 0 1 1 0
94 WDR37 2 2 2 2
95 CTBP2 0 0 0 1
96 ASAH2C 2 1 1 0
97 DHODH 1 0 0 0
98
99 **--calpha**
100
101 If your database has been loaded with a PED file describing case and control samples, you can calculate the c-alpha statistic for cases vs. control.
102
103 GEMINI output with setting --calpha::
104
105 gene T c Z p_value
106 SYCE1 -0.5 0.25 -1.0 0.841344746069
107 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
108 CTBP2 0.0 0.0 nan nan
109 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
110 DHODH 0.0 0.0 nan nan
111
112 To calculate the **P-value** using a permutation test, use the --permutations option, specifying the number of permutations of the case/control labels you want to use.
113
114 **--min-aaf and --max-aaf for --calpha**
115
116 By default, all variants affecting a given gene will be included in the C-alpha computation. However, one may establish alternate allele frequency boundaries for the variants included using the --min-aaf and --max-aaf options.
117
118 Used settings:
119
120 - -calpha test.burden.db
121 - -min-aaf 0.0
122 - -max-aaf 0.01
123 - -cases
124 - -controls for --calpha
125
126 If you do not have a PED file loaded, or your PED file does not follow the standard PED phenotype encoding format you can still perform the c-alpha test, but you have to specify which samples are the control samples and which are the case samples.
127
128 Used settings:
129
130 - -controls M10475 M10478
131 - -cases M10500 M128215
132 - -calpha
133
134 Output::
135
136 gene T c Z p_value
137 SYCE1 -0.5 0.25 -1.0 0.841344746069
138 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
139 CTBP2 0.0 0.0 nan nan
140 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
141 DHODH 0.0 0.0 nan nan
142
143 **--nonsynonymous --calpha**
144
145 If you would rather consider all nonsynonymous variants for the C-alpha test rather than just the medium and high impact variants, add the --nonsynonymous flag.
146
147
148 ]]></help>
149 <expand macro="citations">
150 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
151 </expand>
152 </tool>