|
0
|
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
|
|
|
2 <description>perform sample-wise gene-level burden calculations</description>
|
|
|
3 <expand macro="requirements" />
|
|
|
4 <expand macro="version_command" />
|
|
|
5 <macros>
|
|
|
6 <import>gemini_macros.xml</import>
|
|
|
7 <token name="@BINARY@">burden</token>
|
|
|
8 </macros>
|
|
|
9 <command>
|
|
|
10 <![CDATA[
|
|
|
11 gemini @BINARY@
|
|
|
12 --cases $cases
|
|
|
13 --controls $controls
|
|
|
14 $save_tscores
|
|
|
15 $nonsynonymous
|
|
|
16 $calpha
|
|
|
17 --permutations $permutations
|
|
8
|
18 #if float( str($min_aaf) ) >= 0.0:
|
|
0
|
19 --min-aaf $min_aaf
|
|
|
20 #end if
|
|
8
|
21 #if float( str($max_aaf) ) >= 0.0:
|
|
0
|
22 --max-aaf $max_aaf
|
|
|
23 #end if
|
|
|
24 "${ infile }"
|
|
|
25 > "${ outfile }"
|
|
|
26 ]]>
|
|
|
27
|
|
|
28 </command>
|
|
|
29 <expand macro="stdio" />
|
|
|
30 <inputs>
|
|
11
|
31 <expand macro="infile" />
|
|
0
|
32
|
|
|
33 <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
|
|
|
34 <param name="controls" size="30" 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" size="5" label="The min. alt. allele frequency for a variant to be included"
|
|
|
44 help="(--min-aaf)">
|
|
2
|
45 <!--validator type="in_range" min="0.0"/-->
|
|
0
|
46 </param>
|
|
|
47 <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included"
|
|
|
48 help="(--max-aaf)">
|
|
2
|
49 <!--validator type="in_range" min="0.0"/-->
|
|
0
|
50 </param>
|
|
|
51
|
|
|
52 <param name="permutations" type="integer" value="1000" size="10" 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>
|
|
11
|
59 <data name="outfile" format="tabular" />
|
|
0
|
60 </outputs>
|
|
|
61 <tests>
|
|
|
62 <test>
|
|
|
63 </test>
|
|
|
64 </tests>
|
|
|
65 <help>
|
|
|
66 **What it does**
|
|
|
67
|
|
|
68 The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis.
|
|
|
69 By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample.
|
|
|
70
|
|
|
71 $ gemini burden test.burden.db
|
|
|
72 gene M10475 M10478 M10500 M128215
|
|
|
73 WDR37 2 2 2 2
|
|
|
74 CTBP2 0 0 0 1
|
|
|
75 DHODH 1 0 0 0
|
|
|
76
|
|
|
77 @CITATION@
|
|
|
78 </help>
|
|
|
79 <expand macro="citations">
|
|
|
80 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
|
|
|
81 </expand>
|
|
|
82 </tool>
|
