Mercurial > repos > iuc > gemini_burden

annotate gemini_burden.xml @ 3:dc9aaf902982 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 e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:50:24 -0500
parents 393dd589e086
children b68d53454144
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
dc9aaf902982 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
2 <description>perform sample-wise gene-level burden calculations</description>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
3 <macros>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
4 <import>gemini_macros.xml</import>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
5 <token name="@BINARY@">burden</token>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
6 </macros>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
7 <expand macro="requirements" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
8 <expand macro="stdio" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
9 <expand macro="version_command" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
10 <command>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
11 <![CDATA[
3
dc9aaf902982 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
12 @PROVIDE_ANNO_DATA@
dc9aaf902982 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
13
0
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
14 gemini @BINARY@
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
15 --cases $cases
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
16 --controls $controls
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
17 $save_tscores
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
18 $nonsynonymous
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
19 $calpha
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
20 --permutations $permutations
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
21 #if float( str($min_aaf) ) >= 0.0:
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
22 --min-aaf $min_aaf
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
23 #end if
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
24 #if float( str($max_aaf) ) >= 0.0:
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
25 --max-aaf $max_aaf
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
26 #end if
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
27 "${ infile }"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
28 > "${ outfile }"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
29 ]]>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
30
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
31 </command>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
32 <inputs>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
33 <expand macro="infile" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
34
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
35 <param name="cases" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
36 <param name="controls" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
37
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
38 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
39 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
40
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
41 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
42 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
43 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
44 label="Run the C-alpha association test" help="(--calpha)"/>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
45 <param name="min_aaf" type="float" value="-1" label="The min. alt. allele frequency for a variant to be included"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
46 help="(--min-aaf)">
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
47 <!--validator type="in_range" min="0.0"/-->
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
48 </param>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
49 <param name="max_aaf" type="float" value="-1" label="The max. alt. allele frequency for a variant to be included"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
50 help="(--max-aaf)">
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
51 <!--validator type="in_range" min="0.0"/-->
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
52 </param>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
53
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
54 <param name="permutations" type="integer" value="1000" label="Number of permutations to run for the C-alpha test"
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
55 help="(--permutations)">
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
56 <validator type="in_range" min="0"/>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
57 </param>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
58
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
59 </inputs>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
60 <outputs>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
61 <data name="outfile" format="tabular" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
62 </outputs>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
63 <tests>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
64 <test>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
65 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
66 <param name="controls" value="M10475 M10478" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
67 <param name="cases" value="M10500 M128215" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
68 <param name="calpha" value="True" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
69 <output name="outfile" file="gemini_burden_result.tabular" />
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
70 </test>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
71 </tests>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
72 <help><![CDATA[
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
73 **What it does**
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
74
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
75 Burden performs sample-wise gene-level burden calculations.
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
76
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
77 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:
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
78
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
79 GEMINI burden example::
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
80
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
81 gene M10475 M10478 M10500 M128215
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
82 WDR37 2 2 2 2
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
83 CTBP2 0 0 0 1
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
84 DHODH 1 0 0 0
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
85
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
86 **Setting examples**
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
87
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
88 **--nonsynonymous**
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
89
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
90 If you want to be a little bit less restrictive, you can include all non-synonymous variants instead.
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
91
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
92 GEMINI output with setting --nonsynonymous::
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
93
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
94 gene M10475 M10478 M10500 M128215
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
95 SYCE1 0 1 1 0
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
96 WDR37 2 2 2 2
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
97 CTBP2 0 0 0 1
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
98 ASAH2C 2 1 1 0
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
99 DHODH 1 0 0 0
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
100
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
101 **--calpha**
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
102
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
103 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.
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
104
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
105 GEMINI output with setting --calpha::
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
106
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
107 gene T c Z p_value
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
108 SYCE1 -0.5 0.25 -1.0 0.841344746069
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
109 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
110 CTBP2 0.0 0.0 nan nan
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
111 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
112 DHODH 0.0 0.0 nan nan
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
113
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
114 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.
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
115
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
116 **--min-aaf and --max-aaf for --calpha**
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
117
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
118 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.
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
119
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
120 Used settings:
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
121
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
122 - -calpha test.burden.db
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
123 - -min-aaf 0.0
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
124 - -max-aaf 0.01
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
125 - -cases
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
126 - -controls for --calpha
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
127
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
128 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.
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
129
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
130 Used settings:
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
131
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
132 - -controls M10475 M10478
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
133 - -cases M10500 M128215
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
134 - -calpha
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
135
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
136 Output::
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
137
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
138 gene T c Z p_value
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
139 SYCE1 -0.5 0.25 -1.0 0.841344746069
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
140 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
141 CTBP2 0.0 0.0 nan nan
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
142 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
143 DHODH 0.0 0.0 nan nan
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
144
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
145 **--nonsynonymous --calpha**
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
146
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
147 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.
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
148
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
149
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
150 ]]></help>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
151 <expand macro="citations">
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
152 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
153 </expand>
393dd589e086 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
154 </tool>