Mercurial > repos > iuc > gemini_burden
annotate gemini_burden.xml @ 7:df57188562f0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
author | iuc |
---|---|
date | Tue, 10 Mar 2020 06:17:40 -0400 (2020-03-10) |
parents | 699ce2631e79 |
children | f0bf88e9e689 |
rev | line source |
---|---|
5
699ce2631e79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
|
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@"> |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
2 <description>perform sample-wise gene-level burden calculations</description> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
3 <macros> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
4 <import>gemini_macros.xml</import> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
5 <token name="@BINARY@">burden</token> |
4
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
6 <token name="@GEMINI_BUG_WARNING@">Caveat: due to a bug in this version of GEMINI, filtering on alternate allele frequency will get disabled when you select 'All non-synonymous variants' as the types of variants to be used for the burden calculations above.</token> |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
7 </macros> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
8 <expand macro="requirements" /> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
9 <expand macro="stdio" /> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
10 <expand macro="version_command" /> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
11 <command> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
12 <![CDATA[ |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
13 gemini @BINARY@ |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
14 $nonsynonymous |
4
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
15 #if str($analysis.mode) == "c-alpha": |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
16 --calpha |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
17 #if str($analysis.casecontrol.source) == "custom": |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
18 --cases |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
19 #echo (" ".join("'" + token + "'" for token in $analysis.casecontrol.cases.strip().split()))# |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
20 --controls |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
21 #echo (" ".join("'" + token + "'" for token in $analysis.casecontrol.controls.strip().split()))# |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
22 #end if |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
23 --min-aaf ${analysis.min_aaf} |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
24 --max-aaf ${analysis.max_aaf} |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
25 --permutations ${analysis.permutations} |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
26 ${analysis.save_tscores} |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
27 #end if |
5
699ce2631e79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
|
28 '$infile' |
699ce2631e79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
|
29 > '$outfile' |
4
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
30 #if str($analysis.mode) == "c-alpha" and $analysis.save_tscores: |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
31 && touch permutated_t_scores.txt |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
32 && mv permutated_t_scores.txt $t_scores |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
33 #end if |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
34 ]]> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
35 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
36 </command> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
37 <inputs> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
38 <expand macro="infile" /> |
4
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
39 <param argument="--non-synonymous" name="nonsynonymous" type="select" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
40 label="Use the following types of variants for the burden calculation"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
41 <option value="">High impact variants only</option> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
42 <option value="--nonsynonymous">All non-synonymous variants</option> |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
43 </param> |
4
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
44 <conditional name="analysis"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
45 <param argument="--calpha" name="mode" type="select" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
46 label="Which type of burden calculation should be performed?"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
47 <option value="counts">Count of variants per gene and sample</option> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
48 <option value="c-alpha">C-alpha association test per gene</option> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
49 </param> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
50 <when value="counts" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
51 <when value="c-alpha"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
52 <conditional name="casecontrol"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
53 <param name="source" type="select" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
54 label="Selection of case and control samples" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
55 help="Specify how case and control samples for the C-alpha association test should be selected"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
56 <option value="ped">Use PED file information</option> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
57 <option value="custom">Custom selection</option> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
58 </param> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
59 <when value="ped" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
60 <when value="custom"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
61 <param argument="--cases" name="cases" type="text" value="" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
62 label="Space separated list of cases for association testing"/> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
63 <param argument="--controls" name="controls" type="text" value="" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
64 label="Space separated list of controls for association testing" help="(--controls)"/> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
65 </when> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
66 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
67 <param argument="--min-aaf" name="min_aaf" type="float" min="0" max="1" value="0" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
68 label="The min. alt. allele frequency for a variant to be included" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
69 help="@GEMINI_BUG_WARNING@" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
70 <param argument="--max-aaf" name="max_aaf" type="float" min="0" max="1" value="1" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
71 label="The max. alt. allele frequency for a variant to be included" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
72 help="@GEMINI_BUG_WARNING@" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
73 <param argument="--permutations" name="permutations" type="integer" min="1" value="100" label="Number of permutations to run for the C-alpha test" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
74 <param argument="--save_tscores" name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
75 label="Save the list of individual T-scores from all permutations as an extra dataset" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
76 </when> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
77 </conditional> |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
78 </inputs> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
79 <outputs> |
4
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
80 <data name="outfile" format="tabular" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
81 label="GEMINI burden ${analysis.mode} on ${on_string}" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
82 <data name="t_scores" format="tabular" |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
83 label="GEMINI burden permuted T scores on ${on_string}"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
84 <filter>analysis['mode'] == 'c-alpha' and analysis['save_tscores']</filter> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
85 </data> |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
86 </outputs> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
87 <tests> |
4
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
88 <test expect_num_outputs="1"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
89 <!-- test counts mode with defaults --> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
90 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
91 <conditional name="analysis"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
92 <param name="mode" value="counts" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
93 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
94 <output name="outfile" file="gemini_burden_count_highimpact_result.tabular" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
95 </test> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
96 <test expect_num_outputs="1"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
97 <!-- test nonsynonymous parameter --> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
98 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
99 <param name="nonsynonymous" value="--nonsynonymous" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
100 <conditional name="analysis"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
101 <param name="mode" value="counts" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
102 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
103 <output name="outfile" file="gemini_burden_count_nonsynonymous_result.tabular" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
104 </test> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
105 <test expect_num_outputs="1"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
106 <!-- test c-alpha mode with defaults --> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
107 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
108 <conditional name="analysis"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
109 <param name="mode" value="c-alpha" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
110 <conditional name="casecontrol"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
111 <param name="source" value="ped" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
112 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
113 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
114 <output name="outfile" file="gemini_burden_calpha_template.tabular" compare="re_match" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
115 </test> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
116 <test expect_num_outputs="1"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
117 <!-- test c-alpha mode with user-supplied case/control samples --> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
118 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
119 <conditional name="analysis"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
120 <param name="mode" value="c-alpha" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
121 <conditional name="casecontrol"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
122 <param name="source" value="custom" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
123 <param name="controls" value="1_kid 3_kid" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
124 <param name="cases" value="1_dad 1_mom 3_dad 3_mom" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
125 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
126 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
127 <output name="outfile" file="gemini_burden_calpha_template.tabular" compare="re_match" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
128 </test> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
129 <test expect_num_outputs="2"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
130 <!-- test additional T scores output generation --> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
131 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
132 <conditional name="analysis"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
133 <param name="mode" value="c-alpha" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
134 <conditional name="casecontrol"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
135 <param name="source" value="custom" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
136 <param name="controls" value="1_kid 3_kid" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
137 <param name="cases" value="1_dad 1_mom 3_dad 3_mom" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
138 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
139 <param name="permutations" value="2" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
140 <param name="save_tscores" value="True" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
141 </conditional> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
142 <output name="t_scores"> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
143 <assert_contents> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
144 <has_line_matching expression="WDR37	.+	.+" /> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
145 </assert_contents> |
c70d79e0eed7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
0
diff
changeset
|
146 </output> |
0
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
147 </test> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
148 </tests> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
149 <help><![CDATA[ |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
150 **What it does** |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
151 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
152 Burden performs sample-wise gene-level burden calculations. |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
153 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
154 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: |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
155 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
156 GEMINI burden example:: |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
157 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
158 gene M10475 M10478 M10500 M128215 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
159 WDR37 2 2 2 2 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
160 CTBP2 0 0 0 1 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
161 DHODH 1 0 0 0 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
162 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
163 **Setting examples** |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
164 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
165 **--nonsynonymous** |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
166 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
167 If you want to be a little bit less restrictive, you can include all non-synonymous variants instead. |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
168 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
169 GEMINI output with setting --nonsynonymous:: |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
170 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
171 gene M10475 M10478 M10500 M128215 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
172 SYCE1 0 1 1 0 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
173 WDR37 2 2 2 2 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
174 CTBP2 0 0 0 1 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
175 ASAH2C 2 1 1 0 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
176 DHODH 1 0 0 0 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
177 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
178 **--calpha** |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
179 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
180 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. |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
181 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
182 GEMINI output with setting --calpha:: |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
183 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
184 gene T c Z p_value |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
185 SYCE1 -0.5 0.25 -1.0 0.841344746069 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
186 WDR37 -1.0 1.5 -0.816496580928 0.792891910879 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
187 CTBP2 0.0 0.0 nan nan |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
188 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
189 DHODH 0.0 0.0 nan nan |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
190 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
191 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. |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
192 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
193 **--min-aaf and --max-aaf for --calpha** |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
194 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
195 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. |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
196 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
197 Used settings: |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
198 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
199 - -calpha test.burden.db |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
200 - -min-aaf 0.0 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
201 - -max-aaf 0.01 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
202 - -cases |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
203 - -controls for --calpha |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
204 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
205 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. |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
206 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
207 Used settings: |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
208 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
209 - -controls M10475 M10478 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
210 - -cases M10500 M128215 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
211 - -calpha |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
212 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
213 Output:: |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
214 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
215 gene T c Z p_value |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
216 SYCE1 -0.5 0.25 -1.0 0.841344746069 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
217 WDR37 -1.0 1.5 -0.816496580928 0.792891910879 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
218 CTBP2 0.0 0.0 nan nan |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
219 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
220 DHODH 0.0 0.0 nan nan |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
221 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
222 **--nonsynonymous --calpha** |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
223 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
224 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. |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
225 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
226 |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
227 ]]></help> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
228 <expand macro="citations"> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
229 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation --> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
230 </expand> |
e799c1a6854b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
231 </tool> |