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comparison gemini_burden.xml @ 20:b5207530f991 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:19:47 -0500
parents 27ce3de83007
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19:27ce3de83007 20:b5207530f991
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>perform sample-wise gene-level burden calculations</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">burden</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13 --cases $cases
14 --controls $controls
15 $save_tscores
16 $nonsynonymous
17 $calpha
18 --permutations $permutations
19 #if float( str($min_aaf) ) >= 0.0:
20 --min-aaf $min_aaf
21 #end if
22 #if float( str($max_aaf) ) >= 0.0:
23 --max-aaf $max_aaf
24 #end if
25 "${ infile }"
26 > "${ outfile }"
27 ]]>
28
29 </command>
30 <inputs>
31 <expand macro="infile" />
32
33 <param name="cases" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
34 <param name="controls" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
35
36 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False"
37 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
38
39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False"
40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False"
42 label="Run the C-alpha association test" help="(--calpha)"/>
43 <param name="min_aaf" type="float" value="-1" label="The min. alt. allele frequency for a variant to be included"
44 help="(--min-aaf)">
45 <!--validator type="in_range" min="0.0"/-->
46 </param>
47 <param name="max_aaf" type="float" value="-1" label="The max. alt. allele frequency for a variant to be included"
48 help="(--max-aaf)">
49 <!--validator type="in_range" min="0.0"/-->
50 </param>
51
52 <param name="permutations" type="integer" value="1000" label="Number of permutations to run for the C-alpha test"
53 help="(--permutations)">
54 <validator type="in_range" min="0"/>
55 </param>
56
57 </inputs>
58 <outputs>
59 <data name="outfile" format="tabular" />
60 </outputs>
61 <tests>
62 <test>
63 </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>