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comparison gemini_burden.xml @ 17:65f742e605ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:46:38 -0400
parents 53a5647e5271
children ce61d4876838
comparison
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16:ae03de7a9fee 17:65f742e605ec
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>perform sample-wise gene-level burden calculations</description> 2 <description>perform sample-wise gene-level burden calculations</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">burden</token> 5 <token name="@BINARY@">burden</token>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 gemini @BINARY@ 12 gemini @BINARY@
12 --cases $cases 13 --cases $cases
13 --controls $controls 14 --controls $controls
24 "${ infile }" 25 "${ infile }"
25 > "${ outfile }" 26 > "${ outfile }"
26 ]]> 27 ]]>
27 28
28 </command> 29 </command>
29 <expand macro="stdio" />
30 <inputs> 30 <inputs>
31 <expand macro="infile" /> 31 <expand macro="infile" />
32 32
33 <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/> 33 <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
34 <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/> 34 <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
35 35
36 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" 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)"/> 37 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
38 38
39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False" 39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False"
40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/> 40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False" 41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False"
42 label="Run the C-alpha association test" help="(--calpha)"/> 42 label="Run the C-alpha association test" help="(--calpha)"/>
43 <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included" 43 <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included"
44 help="(--min-aaf)"> 44 help="(--min-aaf)">
45 <!--validator type="in_range" min="0.0"/--> 45 <!--validator type="in_range" min="0.0"/-->
46 </param> 46 </param>
47 <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included" 47 <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included"
48 help="(--max-aaf)"> 48 help="(--max-aaf)">
49 <!--validator type="in_range" min="0.0"/--> 49 <!--validator type="in_range" min="0.0"/-->
50 </param> 50 </param>
51 51
52 <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test" 52 <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test"
53 help="(--permutations)"> 53 help="(--permutations)">
54 <validator type="in_range" min="0"/> 54 <validator type="in_range" min="0"/>
55 </param> 55 </param>
56 56
57 </inputs> 57 </inputs>
63 </test> 63 </test>
64 </tests> 64 </tests>
65 <help> 65 <help>
66 **What it does** 66 **What it does**
67 67
68 The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. 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. 69 By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample.
70 70
71 $ gemini burden test.burden.db 71 $ gemini burden test.burden.db
72 gene M10475 M10478 M10500 M128215 72 gene M10475 M10478 M10500 M128215
73 WDR37 2 2 2 2 73 WDR37 2 2 2 2