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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:21:14 -0500
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Find genes among variants that are interacting partners</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">interactions</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini
13 #if $annotation_databases:
14 --annotation-dir ${annotation_databases.fields.path}
15 #end if
16
17 #if $gene.gene_selector == 'lof':
18 ## lof interactions is a separate program
19 lof_interactions
20 #else:
21 ## use normal gemini interactions program
22 @BINARY@
23 -g "${gene.gene}"
24 #end if
25
26 -r "${radius}"
27 $variant_mode
28 "${ infile }"
29 > "${ outfile }"
30 ]]>
31 </command>
32 <inputs>
33 <expand macro="infile" />
34
35 <conditional name="gene">
36 <param name="gene_selector" type="select" label="Studying" help="">
37 <option value="gene">Interesting gene</option>
38 <option value="lof">All loss-of-function variants</option>
39 </param>
40 <when value="gene">
41 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
42 </when>
43 <when value="lof"/>
44 </conditional>
45 <expand macro="annotation_dir" />
46 <expand macro="radius" />
47 <expand macro="variant_mode" />
48 </inputs>
49 <outputs>
50 <data name="outfile" format="tabular" />
51 </outputs>
52 <tests>
53 <test>
54 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
55 <param name="gene" value="CTBP2" />
56 <param name="radius" value="5" />
57 <output name="outfile" file="gemini_interactions_result.tabular" />
58 </test>
59 </tests>
60 <help><![CDATA[
61 **What it does**
62
63 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data.
64 Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the
65 protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI.
66
67 .. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627
68
69 **Details**
70
71 *interactions: Find genes among variants that are interacting partners.*
72
73 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the protein itself. We have used the HPRD binary interaction data to build a p-p network graph which can be explored by GEMINI.
74
75 **Examples**
76
77 EXAMPLE with setting -g CTBP2 and -r 3::
78
79 sample gene order_of_interaction interacting_gene
80 M128215 CTBP2 0_order: CTBP2
81 M128215 CTBP2 1_order: RAI2
82 M128215 CTBP2 2_order: RB1
83 M128215 CTBP2 3_order: TGM2,NOTCH2NL
84
85 Return CTBP2 (-g) interacting gene variants till the third order (-r)
86
87 EXAMPLE lof_interactions (use this option to restrict your analysis to only LoF variants); lof_interactions and -r 3::
88
89 sample lof_gene order_of_interaction interacting_gene
90 M128215 TGM2 1_order: RB1
91 M128215 TGM2 2_order: none
92 M128215 TGM2 3_order: NOTCH2NL,CTBP2
93
94 Meaning to say return all LoF gene TGM2 (in sample M128215) interacting partners to a 3rd order of interaction.
95
96 EXAMPLE --var. An extended variant information (chrom, start, end etc.) for the interacting gene may be achieved with the –var option for both the interactions and the lof_interactions. Settings '-g CTBP2', '-r 3' and '--var'::
97
98 sample gene order_of_interaction interacting_gene var_id chrom start end impact biotype in_dbsnp clinvar_sig clinvar_disease_name aaf_1kg_all aaf_esp_all
99 M128215 CTBP2 0 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None
100 M128215 CTBP2 1 RAI2 9 chrX 17819376 17819377 non_syn_coding protein_coding 1 None None 1 0.000473
101 M128215 CTBP2 2 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None
102 M128215 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None
103 M128215 CTBP2 3 TGM2 8 chr20 36779423 36779424 stop_gain protein_coding 0 None None None None
104
105 EXAMPLE with the following settings; '-r 3', '--var'::
106
107 sample lof_gene order_of_interaction interacting_gene var_id chrom start end impact biotype in_dbsnp clinvar_sig clinvar_disease_name aaf_1kg_all aaf_esp_all
108 M128215 TGM2 1 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None
109 M128215 TGM2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None
110 M128215 TGM2 3 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None
111
112 ]]></help>
113 <expand macro="citations">
114 <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation -->
115 </expand>
116 </tool>