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date Thu, 20 May 2021 08:44:12 +0000
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1 <tool id="methylGSA" name="methylGSA" version="0.1.0" python_template_version="3.5">
2 <description>Gene Set Analysis for DNA Methylation data</description>
3
4 <requirements>
5 <requirement type="package" version="0.6.0">bioconductor-IlluminaHumanMethylationEPICanno.ilm10b4.hg19</requirement>
6 <requirement type="package" version="0.6.0">bioconductor-IlluminaHumanMethylation450kanno.ilmn12.hg19</requirement>
7 <requirement type="package" version="1.8.0">bioconductor-methylGSA</requirement>
8 <requirement type="package" version="1.20.3">r-getopt</requirement>
9 </requirements>
10
11 <command detect_errors="exit_code"><![CDATA[
12 Rscript '$__tool_directory__/methylGSA.R'
13 --data_file '$data_file'
14 --test_method '$method'
15 --array_type '$array_type'
16 --group '$Group'
17 --GS_list '$geneset'
18 --minsize '$minSize'
19 --maxsize '$maxSize'
20 --result '$gsa_result'
21
22 ]]></command>
23
24 <inputs>
25 <param name="data_file" type="data" format="txt" label="CpG IDs and their p-value" help="A text file with two columns: The CpG IDs and their p-values." />
26 <param name="array_type" type="select" label="Array_type" help="450K or EPIC." >
27 <option value="450K">450K</option>
28 <option value="EPIC">EPIC</option>
29 </param>
30 <param name="Group" type="select" label="Group" help="See help for more details.">
31 <option value="all">all</option>
32 <option value="body">body</option>
33 <option value="promoter1">promoter1</option>
34 <option value="promoter2">promoter2</option>
35 </param>
36 <param name="method" type="select" label="Test method" display="radio" help="See help for more details." >
37 <option value="methylglm">methylglm</option>
38 <option value="gometh">gometh</option>
39 <option value="RRA_ORA">RRA(ORA)</option>
40 <option value="RRA_GSEA">RRA(GSEA)</option>
41 </param>
42 <param name="geneset" type="select" label="Gene sets" help="Select gene sets to test." >
43 <option value="GO">Gene Ontology</option>
44 <option value="KEGG">KEGG</option>
45 <option value="Reactome">Reactome</option>
46 </param>
47
48 <param name="minSize" type="integer" label="Minimum gene set size" value="15" min="1" max="1000" help="Gene sets with less than this number of elements will not be included in the analysis." />
49 <param name="maxSize" type="integer" label="Maximum gene set size" value="500" min="1" max="1000" help="Gene sets with more than this number of elements will not be included in the analysis." />
50
51 </inputs>
52
53 <outputs>
54 <data name="gsa_result" format="csv" label="methylGSA_result" />
55 </outputs>
56
57 <tests>
58 <test>
59 <param name="data_file" value="cpg.csv" ftype="txt" />
60 <param name="array_type" value="450K"/>
61 <param name="Group" value="all" />
62 <param name="method" value="methylglm" />
63 <param name="geneset" value="GO" />
64 <param name="minSize" value="15" />
65 <param name="maxSize" value="500" />
66 <output name="gsa_result" file="methylGSA_result.csv" ftype="csv" />
67 </test>
68 </tests>
69
70 <help><![CDATA[
71
72 .. class:: infomark
73
74 **What it does**
75
76 **methylGSA** is a tool for gene set testing with length bias adjustment for DNA methylation data.
77 It allows users to identify enriched or over-represented gene sets or pathways from the Gene
78 Ontology, KEGG and Reactome databases.
79
80 -------
81
82 =========
83 **Input**
84 =========
85
86 **CpG IDs and their p-value**
87
88 Users are expected to upload a txt file with two columns: The fist column with the CpG IDs, and the second column with the p-values correspond to the CpGs. For example:
89
90 =========== ===========
91 cg13869341 0.307766
92 cg14008030 0.257672
93 cg12045430 0.552322
94 cg20826792 0.056383
95 cg00381604 0.468549
96 cg20253340 0.483770
97 cg21870274 0.812402
98 =========== ===========
99
100 Files should be no more than 100MB.
101
102 **array_type**
103
104 `450K`: Illumina 450 K Beadchip
105
106 `EPIC`: Illumina EPIC Beadchip
107
108 **Group**
109
110 **Group** defines the type of CpG to be considered by the `methylRRA` or `methylglm` functions. By default,
111 group is set to `all`, which means that all CpGs are considered regardless of their gene group.
112 If group is set to `body`, only CpGs on gene body will be considered. If group is `promoter1`
113 or `promoter2`, only CpGs on promoters will be considered.
114 Based on the annotation in IlluminaHumanMethylation450kanno.ilmn12.hg19
115 and IlluminaHumanMethylationEPICanno.ilm10b4.hg19, `body`, `promoter1` and `promoter2` are defined as:
116
117 * body: CpGs whose gene group correspond to “Body” or “1stExon”
118 * promoter1: CpGs whose gene group correspond to “TSS1500” or “TSS200”
119 * promoter2: CpGs whose gene group correspond to “TSS1500”, “TSS200”, “1stExon”, or “5’UTR”
120
121 **Test method**
122
123 * methylglm: Implement logistic regression adjusting for number of probes in enrichment analysis
124 * gometh: Gene ontology testing for Illumina methylation array data
125 * RRA(ORA): Enrichment analysis with ORA method after adjusting multiple p-values of each gene by Robust Rank Aggregation
126 * RRA(GSEA): Enrichment analysis with GSEA method after adjusting multiple p-values of each gene by Robust Rank Aggregation
127
128 **Gene sets tested**
129
130 * Gene Ontology: http://www.geneontology.org
131 * KEGG (Kyoto Encyclopedia of Genes and Genomes): https://www.genome.jp/kegg/
132 * Reactome: https://reactome.org
133
134 ==========
135 **Output**
136 ==========
137
138 **methylGSA_result**
139 This file is a csv file which contains gene set tests results.
140
141 ]]></help>
142
143 <citations>
144 <citation type="doi">10.1093/bioinformatics/bty892</citation>
145 </citations>
146
147 </tool>