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date Thu, 01 Apr 2021 11:20:20 +0000
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1 <tool id="GSVA" name="Gene Set Variation Analysis" version="0.1.0">
2 <description>Estimates GSVA enrichment scores</description>
3 <requirements>
4 <requirement type="package" version="1.38.0">bioconductor-GSVA</requirement>
5 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
6 <requirement type="package" version="1.20.3">r-getopt</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '$__tool_directory__/GSVA.R'
10 --expr '$expression_data'
11 --geneSet '$geneSet'
12 --method '$method'
13 --img_type '$imgfile.img_args.img_type'
14 --img_width '$imgfile.img_args.img_width'
15 --img_height '$imgfile.img_args.img_height'
16 --img_file '$output_img_file'
17 --GSVA_result '$GSVA_result'
18 ]]></command>
19 <inputs>
20 <param name="expression_data" type="data" format="csv" label="Gene expression data" help="An CSV file that is a matrix of expression values where rows correspond to genes and columns correspond to samples." />
21
22 <param name="geneSet" type="data" format="rdata" label="Gene Sets" help="An rdata file included geneSetCollection object 'geneSet' as name."/>
23
24 <param name="method" type="select" label="Method" display="radio" help="Supposted four method: GSVA, ssGSEA, z-score and PLAGE. Details in help.">
25 <option value="gsva">GSVA</option>
26 <option value="ssgsea">ssGSEA</option>
27 <option value="zscore">z-score</option>
28 <option value="plage">PLAGE</option>
29 </param>
30
31 <section name="imgfile" title="Heatmap" expanded="false">
32 <conditional name="img_args">
33 <param name="img_type" type="select" label="Heatmap file type">
34 <option value="PNG" selected="true">PNG</option>
35 <option value="PDF">PDF</option>
36 <option value="JPG">JPG</option>
37 </param>
38
39 <when value="PNG">
40 <param name="img_width" type="integer" value="480" min="480" label="Img width(px)" />
41 <param name="img_height" type="integer" value="480" min="480" label="Img height(px)" />
42 </when>
43
44 <when value="JPG">
45 <param name="img_width" type="integer" value="480" min="480" label="Img width(px)" />
46 <param name="img_height" type="integer" value="480" min="480" label="Img height(px)" />
47 </when>
48
49 <when value="PDF">
50 <param name="img_width" type="integer" value="7" min="7" label="Img width(inches)" />
51 <param name="img_height" type="integer" value="7" min="7" label="Img height(inches)" />
52 </when>
53
54 </conditional>
55 </section>
56
57 </inputs>
58 <outputs>
59 <data name="GSVA_result" format="csv" label="GSVA_enrich_result" />
60 <data format="pdf" name="output_img_file" label="GSVA_heatmap">
61 <change_format>
62 <when input="imgfile.img_args.img_type" value="PNG" format="png"/>
63 <when input="imgfile.img_args.img_type" value="JPG" format="jpg"/>
64 </change_format>
65 </data>
66 </outputs>
67 <tests>
68 <test>
69 <param name="expression_data" value="gsva_input2_GSE10245.csv" ftype="csv" />
70 <param name="geneSet" value="GeneSet_from_Msigdb_KEGG.rdata" ftype="rdata" />
71 <param name="method" value="gsva" />
72 <section name="imgfile">
73 <conditional name="img_args">
74 <param name="img_type" value="PNG" />
75 <param name="img_width" value="480" />
76 <param name="img_height" value="480" />
77 </conditional>
78 </section>
79 <output name="GSVA_result" file="GSVA_enrich_result.csv" ftype="csv" />
80 <output name="output_img_file" file="GSVA_heatmap.png" ftype="png" />
81 </test>
82 </tests>
83
84
85 <help><![CDATA[
86
87 .. class:: infomark
88
89 **What it does**
90
91 Gene Set Variation Analysis (GSVA) is a Gene Set Enrichment (GSE) method that estimates variation of pathway activity over a sample population in an unsupervised manner.
92
93 This tool is built from function `gsva()` bioconductor package `GSVA`, which included four method to analyze microarray and RNG-seq data.
94
95 - **GSVA**: GSVA calculates sample-wise gene set enrichment scores as a function of genes inside and outside the gene set, analogously to a competitive gene set test. And it estimates variation of gene set enrichment over the samples independently of any class label.
96
97 - **PLAGSE**: Pathway Level analysis of Gene Expression (PLAGE) standardizes each gene expression profile over the samples and then estimates the pathway activity profiles for each gene set as the coefficients of the first right-singular vector of the singular value.
98
99 - **z-score**: The combined z-score method also standardizes each gene expression profile into z-scores and combine the individual gene z-scores per sample to pathway activity profile.
100
101 - **ssGSEA**: The ssGSEA method uses the difference in empirical cumulative distribution functions of gene expression rank inside and outside the gene set to calculate an enrichment statistic per sample which is further normalized by the range of values taken throughout all gene sets amd samples.
102
103 --------
104
105 =========
106 **Input**
107 =========
108
109
110 **Gene expression data**
111
112 The input data is an CSV file, which included a matrix of expression values where rows correspond to genes and columns correspond to samples.
113 Recommend gene id is Entrez ID.
114
115 **Gene Sets**
116
117 Gene Sets is an rdata file which included object `geneSet` that is geneSetCollection built by `GSEABase` of bioconductor package. You can use
118 GeneSet from Msigdb/KEGG to get this file.
119
120 **Method**
121
122 Method to employ in the estimation of gene-set enrichment scores per sample. By default this is set to `GSVA` and other options are `ssGSEA`, `z-score` or `PLAGE`. The latter two standardize first expression profiles into z-scores over the samples and, in the case of zscore, it combines them together as their sum divided by the square-root of the size of the gene set, while in the case of plage they are used to calculate the singular value decomposition (SVD) over the genes in the gene set and use the coefficients of the first right-singular vector as pathway activity profile.
123
124 --------
125
126 ==========
127 **Output**
128 ==========
129
130 **1. A gene-set by sample matrix GSVA enrichment scores**
131
132 ========= ========== ======== ======== ======== ==== =========
133 geneSet sample_1 sample_2 sample_3 sample_4 ... sample_n
134 ========= ========== ======== ======== ======== ==== =========
135 pathway_1
136 pathway_2
137 pathway_3
138 pathway_4
139 ...
140 pathway_n
141 ========= ========== ======== ======== ======== ==== =========
142
143
144 **2. Heatmap for the matrix GSVA enrichment scores**
145
146 You can define the heatmap file type, width and height in the part of input.
147
148 ]]></help>
149
150 <citations>
151 <citation type="doi">10.1186/1471-2105-14-7</citation>
152 </citations>
153
154
155 </tool>