Mercurial > repos > mora-lab > reactomepa
comparison ReactomePA.xml @ 0:f6a9fe7e8066 draft
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author | mora-lab |
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date | Thu, 20 May 2021 08:39:19 +0000 |
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1 <tool id="ReactomePA" name="ReactomePA" version="0.1.0"> | |
2 <description>Reactome Pathway Analysis</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="1.20.3">r-getopt</requirement> | |
6 <requirement type="package" version="1.34.0">bioconductor-ReactomePA</requirement> | |
7 <requirement type="package" version="3.12.0">bioconductor-org.Hs.eg.db</requirement> | |
8 </requirements> | |
9 | |
10 <command detect_errors="exit_code" interpreter="Rscript --vanilla"><![CDATA[ | |
11 $__tool_directory__/ReactomePA.R | |
12 -g '$gene_list_file' | |
13 -s '$Significant_Reactome_Pathway_result' | |
14 | |
15 -o '$organism' | |
16 | |
17 -p '$adv.pvalueCutoff' | |
18 -w '$adv.pAdjustMethod' | |
19 #if $adv.convertId=="TRUE": | |
20 -c | |
21 #end if | |
22 -i '$adv.minGSSize' | |
23 -a '$adv.maxGSSize' | |
24 ]]></command> | |
25 | |
26 <inputs> | |
27 <param type="data" name="gene_list_file" format="csv" label="Differentially expressed gene list" help="A csv file including a DEgenes column, that is, the Entrez ID of all differentially expressed genes." /> | |
28 <param type="select" name="organism" label="Organism" help="Choose organism. Only human, rat, mouse, celegans, yeast, zebrafish and fly are included."> | |
29 <option value="human" selected="True">human (H sapiens)</option> | |
30 <option value="rat">rat (R norvegicus)</option> | |
31 <option value="mouse">house mouse (M musculus)</option> | |
32 <option value="celegans">roundworm (C elegans)</option> | |
33 <option value="yeast">yeast (S cerevisiae)</option> | |
34 <option value="zebrafish">zebrafish (D rerio)</option> | |
35 <option value="fly">fruit fly (D melanogaster)</option> | |
36 </param> | |
37 | |
38 <section name="adv" title="Advanced Options" expanded="false"> | |
39 <param type="float" name="pvalueCutoff" value="0.05" min="0.00" max="1.00" label="P-value threshold" help="This is the cutoff p-value to determine significant enrichment of a pathway. Default is 0.05."/> | |
40 <param type="select" name="pAdjustMethod" label="Method to adjust pathway p-values for multiple testing" help="Choose one method to adjust pathway p-values."> | |
41 <option value="BH" selected="True">BH</option> | |
42 <option value="holm">holm</option> | |
43 <option value="hochberg">hochberg</option> | |
44 <option value="hommel">hommel</option> | |
45 <option value="bonferroni">bonferroni</option> | |
46 <option value="BY">BY</option> | |
47 <option value="fdr">fdr</option> | |
48 <option value="none">none</option> | |
49 </param> | |
50 <param type="boolean" name="convertId" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Convert gene ID to SYMBOL" help="Select Yes if you want to convert entrez gene IDs to gene names (see the Help section below). Default: No." /> | |
51 <param type="integer" name="minGSSize" value="10" label="Minimum size of each geneSet" help="Gene sets with less genes than this value will be ignored."/> | |
52 <param type="integer" name="maxGSSize" value="500" label="Maximum size of each geneSet" help="Gene sets with more genes than this value will be ignored." /> | |
53 </section> | |
54 | |
55 </inputs> | |
56 | |
57 <outputs> | |
58 <data name="Significant_Reactome_Pathway_result" format="csv" label="Significant_Reactome_Pathway_result" /> | |
59 </outputs> | |
60 | |
61 <tests> | |
62 <test> | |
63 <param name="gene_list_file" value="Different_expression_gene.csv" ftype="csv" /> | |
64 <param name="organism" value="human"/> | |
65 <param name="minGSSize" value="15"/> | |
66 <param name="maxGSSize" value="200"/> | |
67 <param name="pvalueCutoff" value="0.06"/> | |
68 <param name="pAdjustMethod" value="holm"/> | |
69 <param name="input7" value="true"/> | |
70 <output name="Significant_Reactome_Pathway_result" file="t1.csv" ftype="csv" /> | |
71 </test> | |
72 </tests> | |
73 | |
74 <help><![CDATA[ | |
75 | |
76 .. class:: infomark | |
77 | |
78 **What it does** | |
79 | |
80 Reactome_ is a free, open-source, curated and peer-reviewed pathway database. | |
81 Their goal is to provide intuitive bioinformatics tools for the visualization, | |
82 interpretation and analysis of pathway knowledge. | |
83 | |
84 .. _Reactome: https://reactome.org | |
85 | |
86 **ReactomePA** is a tool to enrich Significant Reactome Pathways with a list of differentially expressed genes. | |
87 | |
88 This tool uses the function `enrichPathway` in the ReactomePA_ package. | |
89 | |
90 .. _ReactomePA: http://www.bioconductor.org/packages/release/bioc/html/ReactomePA.html | |
91 | |
92 --------- | |
93 | |
94 ========== | |
95 **Inputs** | |
96 ========== | |
97 | |
98 Basic Options | |
99 -------------- | |
100 | |
101 **Differentially expressed gene list** | |
102 | |
103 This tool requires a csv file which has a `DEgenes` column containing the entrez gene ID of all differentially expressed genes. | |
104 | |
105 Example: | |
106 | |
107 ========== === | |
108 DEgenes | |
109 ========== === | |
110 4312 | |
111 8318 | |
112 10874 | |
113 55143 | |
114 55388 | |
115 991 | |
116 ========== === | |
117 | |
118 **Organism** | |
119 | |
120 Choose the right organism for your data. Only human, rat, mouse, celegans, yeast, zebrafish and fly are included. | |
121 | |
122 Advanced Options | |
123 ----------------- | |
124 | |
125 **P-value threshold** | |
126 | |
127 This is the cutoff p-value to determine significant enrichment of a pathway. Default is 0.05. | |
128 | |
129 **Method to adjust pathway p-values for multiple testing** | |
130 | |
131 Choose one method to adjust pathway p-values. Included methods are: `"BH"`, `"holm"`, `"hochberg"`, `"hommel"`, `"bonferroni"`, `"BY"`, `"fdr"` and `"none"`. Default is `"BH"`. | |
132 | |
133 **Convert gene ID to SYMBOL** | |
134 | |
135 If you want to convert entrez gene ID to gene SYMBOL name, choose Yes. Default: No. | |
136 | |
137 **Minimum and maximum size of each geneSet** | |
138 | |
139 Set minimum and maximum size of each gene set to be included in the analysis. Default are 10 and 500. | |
140 | |
141 ------ | |
142 | |
143 ========== | |
144 **Output** | |
145 ========== | |
146 | |
147 A csv file including all enriched pathways. | |
148 | |
149 Example - **Single Count Matrix**: | |
150 | |
151 =============== =============================================== =========== =========== | |
152 ID Description GeneRatio BgRatio | |
153 =============== =============================================== =========== =========== | |
154 R-HSA-69618 Mitotic Spindle Checkpoint 22/326 113/10704 | |
155 R-HSA-2500257 Resolution of Sister Chromatid Cohesion 23/326 126/10704 | |
156 R-HSA-141424 Amplification of signal from the kinetochores 20/326 96/10704 | |
157 R-HSA-9648025 EML4 and NUDC in mitotic spindle formation 20/326 117/10704 | |
158 R-HSA-5663220 RHO GTPases Activate Formins 21/326 140/10704 | |
159 =============== =============================================== =========== =========== | |
160 | |
161 | |
162 ]]></help> | |
163 | |
164 <citations> | |
165 <citation type="doi">10.1039/c5mb00663e</citation> | |
166 </citations> | |
167 | |
168 </tool> |