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comparison msigdb_kegg_geneSet.xml @ 1:0c0d33699925 draft default tip

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date Thu, 20 May 2021 08:37:05 +0000
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1 <tool id="msigdb_kegg_geneSet" name="Get gene sets from Msigdb/KEGG" version="0.1.0">
2 <description>Get a geneSet object from Msigdb or KEGG</description>
3
4 <requirements>
5 <requirement type="package" version="1.30.0">bioconductor-KEGGREST</requirement>
6 <requirement type="package" version="7.2.1">r-msigdbr</requirement>
7 <requirement type="package" version="1.52.1">bioconductor-GSEABase</requirement>
8 <requirement type="package" version="1.20.3">r-getopt</requirement>
9 </requirements>
10
11 <command detect_errors="exit_code"><![CDATA[
12 Rscript '$__tool_directory__/msigdb_kegg_geneSet.R'
13
14 --source '$input_args.source'
15
16 #if str($input_args.source) == 'KEGG':
17 --organism '$input_args.organism'
18 #end if
19
20 #if str($input_args.source) == 'Msigdb':
21 --species '$input_args.species'
22 --category '$input_args.cat.category'
23 --geneIdType '$input_args.geneIdType'
24
25 #if str($input_args.cat.category) == 'C2':
26 --subcategory '$input_args.cat.subcategory'
27 #end if
28
29 #if str($input_args.cat.category) == 'C3':
30 --subcategory '$input_args.cat.subcategory'
31 #end if
32
33 #if str($input_args.cat.category) == 'C4':
34 --subcategory '$input_args.cat.subcategory'
35 #end if
36
37 #if str($input_args.cat.category) == 'C5':
38 --subcategory '$input_args.cat.subcategory'
39 #end if
40
41 #end if
42
43 --outputRData '$outputRData'
44
45 ]]></command>
46
47 <inputs>
48 <conditional name="input_args">
49 <param type="select" name="source" label="KEGG or MSigDB" help="Choose gene set from KEGG or MSigDB.">
50 <option value="KEGG" selected="true">KEGG</option>
51 <option value="Msigdb" >MSigDB</option>
52 </param>
53
54 <when value="KEGG">
55 <param type="text" name="organism" value="hsa" label="organism" help="A KEGG organism code (see https://www.kegg.jp/kegg/catalog/org_list.html). For example, human is `hsa`, Mus musculus is `mmu`."/>
56 </when>
57 <when value="Msigdb">
58 <param type="select" name="species" label="Species" help="Species name, such as Homo sapiens or Mus musculus.">
59 <option value="Homo sapiens" selected="true">human (H sapiens)</option>
60 <option value="Bos taurus">cattle (B taurus)</option>
61 <option value="Caenorhabditis elegans">roundworm (C elegans)</option>
62 <option value="Canis lupus familiaris">dog (C familiaris)</option>
63 <option value="Danio rerio">zebrafish (D rerio)</option>
64 <option value="Drosophila melanogaster">fruit fly (D melanogaster)</option>
65 <option value="Gallus gallus">chicken (G gallus)</option>
66 <option value="Mus musculus">house mouse (M musculus)</option>
67 <option value="Rattus norvegicus">Rat (R norvegicus)</option>
68 <option value="Saccharomyces cerevisiae">baker's or brewer's yeast (S cerevisiae)</option>
69 <option value="Sus scrofa">pig (S scrofa)</option>
70 </param>
71
72 <conditional name="cat">
73 <param type="select" name="category" label="Category" help="MSigDB collection abbreviation, such as H or C1.">
74 <option value="H">h: hallmark gene sets</option>
75 <option value="C1">c1: positional gene sets</option>
76 <option value="C2" selected="true">c2: curated gene sets</option>
77 <option value="C3">c3: regulatory target gene sets</option>
78 <option value="C4">c4: computational gene sets</option>
79 <option value="C5">c5: Ontology gene sets</option>
80 <option value="C6">c6: oncogenic signature gene sets</option>
81 <option value="C7">c7: immunologic signature gene sets</option>
82 <option value="C8">c8: cell type signature gene sets</option>
83 </param>
84 <when value="H"></when>
85 <when value="C1"></when>
86 <when value="C2">
87 <param type="select" name="subcategory" label="Sub Category" multiple="true" display="checkboxes">
88 <option value="CGP">chemical and genetic perturbations</option>
89 <option value="CP">all canonical pathways</option>
90 <option value="CP:BIOCARTA">BioCarta gene sets</option>
91 <option value="CP:KEGG" selected="true">KEGG gene sets</option>
92 <option value="CP:PID">PID gene sets</option>
93 <option value="CP:REACTOME">Reactome gene sets</option>
94 <option value="CP:WIKIPATHWAYS">WikiPathways gene sets</option>
95 </param>
96 </when>
97
98 <when value="C3">
99 <param type="select" name="subcategory" label="Sub Category" multiple="true" display="checkboxes">
100 <option value="MIR:MIR_Legacy">legacy microRNA targets</option>
101 <option value="MIR:MIRDB">MIRDB targets</option>
102 <option value="TFT:GTRD">GTRD targets </option>
103 <option value="TFT:TFT_Legacy">legacy transcription factor targets</option>
104 </param>
105 </when>
106
107 <when value="C4">
108 <param type="select" name="subcategory" label="Sub Category" multiple="true" display="checkboxes">
109 <option value="CGN">cancer gene neighborhoods</option>
110 <option value="CM">cancer modules</option>
111 </param>
112 </when>
113
114 <when value="C5">
115 <param type="select" name="subcategory" label="Sub Category" multiple="true" display="checkboxes">
116 <option value="GO:BP">GO biological processes</option>
117 <option value="GO:CC">GO cellular components</option>
118 <option value="GO:MF">GO molecular functions</option>
119 <option value="HPO">Human Phenotype Ontology</option>
120 </param>
121 </when>
122 <when value="C6"></when>
123 <when value="C7"></when>
124 <when value="C8"></when>
125
126 </conditional>
127 <param type="select" name="geneIdType" label="gene ID type" help="Specify gene ID type in pathway. Default is Entrez ID.">
128 <option value="entrez" selected="true">Entrez</option>
129 <option value="symbol">Symbol</option>
130 </param>
131 </when>
132
133 </conditional>
134
135 <!--<param type="boolean" name="whetherOutputfile" truevalue="True" false="False" checked="False" label="Output GMT file" />-->
136
137 </inputs>
138
139 <outputs>
140 <!--<data name="outputGMTFile" format="gmt" />-->
141 <data name="outputRData" format="rdata" label="GeneSet object from MSigDB/KEGG" />
142 </outputs>
143
144 <tests>
145 <test>
146 <conditional name="input_args">
147 <param name="source" value="KEGG" />
148 <param name="organism" value="hsa" />
149 </conditional>
150 <output name="outputRData" file="geneSet.RData"/>
151 </test>
152 </tests>
153
154 <help><![CDATA[
155
156 .. class:: infomark
157
158 **What it does**
159
160 This is a tool built to get a 'geneSetCollection' R object from the MSigDB or KEGG database.
161
162 If the gene sets source is KEGG_, it will only receive a KEGG organism code and output an Rdata file which has a `geneSet` object containing all KEGG pathways with their Entrez gene ID.
163
164 If the gene sets source is MSigDB_, you must assign specific species and categories to define the Gene Set collection. Again, the output is an Rdata file which has a `geneSet` object.
165
166 -----
167
168 **More Information**
169
170 **MSigDB Gene Set Colletions**
171
172 The MSigDB_ gene sets are divided into 9 major collections:
173
174 * **H: hallmark gene sets** are coherently expressed signatures derived by aggregating many MSigDB gene sets to represent well-defined biological states or processes.
175 * **C1: positional gene sets** for each human chromosome and cytogenetic band.
176 * **C2: curated gene sets** are from online pathway databases, publications in PubMed, and knowledge of domain experts.
177 * **C3: motif gene sets** are based on conserved cis-regulatory motifs from a comparative analysis of the human, mouse, rat, and dog genomes.
178 * **C4: computational gene sets** are defined by mining large collections of cancer-oriented microarray data.
179 * **C5: GO gene sets** consist of genes annotated by the same GO terms.
180 * **C6: oncogenic gene sets** are defined directly from microarray gene expression data from cancer gene perturbations.
181 * **C7: immunologic gene sets** are defined directly from microarray gene expression data from immunologic studies.
182 * **C8: cell type signature gene sets** curated from cluster markers identified in single-cell sequencing studies of human tissue.
183
184 .. _MSigDB: http://software.broadinstitute.org/gsea/msigdb
185 .. _KEGG: http://www.genome.jp/kegg/
186 ]]></help>
187
188 <citations>
189 <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
190 author = {Xiaowei Huang and Songqing Mei and Antonio Mora},
191 title = {Galaxy-GSA –A suite of tools for advanced gene set analysis in Galaxy},
192 journal = {Bioinformatics},
193 year = {2021},
194 volume = {8},
195 pages = {1-3}
196 }</citation>
197 </citations>
198
199 </tool>