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date Tue, 20 Aug 2013 09:36:33 -0400
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1 <tool id="ctdBatch_1" name="CTD" version="1.0.0">
2 <description>analysis of chemicals, diseases, or genes</description>
3 <command interpreter="perl">#if $inType.inputType=="disease" #ctd.pl $input $numerical_column $inType.inputType $inType.report ANY $out_file1
4 #else if $inType.reportType.report=="cgixns" #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report "$inType.reportType.actType" $out_file1
5 #else #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report ANY $out_file1
6 #end if</command>
7 <inputs>
8 <param name="input" type="data" format="tabular" label="Dataset" />
9 <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" />
10 <conditional name="inType">
11 <param name="inputType" label="Identifier type" type="select">
12 <option value="chem">Chemicals (MeSH names, synonyms or accession IDs, or CAS RNs)</option>
13 <option value="disease">Diseases (MeSH or OMIM names, synonyms or accession IDs)</option>
14 <option value="gene" selected="true">Genes (NCBI official symbols or accession IDs)</option>
15 </param>
16 <when value="chem">
17 <conditional name='reportType'>
18 <param name="report" label="Data to extract" type="select">
19 <option value="cgixns">Curated chemical-gene interactions</option>
20 <option value="genes">Curated gene associations</option>
21 <option value="pathways_inferred">Inferred pathway associations</option>
22 <option value="pathways_enriched">Enriched pathway associations</option>
23 <option value="diseases" selected="true">All disease relationships</option>
24 <option value="diseases_curated"> Curated disease relationships only</option>
25 <option value="diseases_inferred"> Inferred disease relationships only</option>
26 <option value="go">All GO associations</option>
27 <option value="go_enriched">Enriched GO associations only</option>
28 </param>
29 <when value="genes">
30 <!-- do nothing -->
31 </when>
32 <when value="pathways_inferred">
33 <!-- do nothing -->
34 </when>
35 <when value="pathways_enriched">
36 <!-- do nothing -->
37 </when>
38 <when value="diseases">
39 <!-- do nothing -->
40 </when>
41 <when value="diseases_curated">
42 <!-- do nothing -->
43 </when>
44 <when value="diseases_inferred">
45 <!-- do nothing -->
46 </when>
47 <when value="go">
48 <!-- do nothing -->
49 </when>
50 <when value="go_enriched">
51 <!-- do nothing -->
52 </when>
53 <when value="cgixns">
54 <param name="actType" label="Interaction type" type="select">
55 <option value="ANY">ANY</option>
56 <option value="abundance">abundance</option>
57 <option value="activity">activity</option>
58 <option value="binding">binding</option>
59 <option value="cotreatment">cotreatment</option>
60 <option value="expression">expression</option>
61 <option value="folding">folding</option>
62 <option value="localization">localization</option>
63 <option value="metabolic processing">metabolic processing</option>
64 <option value="acetylation">- acetylation</option>
65 <option value="acylation">- acylation</option>
66 <option value="alkylation">- alkylation</option>
67 <option value="amination">- amination</option>
68 <option value="carbamoylation">- carbamoylation</option>
69 <option value="carboxylation">- carboxylation</option>
70 <option value="chemical synthesis">- chemical synthesis</option>
71 <option value="degradation">- degradation</option>
72 <option value="cleavage"> - cleavage</option>
73 <option value="hydrolysis"> - hydrolysis</option>
74 <option value="ethylation">- ethylation</option>
75 <option value="glutathionylation">- glutathionylation</option>
76 <option value="glycation">- glycation</option>
77 <option value="glycosylation">- glycosylation</option>
78 <option value="N-linked glycosylation"> - N-linked glycosylation</option>
79 <option value="O-linked glycosylation"> - O-linked glycosylation</option>
80 <option value="glucuronidation"> - glucuronidation</option>
81 <option value="hydroxylation">- hydroxylation</option>
82 <option value="lipidation">- lipidation</option>
83 <option value="farnesylation"> - farnesylation</option>
84 <option value="geranolyation"> - geranolyation</option>
85 <option value="myristolylation"> - myristolylation</option>
86 <option value="palmitoylation"> - palmitoylation</option>
87 <option value="prenylation"> - prenylation</option>
88 <option value="methylation">- methylation</option>
89 <option value="nitrosation">- nitrosation</option>
90 <option value="nucleotidylation">- nucleotidylation</option>
91 <option value="oxidation">- oxidation</option>
92 <option value="phosphorylation">- phosphorylation</option>
93 <option value="reduction">- reduction</option>
94 <option value="ribosylation">- ribosylation</option>
95 <option value="ADP-ribosylation"> - ADP-ribosylation</option>
96 <option value="sulfation">- sulfation</option>
97 <option value="sumoylation">- sumoylation</option>
98 <option value="ubiquitination">- ubiquitination</option>
99 <option value="mutagenesis">mutagenesis</option>
100 <option value="reaction">reaction</option>
101 <option value="response to chemical">response to chemical</option>
102 <option value="splicing">splicing</option>
103 <option value="stability">stability</option>
104 <option value="transport">transport</option>
105 <option value="secretion">- secretion</option>
106 <option value="export"> - export</option>
107 <option value="uptake">- uptake</option>
108 <option value="import"> - import</option>
109 </param>
110 </when>
111 </conditional>
112 </when>
113 <when value="disease">
114 <param name="report" label="Data to extract" type="select">
115 <option value="chems">Chemical associations</option>
116 <option value="chems_curated">Curated chemical associations only</option>
117 <option value="chems_inferred">Inferred chemical associations only</option>
118 <option value="genes">Gene associations</option>
119 <option value="genes_curated">Curated gene associations</option>
120 <option value="genes_inferred">Inferred gene associations</option>
121 <option value="pathways_inferred">Inferred pathway associations</option>
122 </param>
123 </when>
124 <when value="gene">
125 <conditional name='reportType'>
126 <param name="report" label="Data to extract" type="select">
127 <option value="cgixns">Curated chemical-gene interactions</option>
128 <option value="chems_curated">Curated chemical associations</option>
129 <option value="pathways_curated">Curated pathway associations</option>
130 <option value="diseases" selected="true">All disease relationships</option>
131 <option value="diseases_curated"> Curated disease relationships only</option>
132 <option value="diseases_inferred"> Inferred disease relationships only</option>
133 <option value="go">All GO associations</option>
134 </param>
135 <when value="chems_curated">
136 <!-- do nothing -->
137 </when>
138 <when value="pathways_curated">
139 <!-- do nothing -->
140 </when>
141 <when value="diseases">
142 <!-- do nothing -->
143 </when>
144 <when value="diseases_curated">
145 <!-- do nothing -->
146 </when>
147 <when value="diseases_inferred">
148 <!-- do nothing -->
149 </when>
150 <when value="go">
151 <!-- do nothing -->
152 </when>
153 <when value="cgixns">
154 <param name="actType" label="Interaction type" type="select">
155 <option value="ANY">ANY</option>
156 <option value="abundance">abundance</option>
157 <option value="activity">activity</option>
158 <option value="binding">binding</option>
159 <option value="cotreatment">cotreatment</option>
160 <option value="expression">expression</option>
161 <option value="folding">folding</option>
162 <option value="localization">localization</option>
163 <option value="metabolic processing">metabolic processing</option>
164 <option value="acetylation">- acetylation</option>
165 <option value="acylation">- acylation</option>
166 <option value="alkylation">- alkylation</option>
167 <option value="amination">- amination</option>
168 <option value="carbamoylation">- carbamoylation</option>
169 <option value="carboxylation">- carboxylation</option>
170 <option value="chemical synthesis">- chemical synthesis</option>
171 <option value="degradation">- degradation</option>
172 <option value="cleavage"> - cleavage</option>
173 <option value="hydrolysis"> - hydrolysis</option>
174 <option value="ethylation">- ethylation</option>
175 <option value="glutathionylation">- glutathionylation</option>
176 <option value="glycation">- glycation</option>
177 <option value="glycosylation">- glycosylation</option>
178 <option value="N-linked glycosylation"> - N-linked glycosylation</option>
179 <option value="O-linked glycosylation"> - O-linked glycosylation</option>
180 <option value="glucuronidation"> - glucuronidation</option>
181 <option value="hydroxylation">- hydroxylation</option>
182 <option value="lipidation">- lipidation</option>
183 <option value="farnesylation"> - farnesylation</option>
184 <option value="geranolyation"> - geranolyation</option>
185 <option value="myristolylation"> - myristolylation</option>
186 <option value="palmitoylation"> - palmitoylation</option>
187 <option value="prenylation"> - prenylation</option>
188 <option value="methylation">- methylation</option>
189 <option value="nitrosation">- nitrosation</option>
190 <option value="nucleotidylation">- nucleotidylation</option>
191 <option value="oxidation">- oxidation</option>
192 <option value="phosphorylation">- phosphorylation</option>
193 <option value="reduction">- reduction</option>
194 <option value="ribosylation">- ribosylation</option>
195 <option value="ADP-ribosylation"> - ADP-ribosylation</option>
196 <option value="sulfation">- sulfation</option>
197 <option value="sumoylation">- sumoylation</option>
198 <option value="ubiquitination">- ubiquitination</option>
199 <option value="mutagenesis">mutagenesis</option>
200 <option value="reaction">reaction</option>
201 <option value="response to chemical">response to chemical</option>
202 <option value="splicing">splicing</option>
203 <option value="stability">stability</option>
204 <option value="transport">transport</option>
205 <option value="secretion">- secretion</option>
206 <option value="export"> - export</option>
207 <option value="uptake">- uptake</option>
208 <option value="import"> - import</option>
209 </param>
210 </when>
211 </conditional>
212 </when>
213 </conditional>
214 </inputs>
215 <outputs>
216 <data format="tabular" name="out_file1" />
217 </outputs>
218 <tests>
219 <test>
220 <param name="input" ftype="tabular" value="ctdBatchInput.txt" />
221 <param name="numerical_column" value="1" />
222 <param name="inputType" value="gene" />
223 <param name="report" value="diseases" />
224 <output name="out_file1" file="ctdBatchOut.txt" />
225 </test>
226 </tests>
227 <help>
228
229 **Dataset formats**
230
231 The input and output datasets are tabular_.
232
233 -----
234
235 **What it does**
236
237 This tool extracts data related to the provided list of identifiers
238 from the Comparative Toxicogenomics Database (CTD). The fields
239 extracted vary with the type of data requested; the first row
240 of the output identifies the columns.
241
242 For the curated chemical-gene interactions, you can also choose the
243 interaction type from the search-and-select box. The choices that
244 start with '-' are a subset of a choice above them; you can chose
245 either the general interaction type or a more specific one.
246
247 Home page: http://ctdbase.org
248
249 .. _tabular: ${static_path}/formatHelp.html#tab
250
251 -----
252
253 **Examples**
254
255 - input data file:
256 HBB
257
258 - select column c1, Identifier type = Genes, and Data to extract = All disease relationships
259
260 - output file::
261
262 #Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs
263 hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900
264 hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741
265 etc.
266
267 Another example:
268
269 - same input file:
270 HBB
271
272 - select column c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY
273
274 - output file::
275
276 #Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs
277 hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347
278 hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499
279 etc.
280
281 -----
282
283 **Reference**
284
285 Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical.gene.disease networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92.
286
287
288 </help>
289 </tool>