Mercurial > repos > xuebing > sharplabtool

comparison tools/human_genome_variation/ctd.xml @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 <tool id="hgv_ctdBatch" name="CTD" version="1.0.0">
2 <description>analysis of chemicals, diseases, or genes</description>
3
4 <command interpreter="perl">
5 ctd.pl $input $numerical_column $inType.inputType
6 #if $inType.inputType == "disease"
7 $inType.report ANY
8 #else if $inType.reportType.report == "cgixns"
9 $inType.reportType.report $inType.reportType.actType
10 #else
11 $inType.reportType.report ANY
12 #end if
13 $out_file1
14 </command>
15
16 <inputs>
17 <param name="input" type="data" format="tabular" label="Dataset" />
18 <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" />
19 <conditional name="inType">
20 <param name="inputType" label="Identifier type" type="select">
21 <option value="chem">Chemicals (MeSH names, synonyms or accession IDs, or CAS RNs)</option>
22 <option value="disease">Diseases (MeSH or OMIM names, synonyms or accession IDs)</option>
23 <option value="gene" selected="true">Genes (NCBI official symbols or accession IDs)</option>
24 </param>
25 <when value="chem">
26 <conditional name='reportType'>
27 <param name="report" label="Data to extract" type="select">
28 <option value="cgixns">Curated chemical-gene interactions</option>
29 <option value="genes">Curated gene associations</option>
30 <option value="pathways">Pathway associations</option>
31 <option value="diseases" selected="true">All disease relationships</option>
32 <option value="diseases_direct"> Direct disease relationships only</option>
33 <option value="diseases_inferred"> Inferred disease relationships only</option>
34 <option value="go">All GO associations</option>
35 <option value="go_p"> GO biological Processes only</option>
36 <option value="go_f"> GO molecular Functions only</option>
37 <option value="go_c"> GO cellular Components only</option>
38 </param>
39 <when value="genes">
40 <!-- do nothing -->
41 </when>
42 <when value="pathways">
43 <!-- do nothing -->
44 </when>
45 <when value="diseases">
46 <!-- do nothing -->
47 </when>
48 <when value="diseases_direct">
49 <!-- do nothing -->
50 </when>
51 <when value="diseases_inferred">
52 <!-- do nothing -->
53 </when>
54 <when value="go">
55 <!-- do nothing -->
56 </when>
57 <when value="go_p">
58 <!-- do nothing -->
59 </when>
60 <when value="go_f">
61 <!-- do nothing -->
62 </when>
63 <when value="go_c">
64 <!-- do nothing -->
65 </when>
66 <when value="cgixns">
67 <param name="actType" label="Interaction type" type="select">
68 <option value="ANY">ANY</option>
69 <option value="abundance">abundance</option>
70 <option value="activity">activity</option>
71 <option value="binding">binding</option>
72 <option value="cotreatment">cotreatment</option>
73 <option value="expression">expression</option>
74 <option value="folding">folding</option>
75 <option value="localization">localization</option>
76 <option value="metabolic processing">metabolic processing</option>
77 <option value="acetylation">- acetylation</option>
78 <option value="acylation">- acylation</option>
79 <option value="alkylation">- alkylation</option>
80 <option value="amination">- amination</option>
81 <option value="carbamoylation">- carbamoylation</option>
82 <option value="carboxylation">- carboxylation</option>
83 <option value="chemical synthesis">- chemical synthesis</option>
84 <option value="degradation">- degradation</option>
85 <option value="cleavage"> - cleavage</option>
86 <option value="hydrolysis"> - hydrolysis</option>
87 <option value="ethylation">- ethylation</option>
88 <option value="glutathionylation">- glutathionylation</option>
89 <option value="glycation">- glycation</option>
90 <option value="glycosylation">- glycosylation</option>
91 <option value="N-linked glycosylation"> - N-linked glycosylation</option>
92 <option value="O-linked glycosylation"> - O-linked glycosylation</option>
93 <option value="glucuronidation"> - glucuronidation</option>
94 <option value="hydroxylation">- hydroxylation</option>
95 <option value="lipidation">- lipidation</option>
96 <option value="farnesylation"> - farnesylation</option>
97 <option value="geranolyation"> - geranolyation</option>
98 <option value="myristolylation"> - myristolylation</option>
99 <option value="palmitoylation"> - palmitoylation</option>
100 <option value="prenylation"> - prenylation</option>
101 <option value="methylation">- methylation</option>
102 <option value="nitrosation">- nitrosation</option>
103 <option value="nucleotidylation">- nucleotidylation</option>
104 <option value="oxidation">- oxidation</option>
105 <option value="phosphorylation">- phosphorylation</option>
106 <option value="reduction">- reduction</option>
107 <option value="ribosylation">- ribosylation</option>
108 <option value="ADP-ribosylation"> - ADP-ribosylation</option>
109 <option value="sulfation">- sulfation</option>
110 <option value="sumoylation">- sumoylation</option>
111 <option value="ubiquitination">- ubiquitination</option>
112 <option value="mutagenesis">mutagenesis</option>
113 <option value="reaction">reaction</option>
114 <option value="response to chemical">response to chemical</option>
115 <option value="splicing">splicing</option>
116 <option value="stability">stability</option>
117 <option value="transport">transport</option>
118 <option value="secretion">- secretion</option>
119 <option value="export"> - export</option>
120 <option value="uptake">- uptake</option>
121 <option value="import"> - import</option>
122 </param>
123 </when>
124 </conditional>
125 </when>
126 <when value="disease">
127 <param name="report" label="Data to extract" type="select">
128 <option value="chems">Chemical associations</option>
129 <option value="chems_direct">Chemical associations direct relationships only</option>
130 <option value="chems_inferred">Chemical associations inferred relationships only</option>
131 <option value="genes">Curated gene associations</option>
132 <option value="pathways">Pathway associations</option>
133 </param>
134 </when>
135 <when value="gene">
136 <conditional name='reportType'>
137 <param name="report" label="Data to extract" type="select">
138 <option value="cgixns">Curated chemical-gene interactions</option>
139 <option value="chems">Curated chemical associations</option>
140 <option value="pathways">Pathway associations</option>
141 <option value="diseases" selected="true">All disease relationships</option>
142 <option value="diseases_direct"> Direct disease relationships only</option>
143 <option value="diseases_inferred"> Inferred disease relationships only</option>
144 <option value="go">All GO associations</option>
145 <option value="go_p"> GO biological Processes only</option>
146 <option value="go_f"> GO molecular Functions only</option>
147 <option value="go_c"> GO cellular Components only</option>
148 </param>
149 <when value="chems">
150 <!-- do nothing -->
151 </when>
152 <when value="pathways">
153 <!-- do nothing -->
154 </when>
155 <when value="diseases">
156 <!-- do nothing -->
157 </when>
158 <when value="diseases_direct">
159 <!-- do nothing -->
160 </when>
161 <when value="diseases_inferred">
162 <!-- do nothing -->
163 </when>
164 <when value="go">
165 <!-- do nothing -->
166 </when>
167 <when value="go_p">
168 <!-- do nothing -->
169 </when>
170 <when value="go_f">
171 <!-- do nothing -->
172 </when>
173 <when value="go_c">
174 <!-- do nothing -->
175 </when>
176 <when value="cgixns">
177 <param name="actType" label="Interaction type" type="select">
178 <option value="ANY">ANY</option>
179 <option value="abundance">abundance</option>
180 <option value="activity">activity</option>
181 <option value="binding">binding</option>
182 <option value="cotreatment">cotreatment</option>
183 <option value="expression">expression</option>
184 <option value="folding">folding</option>
185 <option value="localization">localization</option>
186 <option value="metabolic processing">metabolic processing</option>
187 <option value="acetylation">- acetylation</option>
188 <option value="acylation">- acylation</option>
189 <option value="alkylation">- alkylation</option>
190 <option value="amination">- amination</option>
191 <option value="carbamoylation">- carbamoylation</option>
192 <option value="carboxylation">- carboxylation</option>
193 <option value="chemical synthesis">- chemical synthesis</option>
194 <option value="degradation">- degradation</option>
195 <option value="cleavage"> - cleavage</option>
196 <option value="hydrolysis"> - hydrolysis</option>
197 <option value="ethylation">- ethylation</option>
198 <option value="glutathionylation">- glutathionylation</option>
199 <option value="glycation">- glycation</option>
200 <option value="glycosylation">- glycosylation</option>
201 <option value="N-linked glycosylation"> - N-linked glycosylation</option>
202 <option value="O-linked glycosylation"> - O-linked glycosylation</option>
203 <option value="glucuronidation"> - glucuronidation</option>
204 <option value="hydroxylation">- hydroxylation</option>
205 <option value="lipidation">- lipidation</option>
206 <option value="farnesylation"> - farnesylation</option>
207 <option value="geranolyation"> - geranolyation</option>
208 <option value="myristolylation"> - myristolylation</option>
209 <option value="palmitoylation"> - palmitoylation</option>
210 <option value="prenylation"> - prenylation</option>
211 <option value="methylation">- methylation</option>
212 <option value="nitrosation">- nitrosation</option>
213 <option value="nucleotidylation">- nucleotidylation</option>
214 <option value="oxidation">- oxidation</option>
215 <option value="phosphorylation">- phosphorylation</option>
216 <option value="reduction">- reduction</option>
217 <option value="ribosylation">- ribosylation</option>
218 <option value="ADP-ribosylation"> - ADP-ribosylation</option>
219 <option value="sulfation">- sulfation</option>
220 <option value="sumoylation">- sumoylation</option>
221 <option value="ubiquitination">- ubiquitination</option>
222 <option value="mutagenesis">mutagenesis</option>
223 <option value="reaction">reaction</option>
224 <option value="response to chemical">response to chemical</option>
225 <option value="splicing">splicing</option>
226 <option value="stability">stability</option>
227 <option value="transport">transport</option>
228 <option value="secretion">- secretion</option>
229 <option value="export"> - export</option>
230 <option value="uptake">- uptake</option>
231 <option value="import"> - import</option>
232 </param>
233 </when>
234 </conditional>
235 </when>
236 </conditional>
237 </inputs>
238
239 <outputs>
240 <data format="tabular" name="out_file1" />
241 </outputs>
242
243 <!-- broken for now. will be fixed soon.
244 <tests>
245 <test>
246 <param name="input" ftype="tabular" value="ctdBatchInput.txt" />
247 <param name="numerical_column" value="1" />
248 <param name="inputType" value="gene" />
249 <param name="report" value="diseases" />
250 <output name="out_file1" file="ctdBatchOut.txt" />
251 </test>
252 </tests>
253 -->
254
255 <help>
256 **Dataset formats**
257
258 The input and output datasets are tabular_.
259 (`Dataset missing?`_)
260
261 .. _tabular: ./static/formatHelp.html#tab
262 .. _Dataset missing?: ./static/formatHelp.html
263
264 -----
265
266 **What it does**
267
268 This tool extracts data related to the provided list of identifiers
269 from the Comparative Toxicogenomics Database (CTD). The fields
270 extracted vary with the type of data requested; the first row
271 of the output identifies the columns.
272
273 For the curated chemical-gene interactions, you can also choose the
274 interaction type from the search-and-select box. The choices that
275 start with '-' are a subset of a choice above them; you can chose
276 either the general interaction type or a more specific one.
277
278 Website: http://ctd.mdibl.org/
279
280 -----
281
282 **Examples**
283
284 - input data file:
285 HBB
286
287 - select Column = c1, Identifier type = Genes, and Data to extract = All disease relationships
288
289 - output file::
290
291 #Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs
292 hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900
293 hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741
294 etc.
295
296 Another example:
297
298 - same input file:
299 HBB
300
301 - select Column = c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY
302
303 - output file::
304
305 #Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs
306 hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347
307 hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499
308 etc.
309
310 -----
311
312 **Reference**
313
314 Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. (2009)
315 Comparative Toxicogenomics Database: a knowledgebase and discovery tool for
316 chemical-gene-disease networks.
317 Nucleic Acids Res. 37(Database issue):D786-92. Epub 2008 Sep 9.
318
319 </help>
320 </tool>