root/galaxy-central/tools/human_genome_variation/ctd.xml

リビジョン 2, 15.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
258The 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
268This tool extracts data related to the provided list of identifiers
269from the Comparative Toxicogenomics Database (CTD).  The fields
270extracted vary with the type of data requested; the first row
271of the output identifies the columns.
272
273For the curated chemical-gene interactions, you can also choose the
274interaction type from the search-and-select box.  The choices that
275start with '-' are a subset of a choice above them; you can chose
276either the general interaction type or a more specific one.
277
278Website: 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
296Another 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
314Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. (2009)
315Comparative Toxicogenomics Database: a knowledgebase and discovery tool for
316chemical-gene-disease networks.
317Nucleic Acids Res. 37(Database issue):D786-92. Epub 2008 Sep 9.
318
319  </help>
320</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。