Mercurial > repos > iuc > rdavidwebservice
comparison rdavidwebservice.xml @ 0:5aa52484bef2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rdavidwebservice commit b664316c8917dff50de40207c2b3104ed850b90b
author | iuc |
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date | Thu, 23 May 2019 13:44:50 -0400 |
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1 <tool id="rdavidwebservice" name="RDAVIDWebService" version="@TOOL_VERSION@"> | |
2 <description> | |
3 Run functional annotation using DAVID | |
4 </description> | |
5 <macros> | |
6 <import>macros.xml</import> | |
7 </macros> | |
8 <requirements> | |
9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-rdavidwebservice</requirement> | |
10 </requirements> | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 cat '$script' && | |
13 Rscript '$script' | |
14 ]]></command> | |
15 <configfiles> | |
16 <configfile name="script"><![CDATA[ | |
17 ## Setup R error handling to go to stderr | |
18 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) | |
19 ## Unify locale settings | |
20 loc <- Sys.setlocale("LC_MESSAGES", "C.UTF-8") | |
21 ## Import libraries | |
22 library(RDAVIDWebService) | |
23 | |
24 gene_list <- scan('$input1', what="character") | |
25 gene_identifier_type <- '$identifier1' | |
26 | |
27 #if str('$__user_email__') != "": | |
28 email <- '$__user_email__' | |
29 #else: | |
30 email <- 'galaxy_user@galaxy.org' | |
31 #end if | |
32 | |
33 david <- DAVIDWebService(email=email, url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/") | |
34 | |
35 geneList <- addList(david, gene_list, idType=gene_identifier_type, | |
36 listName="genelist", listType="Gene") | |
37 | |
38 #if str($background.background_selector) == "with_background": | |
39 background_list <- scan('$background.input2', what="character") | |
40 background_identifier_type <- '$background.identifier2' | |
41 background <- addList(david, background_list, idType=background_identifier_type, | |
42 listName="backgroundlist",listType="Background") | |
43 #end if | |
44 | |
45 #if str($AnnotationCategories.setAnnotationCategories) == "Yes": | |
46 annocategories <- c('$AnnotationCategories.Disease', '$AnnotationCategories.Functional_Categories', '$AnnotationCategories.Gene_Ontology', '$AnnotationCategories.General_Annotations', '$AnnotationCategories.Literature', '$AnnotationCategories.Main_Accessions', '$AnnotationCategories.Pathways', '$AnnotationCategories.Protein_Domains', '$AnnotationCategories.Tissue_Expression') | |
47 annocategories <- annocategories[annocategories != 'None'] | |
48 annocategories <- unlist(strsplit(annocategories, split = ",")) | |
49 setAnnotationCategories(david, annocategories) | |
50 #end if | |
51 | |
52 #if str($FunctionalAnnotationCluster.set_FACluster_params) == "Yes": | |
53 getClusterReportFile(david, '$output1', | |
54 kappa = as.integer('$FunctionalAnnotationCluster.kappa'), | |
55 overlap = as.integer('$FunctionalAnnotationCluster.overlap'), | |
56 initialSeed = as.integer('$FunctionalAnnotationCluster.initialSeed'), | |
57 finalSeed = as.integer('$FunctionalAnnotationCluster.finalSeed'), | |
58 linkage = as.double('$FunctionalAnnotationCluster.linkage')) | |
59 #end if | |
60 | |
61 #if str($FunctionalAnnotationChart.set_FAChart_params) == "Yes" : | |
62 getFunctionalAnnotationChartFile(david, '$output2', | |
63 count = as.integer('$FunctionalAnnotationChart.count'), | |
64 threshold = as.double('$FunctionalAnnotationChart.threshold')) | |
65 #end if | |
66 | |
67 #if str($FunctionalAnnotationTable.set_FATable_params) == "Yes": | |
68 getFunctionalAnnotationTableFile(david, '$output3') | |
69 #end if | |
70 | |
71 #if str($GeneListReport.set_GLReport_params) == "Yes": | |
72 getGeneListReportFile(david, '$output4') | |
73 #end if | |
74 ]]></configfile> | |
75 </configfiles> | |
76 <inputs> | |
77 <param name="input1" type="data" format="txt" label="Select gene list"/> | |
78 <param name="identifier1" type="select" label="Select gene list identifier type"> | |
79 <expand macro="identifier_options" /> | |
80 </param> | |
81 <param name="email" type="text" label="I acknowledge that this services will send my galaxy_user email address to an external service: DAVIDWebService. Please confirm with 'yes'." help="E-Mail has to be registered at https://david.ncifcrf.gov/webservice/register.htm in order to get access to DAVID (webservice)"> | |
82 <validator type="regex" message="You need to agree the terms to continue by typing 'yes'">^'*[Yy]es'*$</validator> | |
83 </param> | |
84 <conditional name="background"> | |
85 <param name="background_selector" type="select" label="Background" help="Default: entire species as background"> | |
86 <option value="without_background">Use default Background</option> | |
87 <option value="with_background">Use specify Background</option> | |
88 </param> | |
89 <when value="with_background"> | |
90 <param name="input2" type="data" format="txt" label="Select gene list for background"/> | |
91 <param name="identifier2" type="select" label="Select background list identifier type"> | |
92 <expand macro="identifier_options" /> | |
93 </param> | |
94 </when> | |
95 <when value="without_background"> | |
96 </when> | |
97 </conditional> | |
98 <conditional name="AnnotationCategories"> | |
99 <param name="setAnnotationCategories" type="select" label="Annotation Categories" help="Default: OMIM_DISEASE, COG_ONTOLOGY, UP_KEYWORDS, UP_SEQ_FEATURE, GOTERM_BP_DIRECT, GOTERM_MF_DIRECT, GOTERM_CC_DIRECT, BBID, BIOCARTA, KEGG_PATHWAY, INTERPRO, PIR_SUPERFAMILY, SMART"> | |
100 <option value="without_AnnotationCategories">Use default Annotation Categories</option> | |
101 <option value="with_AnnotationCategories">Use specify Annotation Categories</option> | |
102 </param> | |
103 <when value="with_AnnotationCategories"> | |
104 <param name="Disease" type="select" display="checkboxes" multiple="true" label="Disease"> | |
105 <option value="GAD_DISEASE">GAD_DISEASE</option> | |
106 <option value="GAD_DISEASE_CLASS">GAD_DISEASE_CLASS</option> | |
107 <option value="OMIM_DISEASE">OMIM_DISEASE</option> | |
108 </param> | |
109 <param name="Functional_Categories" type="select" display="checkboxes" multiple="true" label="Functional_Categories"> | |
110 <option value="COG_ONTOLOGY">COG_ONTOLOGY</option> | |
111 <option value="PIR_SEQ_FEATURE">PIR_SEQ_FEATURE</option> | |
112 <option value="SP_COMMENT_TYPE">SP_COMMENT_TYPE</option> | |
113 <option value="UP_KEYWORDS">UP_KEYWORDS</option> | |
114 <option value="UP_SEQ_FEATURE">UP_SEQ_FEATURE</option> | |
115 </param> | |
116 <param name="Gene_Ontology" type="select" display="checkboxes" multiple="true" label="Gene_Ontology"> | |
117 <option value="GOTERM_BP_1">GOTERM_BP_1</option> | |
118 <option value="GOTERM_BP_2">GOTERM_BP_2</option> | |
119 <option value="GOTERM_BP_3">GOTERM_BP_3</option> | |
120 <option value="GOTERM_BP_4">GOTERM_BP_4</option> | |
121 <option value="GOTERM_BP_5">GOTERM_BP_5</option> | |
122 <option value="GOTERM_BP_ALL">GOTERM_BP_ALL</option> | |
123 <option value="GOTERM_BP_DIRECT">GOTERM_BP_DIRECT</option> | |
124 <option value="GOTERM_BP_FAT" selected="True">GOTERM_BP_FAT</option> | |
125 <option value="GOTERM_CC_1">GOTERM_CC_1</option> | |
126 <option value="GOTERM_CC_2">GOTERM_CC_2</option> | |
127 <option value="GOTERM_CC_3">GOTERM_CC_3</option> | |
128 <option value="GOTERM_CC_4">GOTERM_CC_4</option> | |
129 <option value="GOTERM_CC_5">GOTERM_CC_5</option> | |
130 <option value="GOTERM_CC_ALL">GOTERM_CC_ALL</option> | |
131 <option value="GOTERM_BP_DIRECT">GOTERM_BP_DIRECT</option> | |
132 <option value="GOTERM_CC_1">GOTERM_CC_1</option> | |
133 <option value="GOTERM_CC_2">GOTERM_CC_2</option> | |
134 <option value="GOTERM_CC_3">GOTERM_CC_3</option> | |
135 <option value="GOTERM_CC_4">GOTERM_CC_4</option> | |
136 <option value="GOTERM_CC_5">GOTERM_CC_5</option> | |
137 <option value="GOTERM_CC_ALL">GOTERM_CC_ALL</option> | |
138 <option value="GOTERM_CC_FAT" selected="True">GOTERM_CC_FAT</option> | |
139 <option value="GOTERM_MF_1">GOTERM_MF_1</option> | |
140 <option value="GOTERM_MF_2">GOTERM_MF_2</option> | |
141 <option value="GOTERM_MF_3">GOTERM_MF_3</option> | |
142 <option value="GOTERM_MF_4">GOTERM_MF_4</option> | |
143 <option value="GOTERM_MF_5">GOTERM_MF_5</option> | |
144 <option value="GOTERM_MF_ALL">GOTERM_MF_ALL</option> | |
145 <option value="GOTERM_MF_FAT" selected="True">GOTERM_MF_FAT</option> | |
146 </param> | |
147 <param name="General_Annotations" type="select" display="checkboxes" multiple="true" label="General_Annotations"> | |
148 <option value="CHROMOSOME">CHROMOSOME</option> | |
149 <option value="CYTOBAND">CYTOBAND</option> | |
150 <option value="ENTREZ_GENE_SUMMARY">ENTREZ_GENE_SUMMARY</option> | |
151 <option value="OFFICIAL_GENE_SYMBOL">OFFICIAL_GENE_SYMBOL</option> | |
152 <option value="PIR_SUMMARY">PIR_SUMMARY</option> | |
153 <option value="SP_COMMENT">SP_COMMENT</option> | |
154 </param> | |
155 <param name="Literature" type="select" display="checkboxes" multiple="true" label="Literature"> | |
156 <option value="GENERIF_SUMMARY">GENERIF_SUMMARY</option> | |
157 <option value="HIV_INTERACTION_PUBMED_ID">HIV_INTERACTION_PUBMED_ID</option> | |
158 <option value="PUBMED_ID">PUBMED_ID</option> | |
159 </param> | |
160 <param name="Main_Accessions" type="select" display="checkboxes" multiple="true" label="Main_Accessions"> | |
161 <option value="ENSEMBL_GENE_ID">ENSEMBL_GENE_ID</option> | |
162 <option value="ENTREZ_GENE_ID">ENTREZ_GENE_ID</option> | |
163 </param> | |
164 <param name="Pathways" type="select" display="checkboxes" multiple="true" label="Pathways"> | |
165 <option value="BBID">BBID</option> | |
166 <option value="BIOCARTA">BIOCARTA</option> | |
167 <option value="EC_NUMBER">EC_NUMBER</option> | |
168 <option value="KEGG_PATHWAY" selected="True">KEGG_PATHWAY</option> | |
169 <option value="REACTOME_PATHWAY">REACTOME_PATHWAY</option> | |
170 </param> | |
171 <param name="Protein_Domains" type="select" display="checkboxes" multiple="true" label="Protein_Domains"> | |
172 <option value="GENE3D">GENE3D</option> | |
173 <option value="INTERPRO">INTERPRO</option> | |
174 <option value="PFAM">PFAM</option> | |
175 <option value="PIR_SUPERFAMILY">PIR_SUPERFAMILY</option> | |
176 <option value="PRINTS">PRINTS</option> | |
177 <option value="PRODOM">PRODOM</option> | |
178 <option value="PROSITE">PROSITE</option> | |
179 <option value="SMART">SMART</option> | |
180 <option value="SUPFAM">SUPFAM</option> | |
181 <option value="TIGRFAMS">TIGRFAMS</option> | |
182 </param> | |
183 <param name="Protein_Interactions" type="select" display="checkboxes" multiple="true" label="Protein_Interactions"> | |
184 <option value="BIOGRID_INTERACTION">BIOGRID_INTERACTION</option> | |
185 <option value="DIP">DIP</option> | |
186 <option value="HIV_INTERACTION">HIV_INTERACTION</option> | |
187 <option value="HIV_INTERACTION_CATEGORY">HIV_INTERACTION_CATEGORY</option> | |
188 <option value="INTACT">INTACT</option> | |
189 <option value="MINT">MINT</option> | |
190 <option value="UCSC_TFBS">UCSC_TFBS</option> | |
191 </param> | |
192 <param name="Tissue_Expression" type="select" display="checkboxes" multiple="true" label="Tissue_Expression"> | |
193 <option value="CGAP_EST_QUARTILE">CGAP_EST_QUARTILE</option> | |
194 <option value="CGAP_SAGE_QUARTILE">CGAP_SAGE_QUARTILE</option> | |
195 <option value="GNF_U133A_QUARTILE">GNF_U133A_QUARTILE</option> | |
196 <option value="UNIGENE_EST_QUARTILE">UNIGENE_EST_QUARTILE</option> | |
197 <option value="UP_TISSUE">UP_TISSUE</option> | |
198 </param> | |
199 </when> | |
200 <when value="without_AnnotationCategories"> | |
201 </when> | |
202 </conditional> | |
203 <conditional name="FunctionalAnnotationCluster"> | |
204 <param name="set_FACluster_params" type="select" label="Functional Annotation Clustering"> | |
205 <option value="Yes">Yes</option> | |
206 <option value="No">No</option> | |
207 </param> | |
208 <when value="Yes"> | |
209 <param name="overlap" type="integer" min="3" max="10" value="3" label="Similarity Term Overlap"/> | |
210 <param name="kappa" type="select" label="Similarity Threshold"> | |
211 <option value="20">0.20</option> | |
212 <option value="25">0.25</option> | |
213 <option value="30">0.30</option> | |
214 <option value="35">0.35</option> | |
215 <option value="40">0.40</option> | |
216 <option value="45">0.45</option> | |
217 <option value="50" selected="True">0.50</option> | |
218 <option value="55">0.55</option> | |
219 <option value="60">0.60</option> | |
220 <option value="65">0.65</option> | |
221 <option value="70">0.70</option> | |
222 <option value="75">0.75</option> | |
223 <option value="80">0.80</option> | |
224 <option value="85">0.85</option> | |
225 <option value="90">0.90</option> | |
226 <option value="95">0.95</option> | |
227 <option value="100">1.00</option> | |
228 </param> | |
229 <param name="initialSeed" type="integer" min="2" max="10" value="3" label="Initial Group Membership"/> | |
230 <param name="finalSeed" type="integer" min="2" max="10" value="3" label="Initial Group Membership"/> | |
231 <param name="linkage" type="select" label="Multiple Linkage Threshold"> | |
232 <option value="0.0">0.00</option> | |
233 <option value="0.05">0.05</option> | |
234 <option value="0.10">0.10</option> | |
235 <option value="0.15">0.15</option> | |
236 <option value="0.20">0.20</option> | |
237 <option value="0.25">0.25</option> | |
238 <option value="0.30">0.30</option> | |
239 <option value="0.35">0.35</option> | |
240 <option value="0.40">0.40</option> | |
241 <option value="0.45">0.45</option> | |
242 <option value="0.50" selected="True">0.50</option> | |
243 <option value="0.55">0.55</option> | |
244 <option value="0.60">0.60</option> | |
245 <option value="0.65">0.65</option> | |
246 <option value="0.70">0.70</option> | |
247 <option value="0.75">0.75</option> | |
248 <option value="0.80">0.80</option> | |
249 <option value="0.85">0.85</option> | |
250 <option value="0.90">0.90</option> | |
251 <option value="0.95">0.95</option> | |
252 <option value="1.0">1.00</option> | |
253 </param> | |
254 </when> | |
255 <when value="No"> | |
256 </when> | |
257 </conditional> | |
258 <conditional name="FunctionalAnnotationChart"> | |
259 <param name="set_FAChart_params" type="select" label="Functional Annotation Chart"> | |
260 <option value="Yes">Yes</option> | |
261 <option value="No" selected="True">No</option> | |
262 </param> | |
263 <when value="Yes"> | |
264 <param name="count" type="integer" label="Count" value="2" /> | |
265 <param name="threshold" type="float" label="EASE" value="0.1" /> | |
266 </when> | |
267 <when value="No"> | |
268 </when> | |
269 </conditional> | |
270 <conditional name="FunctionalAnnotationTable"> | |
271 <param name="set_FATable_params" type="select" label="Functional Annotation Table"> | |
272 <option value="Yes">Yes</option> | |
273 <option value="No" selected="True">No</option> | |
274 </param> | |
275 <when value="Yes"> | |
276 </when> | |
277 <when value="No"> | |
278 </when> | |
279 </conditional> | |
280 <conditional name="GeneListReport"> | |
281 <param name="set_GLReport_params" type="select" label="Gene List Report"> | |
282 <option value="Yes">Yes</option> | |
283 <option value="No" selected="True">No</option> | |
284 </param> | |
285 <when value="Yes"> | |
286 </when> | |
287 <when value="No"> | |
288 </when> | |
289 </conditional> | |
290 </inputs> | |
291 <outputs> | |
292 <data name="output1" format="tabular" label="${tool.name} on ${on_string}: Functional Annotation Cluster"> | |
293 <filter>FunctionalAnnotationCluster['set_FACluster_params'] == 'Yes'</filter> | |
294 </data> | |
295 <data name="output2" format="tabular" label="${tool.name} on ${on_string}: Functional Annotation Chart"> | |
296 <filter>FunctionalAnnotationChart['set_FAChart_params'] == 'Yes'</filter> | |
297 </data> | |
298 <data name="output3" format="tabular" label="${tool.name} on ${on_string}: Functional Annotation Table"> | |
299 <filter>FunctionalAnnotationTable['set_FATable_params'] == 'Yes'</filter> | |
300 </data> | |
301 <data name="output4" format="tabular" label="${tool.name} on ${on_string}: Gene List Report"> | |
302 <filter>GeneListReport['set_GLReport_params'] == 'Yes'</filter> | |
303 </data> | |
304 </outputs> | |
305 <tests> | |
306 <test> | |
307 <param name="input1" value="demolist1" ftype="tabular"/> | |
308 <param name="identifier1" value="AFFYMETRIX_3PRIME_IVT_ID"/> | |
309 <param name="email" value="yes"/> | |
310 <conditional name="AnnotationCategories"> | |
311 <param name="setAnnotationCategories" value="with_AnnotationCategories"/> | |
312 <param name="Disease" value="GAD_DISEASE,GAD_DISEASE_CLASS,OMIM_DISEASE"/> | |
313 <param name="Gene_Ontology" value="GOTERM_MF_FAT,GOTERM_CC_FAT,GOTERM_BP_FAT"/> | |
314 <param name="Pathways" value="KEGG_PATHWAY"/> | |
315 </conditional> | |
316 <conditional name="FunctionalAnnotationCluster"> | |
317 <param name="set_FACluster_params" value="Yes"/> | |
318 </conditional> | |
319 <conditional name="FunctionalAnnotationChart"> | |
320 <param name="set_FAChart_params" value="Yes"/> | |
321 </conditional> | |
322 <conditional name="FunctionalAnnotationTable"> | |
323 <param name="set_FATable_params" value="Yes"/> | |
324 </conditional> | |
325 <conditional name="GeneListReport"> | |
326 <param name="set_GLReport_params" value="Yes"/> | |
327 </conditional> | |
328 <output name="output1"> | |
329 <assert_contents> | |
330 <has_text_matching expression="Annotation Cluster 1	Enrichment Score: \d*\.*\d*"/> | |
331 </assert_contents> | |
332 </output> | |
333 <output name="output2"> | |
334 <assert_contents> | |
335 <has_line_matching expression="Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR"/> | |
336 </assert_contents> | |
337 </output> | |
338 <output name="output3"> | |
339 <assert_contents> | |
340 <has_line_matching expression="ID	Gene Name	Species	BBID	BIOCARTA	COG_ONTOLOGY	GOTERM_BP_DIRECT	GOTERM_CC_DIRECT	GOTERM_MF_DIRECT	INTERPRO	KEGG_PATHWAY	OMIM_DISEASE	PIR_SUPERFAMILY	SMART	UP_KEYWORDS	UP_SEQ_FEATURE"/> | |
341 </assert_contents> | |
342 </output> | |
343 <output name="output4"> | |
344 <assert_contents> | |
345 <has_line_matching expression="ID	Name	Species"/> | |
346 </assert_contents> | |
347 </output> | |
348 </test> | |
349 </tests> | |
350 <help><![CDATA[ | |
351 **What it does** | |
352 | |
353 Retrieve data from the Database for Annotation, Visualization and Integrated Discovery (DAVID) using Web Services into R objects. This tool offers the main functionalities of DAVID website including: | |
354 | |
355 i) user-friendly connectivity to upload gene/background list/s, change gene/background position | |
356 | |
357 ii) Reports of the submitted Gene List, Gene/Term Clusters, Functional Annotation Chart, Functional Annotation Table | |
358 | |
359 | |
360 **Links and registration** | |
361 | |
362 http://david.abcc.ncifcrf.gov/ and | |
363 https://bioconductor.org/packages/release/bioc/html/RDAVIDWebService.html | |
364 | |
365 The used e-mail address has to be registered at https://david.ncifcrf.gov/webservice/register.htm in order to get access to DAVID (WebService) | |
366 | |
367 ]]></help> | |
368 <citations> | |
369 <citation type="doi">10.1093/bioinformatics/btt487</citation> | |
370 <citation type="doi">10.1038/nprot.2008.211</citation> | |
371 </citations> | |
372 </tool> |