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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rdavidwebservice commit b664316c8917dff50de40207c2b3104ed850b90b
author iuc
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&#009;Enrichment Score: \d*\.*\d*"/>
331 </assert_contents>
332 </output>
333 <output name="output2">
334 <assert_contents>
335 <has_line_matching expression="Category&#009;Term&#009;Count&#009;%&#009;PValue&#009;Genes&#009;List Total&#009;Pop Hits&#009;Pop Total&#009;Fold Enrichment&#009;Bonferroni&#009;Benjamini&#009;FDR"/>
336 </assert_contents>
337 </output>
338 <output name="output3">
339 <assert_contents>
340 <has_line_matching expression="ID&#009;Gene Name&#009;Species&#009;BBID&#009;BIOCARTA&#009;COG_ONTOLOGY&#009;GOTERM_BP_DIRECT&#009;GOTERM_CC_DIRECT&#009;GOTERM_MF_DIRECT&#009;INTERPRO&#009;KEGG_PATHWAY&#009;OMIM_DISEASE&#009;PIR_SUPERFAMILY&#009;SMART&#009;UP_KEYWORDS&#009;UP_SEQ_FEATURE"/>
341 </assert_contents>
342 </output>
343 <output name="output4">
344 <assert_contents>
345 <has_line_matching expression="ID&#009;Name&#009;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>