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comparison rgcca.xml @ 1:6bf48c098d36 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
author iuc
date Sun, 18 Jul 2021 18:02:32 +0000
parents 4809cae1b724
children
comparison
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0:4809cae1b724 1:6bf48c098d36
1 <tool id="rgcca" name="RGCCA" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="rgcca" name="RGCCA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 2
3 <description>performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals.</description> 3 <description>performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals.</description>
4 4
5 <macros> 5 <macros>
6 <import>macro.xml</import> 6 <import>macro.xml</import>
16 <edam_operation>operation_0337</edam_operation> 16 <edam_operation>operation_0337</edam_operation>
17 </edam_operations> 17 </edam_operations>
18 18
19 <requirements> 19 <requirements>
20 <requirement type="package" version="@TOOL_VERSION@">rgccacmd</requirement> 20 <requirement type="package" version="@TOOL_VERSION@">rgccacmd</requirement>
21 <requirement type="package" version="4.1">r-base</requirement>
21 </requirements> 22 </requirements>
22 23
23 <command detect_errors="exit_code"><![CDATA[ 24 <command detect_errors="exit_code"><![CDATA[
24 #set data_paths = ",".join([str(_.file_name) for _ in $blocks]) 25 #set data_paths = ",".join([str(_.file_name) for _ in $blocks])
25 #set data_names = ",".join([str(_.element_identifier).replace(',', '_') for _ in $blocks]) 26 #set data_names = ",".join([str(_.element_identifier).replace(',', '_') for _ in $blocks])
27 #set out_files = str($output_selector).split(",")
26 Rscript '$__tool_directory__/launcher.R' 28 Rscript '$__tool_directory__/launcher.R'
27 --datasets '${data_paths}' 29 --datasets '${data_paths}'
28 --names '${data_names}' 30 --names '${data_names}'
29 --o1 '$individual_plot' --o2 '$corcircle' --o3 '$top_variables' --o4 '$ave' --o5 '$design' --o6 '$individual_table' --o7 '$variable_table' --o8 '$rdata' 31 #if 'individuals' in $out_files
32 --o1 '$individual_plot'
33 #end if
34 #if 'corcircle' in $out_files
35 --o2 '$corcircle'
36 #end if
37 #if 'top_variables' in $out_files
38 --o3 '$top_variables'
39 #end if
40 #if 'ave' in $out_files
41 --o4 '$ave'
42 #end if
43 #if 'design' in $out_files
44 --o5 '$design'
45 #end if
46 #if 'individual_table' in $out_files
47 --o6 '$individual_table'
48 #end if
49 #if 'variable_table' in $out_files
50 --o7 '$variable_table'
51 #end if
52 #if 'rdata' in $out_files
53 --o8 '$rdata'
54 #end if
30 $parse.header 55 $parse.header
31 --separator $parse.separator 56 --separator $parse.separator
32 $analyse.superblock 57 $analyse.superblock
33 $analyse.scale 58 $analyse.scale
34 #if $analyse.tau.bool == 'false' 59 #if $analyse.tau.bool == 'false'
35 --penalty $analyse.tau.value 60 --penalty $analyse.tau.value
36 #else 61 #else
37 --penalty $analyse.tau.bool 62 --penalty $analyse.tau.bool
38 #end if 63 #end if
39 --ncomp $analyse.ncomp 64 --ncomp $analyse.ncomp
40 --scheme $analyse.scheme 65 --scheme $analyse.scheme
41 #if $analyse.method.family == '1' 66 #if $analyse.method.family == '1'
42 --type pca 67 --type pca
43 #else 68 #else
44 --type $analyse.method.type 69 --type $analyse.method.type
45 #end if 70 #end if
46 #if $analyse.connection 71 #if $analyse.connection
47 --connection $analyse.connection 72 --connection $analyse.connection
48 #end if 73 #end if
49 #if $analyse.supervised.learning_mode == 'supervised' 74 #if $analyse.supervised.learning_mode == 'supervised'
50 --response $analyse.supervised.block_response 75 --response $analyse.supervised.block_response
51 #end if 76 #end if
52 #if $graphic.response 77 #if $graphic.response
53 --group $graphic.response 78 --group $graphic.response
54 #end if 79 #end if
55 --compx $graphic.compx 80 --compx $graphic.compx
56 --compy $graphic.compy 81 --compy $graphic.compy
57 --nmark $graphic.nmark 82 --nmark $graphic.nmark
58 $graphic.text 83 $graphic.text
179 204
180 <param name="output_selector" type="select" multiple="true" label="Outputs"> 205 <param name="output_selector" type="select" multiple="true" label="Outputs">
181 <option value="individuals" selected="true">Individual plot</option> 206 <option value="individuals" selected="true">Individual plot</option>
182 <option value="corcircle" selected = "true">Corcircle plot</option> 207 <option value="corcircle" selected = "true">Corcircle plot</option>
183 <option value="top_variables">Top variables plot</option> 208 <option value="top_variables">Top variables plot</option>
184 <option value="ave">Averages plot</option> 209 <option value="ave">Explained variance plot</option>
185 <option value="design">Design plot</option> 210 <option value="design">Design plot</option>
186 <option value="individual_table" selected="true">Individual table</option> 211 <option value="individual_table" selected="true">Individual table</option>
187 <option value="variable_table" selected="true">Variable table</option> 212 <option value="variable_table" selected="true">Variable table</option>
188 <option value="rdata">RData file</option> 213 <option value="rdata">RData file</option>
189 </param> 214 </param>
223 <param name="blocks" value="agriculture.tsv" ftype = "tsv"/> 248 <param name="blocks" value="agriculture.tsv" ftype = "tsv"/>
224 <output name="individual_table"> 249 <output name="individual_table">
225 <assert_contents> 250 <assert_contents>
226 <has_n_columns n="4"/> 251 <has_n_columns n="4"/>
227 <has_line_matching 252 <has_line_matching
228 expression='"agriculture.axis1"\s"agriculture.axis2"\s"superblock.axis1"\s"superblock.axis2"'/> 253 expression='"agriculture.component1"\s"agriculture.component2"\s"superblock.component1"\s"superblock.component2"'/>
229 <has_line_matching 254 <has_line_matching
230 expression='^.+(\s\-?\d+.\d+){4}$'/> 255 expression='^.+(\s\-?\d+.\d+){4}$'/>
231 </assert_contents> 256 </assert_contents>
232 </output> 257 </output>
233 </test> 258 </test>
279 <has_text text="sgcca"/> 304 <has_text text="sgcca"/>
280 </assert_command> 305 </assert_command>
281 </test> 306 </test>
282 307
283 <test expect_num_outputs="8" expect_exit_code="0"> 308 <test expect_num_outputs="8" expect_exit_code="0">
284 <expand macro="output_tests" path="2blocks" compx="3" compy="1"/> 309 <expand macro="output_tests" path="2blocks"/>
285 <param name="blocks" value="agriculture.tsv,politic.tsv"/> 310 <param name="blocks" value="agriculture.tsv,politic.tsv"/>
286 <section name="analyse"> 311 <section name="analyse">
287 <param name="scale" value="false"/> 312 <param name="scale" value="false"/>
288 <conditional name="tau"> 313 <conditional name="tau">
289 <param name="bool" value="false"/> 314 <param name="bool" value="false"/>
322 **Author:** 347 **Author:**
323 Etienne CAMENEN 348 Etienne CAMENEN
324 349
325 350
326 **Contact:** 351 **Contact:**
327 arthur.tenenhaus@centralesupelec.fr 352 etienne.camenen@gmail.com
328 353
329 354
330 **R package:** 355 **R package:**
331 The RGCCA package is available from the CRAN repository (https://cran.r-project.org/web/packages/RGCCA). 356 | The RGCCA package is available from the CRAN repository (v2.1.2; https://cran.r-project.org/web/packages/RGCCA).
357 | This tool is based on a version available on github (v3.0; https://github.com/rgcca-factory/RGCCA).
332 358
333 --------------------------------------------------- 359 ---------------------------------------------------
334 360
335 ================================== 361 ==================================
336 R/SGCCA 362 R/SGCCA
338 364
339 A user-friendly multi-blocks analysis (Regularized Generalized Canonical Correlation Analysis, RGCCA) as described in [1] and [2] with all default settings predefined. The software produces figures to explore the analysis' results: individuals and variables projected on two components of the multi-block analysis, list of top variables and explained variance in the model. 365 A user-friendly multi-blocks analysis (Regularized Generalized Canonical Correlation Analysis, RGCCA) as described in [1] and [2] with all default settings predefined. The software produces figures to explore the analysis' results: individuals and variables projected on two components of the multi-block analysis, list of top variables and explained variance in the model.
340 366
341 **Working example** 367 **Working example**
342 368
343 | From Russett data (RGCCA package): https://github.com/rgcca-factory/RGCCA/tree/master/inst/extdata 369 | From Russett data (RGCCA package): https://github.com/BrainAndSpineInstitute/rgcca_ui/tree/master/inst/extdata
344 | Use *agriculture.tsv* as a block. Add *industry.tsv* and *politic.tsv* as new blocks. *connection.tsv* could be used as a design matrix and *political_system.tsv* as a response variable respectively in analysis and graphic settings. 370 | Use *agriculture.tsv* as a block. Add *industry.tsv* and *politic.tsv* for multiblock analysis. *connection.tsv* could be used as a design matrix and *political_system.tsv* as a response variable respectively in analysis and graphic settings.
345 371
346 **Documentation** 372 **Documentation**
347 373
348 - RGCCA: https://cran.r-project.org/web/packages/RGCCA/vignettes/vignette_RGCCA.pdf 374 - RGCCA: https://cran.r-project.org/web/packages/RGCCA/vignettes/vignette_RGCCA.pdf
349 - accepted input / output formats: https://github.com/rgcca-factory/RGCCA#input-files 375 - accepted input / https://github.com/BrainAndSpineInstitute/rgcca_ui#input-files
350 <!-- - tutorial: https://github.com/BrainAndSpineInstitute/rgcca_galaxy/blob/release/0.2/README.md--> 376 - tutorial: https://github.com/BrainAndSpineInstitute/rgcca_galaxy#readme
351 377
352 </help> 378 </help>
353 379
354 <citations> 380 <citations>
355 <citation type="doi">10.1007/s11336-017-9573-x</citation> 381 <citation type="doi">10.1007/s11336-017-9573-x</citation>