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comparison mixomics_blocksplsda.xml @ 5:88c1fd2ac110 draft default tip

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents d4e9f7546dfa
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4:d4e9f7546dfa 5:88c1fd2ac110
1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true"> 1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
2 2
3 <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description> 3 <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
31 --sample_description_col ${sample_description_col} 31 --sample_description_col ${sample_description_col}
32 32
33 --ncomp ${adv.ncomp} 33 --ncomp ${adv.ncomp}
34 ${correlation} 34 ${correlation}
35 ##--scheme ${adv.scheme} 35 ##--scheme ${adv.scheme}
36 ##--mode ${adv.mode}
37 --maxiter ${adv.maxiter} 36 --maxiter ${adv.maxiter}
38 ##${adv.scale} 37 ##${adv.scale}
39 --scale ## always activated hidden param 38 --scale ## always activated hidden param
40 ${adv.check_missing_values} 39 ${adv.check_missing_values}
41 ##--init ${adv.init} 40 ##--init ${adv.init}
77 help="number of new variables (components) computed by the data integration" /> 76 help="number of new variables (components) computed by the data integration" />
78 <!-- <param name="scheme" type="select" label="Scheme"> 77 <!-- <param name="scheme" type="select" label="Scheme">
79 <option value="horst" selected="true">horst</option> 78 <option value="horst" selected="true">horst</option>
80 <option value="factorial" >factorial</option> 79 <option value="factorial" >factorial</option>
81 <option value="centroid" >centroid</option> 80 <option value="centroid" >centroid</option>
82 </param>
83 <param name="mode" type="select" label="Mode">
84 <option value="regression" selected="true">regression</option>
85 <option value="canonical" >canonical</option>
86 <option value="invariant" >invariant</option>
87 <option value="classic" >classic</option>
88 </param> --> 81 </param> -->
89 <param name="maxiter" type="integer" value="100" min="1" 82 <param name="maxiter" type="integer" value="100" min="1"
90 label="Maximum number of iterations" 83 label="Maximum number of iterations"
91 help="maximum number of iterations performed by block.splsda" /> 84 help="maximum number of iterations performed by block.splsda" />
92 <!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true" 85 <!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true"
146 Description 139 Description
147 ----------- 140 -----------
148 141
149 The blocks.splsda function is part of the mixOmics package for exploration and integration of omics datasets. 142 The blocks.splsda function is part of the mixOmics package for exploration and integration of omics datasets.
150 This data integration takes as input parameters different omics datasets 143 This data integration takes as input parameters different omics datasets
151 (transcriptomic, metabolomic, metagenomic, ...) and a response variable (e.g. for a sample, the value of the response 144 (transcriptomics, metabolomics, metagenomics, ...) and a response variable (e.g. for a sample, the value of the response
152 variable is equal to « Treated »  or « Control »). This data integration returns, for each omics dataset, variables 145 variable is equal to « Treated »  or « Control »). This data integration is performed fo the scheme "horst" and the mode "regression". This data integration returns, for each omics dataset, variables
153 which are correlated with the variables of the other omic datasets and the response variable. The other functions of 146 which are correlated with the variables of the other omic datasets and the response variable. The other functions of
154 this pipeline allow visualizing this correlated variables thanks to correlation circles and networks. 147 this pipeline allow visualizing this correlated variables thanks to correlation circles and networks.
155 148
156 ----------------- 149 -----------------
157 Workflow position 150 Workflow position
196 The variables metadata is in tabular format (.tsv). 189 The variables metadata is in tabular format (.tsv).
197 The first colum contains the variables names. 190 The first colum contains the variables names.
198 The first row contains the metadata column names. 191 The first row contains the metadata column names.
199 The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created. 192 The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created.
200 193
201 Variables metadata files are optional.
202 If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
203
204 194
205 Global input files: 195 Global input files:
206 ------------------- 196 -------------------
207 197
208 +-----------------------------+------------+ 198 +-----------------------------+------------+
213 203
214 1. Samples metadata structure 204 1. Samples metadata structure
215 Samples metadata is in tabular format (.tsv). 205 Samples metadata is in tabular format (.tsv).
216 The first column contains the sample names. 206 The first column contains the sample names.
217 The first row contains the metadata column names. 207 The first row contains the metadata column names.
218 Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for integration. 208 Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for data integration.
219 209
220 ---------- 210 ----------
221 Parameters 211 Parameters
222 ---------- 212 ----------
223 213
224 For each block (min 2 blocks):
225 ------------------------------
226
227 Block name
228 Name of the block. If not provided, this will default to the input filename
229
230 Number of variables to select for each component 214 Number of variables to select for each component
231 If set to 0 (default), all variables will be considered in the model 215 tune.block.splsda can be used to set the number of variables to select on each component
232
233 Global parameters:
234 ------------------
235
236 Sample description column number
237
238 Number of components to include in the model
239
240 Correlation between all blocks
241
242 Advanced options:
243 -----------------
244
245 Scheme
246
247 Mode
248
249 Maximum number of iterations
250
251 Scale
252
253 Init
254
255 Convergence stopping value (tol)
256
257 Near zero var
258
259 216
260 @HELP_MANUAL@ 217 @HELP_MANUAL@
261 218
262 ------------ 219 ------------
263 Output files 220 Output files