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comparison mixomics_blocksplsda.xml @ 2:c8533e9298e5 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author ppericard
date Fri, 23 Oct 2020 10:15:56 +0000
parents e93350dc99f1
children d4e9f7546dfa
comparison
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1:e93350dc99f1 2:c8533e9298e5
1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="6.12+galaxy0" profile="16.04" workflow_compatible="true"> 1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy1" 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 <requirements> 5 <macros>
6 <requirement type="package" version="6.12">bioconductor-mixomics</requirement> 6 <import>macros.xml</import>
7 <requirement type="package" version="2.0">r-argparse</requirement> 7 <import>macros_mixomics.xml</import>
8 </requirements> 8 </macros>
9 9
10 <!-- <stdio> 10 <expand macro="requirements"/>
11 <exit_code range="1:" level="fatal" /> 11 <expand macro="stdio"/>
12 </stdio> --> 12
13 13 <command detect_errors="aggressive"><![CDATA[
14 <command detect_errors="aggressive"> 14
15 <![CDATA[
16 mkdir outdir 15 mkdir outdir
17 && Rscript 16 && @COMMAND_RSCRIPT@/mixomics_blocksplsda.R
18 ${__tool_directory__}/mixomics_blocksplsda_script.R 17
19 #for $b in $blocks 18 #for $b in $blocks
20 --block 19 --block
21 #if $b.block_name 20 #if $b.block_name
22 ${b.block_name} 21 ${b.block_name}
23 #else 22 #else
25 #end if 24 #end if
26 ${b.keep} 25 ${b.keep}
27 ${b.data_matrix} 26 ${b.data_matrix}
28 ${b.variable_metadata} 27 ${b.variable_metadata}
29 #end for 28 #end for
29
30 --sample_metadata_in ${sample_metadata_in} 30 --sample_metadata_in ${sample_metadata_in}
31 --sample_description_col ${sample_description_col} 31 --sample_description_col ${sample_description_col}
32
32 --ncomp ${adv.ncomp} 33 --ncomp ${adv.ncomp}
33 ${correlation} 34 ${correlation}
34 ##--scheme ${adv.scheme} 35 ##--scheme ${adv.scheme}
35 ##--mode ${adv.mode} 36 ##--mode ${adv.mode}
36 --maxiter ${adv.maxiter} 37 --maxiter ${adv.maxiter}
38 --scale ## always activated hidden param 39 --scale ## always activated hidden param
39 ${adv.check_missing_values} 40 ${adv.check_missing_values}
40 ##--init ${adv.init} 41 ##--init ${adv.init}
41 ##--tol ${adv.tol} 42 ##--tol ${adv.tol}
42 ##${adv.nearzerovar} 43 ##${adv.nearzerovar}
44
43 --rdata_out ${rdata_out} 45 --rdata_out ${rdata_out}
44 ##--sample_metadata_out ${sample_metadata_out} 46 ##--sample_metadata_out ${sample_metadata_out}
45 --variable_metadata_outdir outdir 47 --variable_metadata_outdir outdir
46 ]]> 48
47 </command> 49 @COMMAND_LOG_EXIT@
50
51 ]]></command>
48 52
49 <inputs> 53 <inputs>
50 <repeat name="blocks" title="Blocks"> 54 <repeat name="blocks" title="Blocks">
51 <param name="block_name" type="text" label="Block name" /> 55 <param name="block_name" type="text" label="Block name" />
52 <param name="keep" type="integer" value="0" min="0" 56 <param name="keep" type="integer" value="0" min="0"
71 help="[design] If set to Yes, data integration will take into account correlations between all the blocks (design matrix with diagonal coefficients set to 0 and the rest of the coefficients set to 1)." /> 75 help="[design] If set to Yes, data integration will take into account correlations between all the blocks (design matrix with diagonal coefficients set to 0 and the rest of the coefficients set to 1)." />
72 <section name="adv" title="Advanced Options" expanded="false"> 76 <section name="adv" title="Advanced Options" expanded="false">
73 <param name="ncomp" type="integer" value="2" min="1" 77 <param name="ncomp" type="integer" value="2" min="1"
74 label="Number of components to include in the model" 78 label="Number of components to include in the model"
75 help="[ncomp] Number of new variables (components) computed by the data integration." /> 79 help="[ncomp] Number of new variables (components) computed by the data integration." />
76 <!-- <param name="scheme" type="select" label="Scheme"> 80 <!-- <param name="scheme" type="select" label="Scheme">
77 <option value="horst" selected="true">horst</option> 81 <option value="horst" selected="true">horst</option>
78 <option value="factorial" >factorial</option> 82 <option value="factorial" >factorial</option>
79 <option value="centroid" >centroid</option> 83 <option value="centroid" >centroid</option>
80 </param> 84 </param>
81 <param name="mode" type="select" label="Mode"> 85 <param name="mode" type="select" label="Mode">
85 <option value="classic" >classic</option> 89 <option value="classic" >classic</option>
86 </param> --> 90 </param> -->
87 <param name="maxiter" type="integer" value="100" min="1" 91 <param name="maxiter" type="integer" value="100" min="1"
88 label="Maximum number of iterations" 92 label="Maximum number of iterations"
89 help="[max.iter] Maximum number of iterations performed by block.splsda." /> 93 help="[max.iter] Maximum number of iterations performed by block.splsda." />
90 <!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true" 94 <!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true"
91 label="Scale" 95 label="Scale"
92 help="if checked, each block is standardized to zero means and unit variances" /> --> 96 help="if checked, each block is standardized to zero means and unit variances" /> -->
93 <param name="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true" 97 <param name="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true"
94 label="Check for missing values" 98 label="Check for missing values"
95 help="will raise an error if missing values are found in data matrices" /> 99 help="will raise an error if missing values are found in data matrices" />
96 <!-- <param name="init" type="select" label="Init"> 100 <!-- <param name="init" type="select" label="Init">
97 <option value="svd" selected="true">svd</option> 101 <option value="svd" selected="true">svd</option>
98 <option value="svd.single" >svd.single</option> 102 <option value="svd.single" >svd.single</option>
99 </param> 103 </param>
100 <param name="tol" type="float" value="1e-06" min="0" 104 <param name="tol" type="float" value="1e-06" min="0"
101 label="Convergence stopping value" 105 label="Convergence stopping value"
104 label="Should be set to TRUE in particular for data with many zero values" /> --> 108 label="Should be set to TRUE in particular for data with many zero values" /> -->
105 </section> 109 </section>
106 </inputs> 110 </inputs>
107 111
108 <outputs> 112 <outputs>
109 <data name="rdata_out" format="rdata" label="${tool.name}_output.rdata" /> 113 <data name="rdata_out" format="rdata" label="${tool.name}_output.RData" />
110 <!-- <data name="sample_metadata_out" format="tabular" 114 <!-- <data name="sample_metadata_out" format="tabular"
111 label="${tool.name}_${sample_metadata_in.name}" /> --> 115 label="${tool.name}_${sample_metadata_in.name}" /> -->
112 <collection name="blocks_output" type="list" label="${tool.name}_blocks_output"> 116 <collection name="blocks_output" type="list" label="${tool.name}_blocks_output">
113 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" 117 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv"
114 directory="outdir" format="tabular" /> 118 directory="outdir" format="tabular" />
125 <param name="block_name" value="Block2" /> 129 <param name="block_name" value="Block2" />
126 <param name="data_matrix" value="in_block2_data.tabular" /> 130 <param name="data_matrix" value="in_block2_data.tabular" />
127 </repeat> 131 </repeat>
128 <param name="sample_metadata_in" value="in_sample_meta.tabular" /> 132 <param name="sample_metadata_in" value="in_sample_meta.tabular" />
129 <output name="rdata_out" value="out_rdata.rdata" /> 133 <output name="rdata_out" value="out_rdata.rdata" />
130 <output name="sample_metadata_out" value="out_sample_meta.tabular" /> 134 <!-- <output name="sample_metadata_out" value="out_sample_meta.tabular" /> -->
131 </test> 135 </test>
132 </tests> 136 </tests>
133 137
134 <help> 138 <help><![CDATA[
135 <![CDATA[ 139
136 .. class:: infomark 140 @HELP_AUTHORS@
137
138 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
139
140 ---------------------------------------------------
141
142 .. class:: infomark
143
144 **Please cite**
145
146 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
147 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
148
149 ---------------------------------------------------
150 141
151 ====================== 142 ======================
152 mixOmics blocks.splsda 143 mixOmics blocks.splsda
153 ====================== 144 ======================
154 145
157 ----------- 148 -----------
158 149
159 The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets. 150 The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets.
160 Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis. 151 Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis.
161 152
153 -----------------
154 Workflow position
155 -----------------
156
157 **Downstream tools**
158
159 ======================= ================================== ==========
160 Name Output file Format
161 ======================= ================================== ==========
162 mixOmics.plotIndiv mixomics_blocksplsda_output.RData rdata
163 ----------------------- ---------------------------------- ----------
164 mixOmics.plotVar mixomics_blocksplsda_output.RData rdata
165 ----------------------- ---------------------------------- ----------
166 visCorVar.matCorAddVar mixomics_blocksplsda_output.RData rdata
167 ======================= ================================== ==========
168
169 ---------------------------------------------------
170
162 ----------- 171 -----------
163 Input files 172 Input files
164 ----------- 173 -----------
165 174
166 For each block (min 2 blocks): 175 For each block (min 2 blocks):
167 ============================== 176 ------------------------------
168 177
169 +------------------------------+------------+ 178 +------------------------------+------------+
170 | Parameter : num + label | Format | 179 | Parameter : num + label | Format |
171 +==============================+============+ 180 +==============================+============+
172 | 1 : Data matrix | tabular | 181 | 1 : Data matrix | tabular |
186 * Rows = variables, Columns = metadata 195 * Rows = variables, Columns = metadata
187 * First row = metadata column names 196 * First row = metadata column names
188 * First column = variables names. MUST be the same and in the same order than in the associated data matrix 197 * First column = variables names. MUST be the same and in the same order than in the associated data matrix
189 198
190 Global input files: 199 Global input files:
191 =================== 200 -------------------
192 201
193 +-----------------------------+------------+ 202 +-----------------------------+------------+
194 | Parameter : num + label | Format | 203 | Parameter : num + label | Format |
195 +=============================+============+ 204 +=============================+============+
196 | 1 : Samples metadata | tabular | 205 | 1 : Samples metadata | tabular |
207 ---------- 216 ----------
208 Parameters 217 Parameters
209 ---------- 218 ----------
210 219
211 For each block (min 2 blocks): 220 For each block (min 2 blocks):
212 ============================== 221 ------------------------------
213 222
214 Block name 223 Block name
215 Name of the block. If not provided, this will default to the input filename 224 Name of the block. If not provided, this will default to the input filename
216 225
217 Number of variables to select for each component 226 Number of variables to select for each component
218 If set to 0 (default), all variables will be considered in the model 227 If set to 0 (default), all variables will be considered in the model
219 228
220 Global parameters: 229 Global parameters:
221 ================== 230 ------------------
222 231
223 Sample description column number 232 Sample description column number
224 233
225 Number of components to include in the model 234 Number of components to include in the model
226 235
227 Correlation between all blocks 236 Correlation between all blocks
228 237
229 Advanced options: 238 Advanced options:
230 ================= 239 -----------------
231 240
232 Scheme 241 Scheme
233 242
234 Mode 243 Mode
235 244
240 Init 249 Init
241 250
242 Convergence stopping value (tol) 251 Convergence stopping value (tol)
243 252
244 Near zero var 253 Near zero var
254
255
256 @HELP_MANUAL@
245 257
246 ------------ 258 ------------
247 Output files 259 Output files
248 ------------ 260 ------------
249 261
250 mixomics_blocksplsda_output.rdata 262 mixomics_blocksplsda_output.RData
251 | rData output 263 | RData output
252 | Contains the `mixomics_result` R object containing the result of the block.splsda function 264 | Contains the `mixomics_result` R object containing the result of the block.splsda function
253
254 mixomics_blocksplsda_{input_sample_metadata_name}
255 | tabular output
256 | Identical to the input Sample metadata file with appended columns from the result of block.splsda function
257 265
258 mixomics_blocksplsda_blocks_output 266 mixomics_blocksplsda_blocks_output
259 A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block 267 A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block
260 268
261 ]]> 269 ]]></help>
262 </help> 270
263 271 <expand macro="citations" />
264 <citations>
265 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
266 </citations>
267 272
268 </tool> 273 </tool>