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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
author ppericard
date Fri, 17 May 2019 05:00:22 -0400
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1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.1.0" profile="16.04" workflow_compatible="true">
2
3 <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description>
4
5 <requirements>
6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
7 <requirement type="package" version="2.0">r-argparse</requirement>
8 </requirements>
9
10 <!-- <stdio>
11 <exit_code range="1:" level="fatal" />
12 </stdio> -->
13
14 <command detect_errors="aggressive">
15 <![CDATA[
16 mkdir outdir
17 && Rscript
18 ${__tool_directory__}/mixomics_blocksplsda_script.R
19 #for $b in $blocks
20 --block
21 #if $b.block_name
22 ${b.block_name}
23 #else
24 ${b.data_matrix.name}
25 #end if
26 ${b.keep}
27 ${b.data_matrix}
28 ${b.variable_metadata}
29 #end for
30 --sample_metadata_in ${sample_metadata_in}
31 --sample_description_col ${sample_description_col}
32 --ncomp ${ncomp}
33 ${correlation}
34 --scheme ${adv.scheme}
35 --mode ${adv.mode}
36 --maxiter ${adv.maxiter}
37 ${adv.scale}
38 --init ${adv.init}
39 --tol ${adv.tol}
40 ${adv.nearzerovar}
41 --rdata_out ${rdata_out}
42 --sample_metadata_out ${sample_metadata_out}
43 --variable_metadata_outdir outdir
44 ]]>
45 </command>
46
47 <inputs>
48 <repeat name="blocks" title="Blocks">
49 <param name="block_name" type="text" label="Block name" />
50 <param name="keep" type="integer" value="0" min="0" label="Number of variables to select for each component" help="Default is to keep all variables" />
51 <param name="data_matrix" type="data" format="tabular" label="Data matrix" help="rows = variables, columns = samples" />
52 <param name="variable_metadata" type="data" format="tabular" optional="true" label="Variables metadata" help="rows = variables" />
53 </repeat>
54 <param name="sample_metadata_in" type="data" format="tabular" label="Samples metadata matrix" />
55 <param name="sample_description_col" type="integer" value="0" min="0" label="Sample description column number" help="Use the last column by default" />
56 <param name="ncomp" type="integer" value="2" min="1" label="Number of components to include in the model" />
57 <param name="correlation" type="boolean" truevalue="--correlation" falsevalue="" checked="false" label="Correlation between all blocks"/>
58 <section name="adv" title="Advanced Options" expanded="false">
59 <param name="scheme" type="select" label="Scheme">
60 <option value="horst" selected="true">horst</option>
61 <option value="factorial" >factorial</option>
62 <option value="centroid" >centroid</option>
63 </param>
64 <param name="mode" type="select" label="Mode">
65 <option value="regression" selected="true">regression</option>
66 <option value="canonical" >canonical</option>
67 <option value="invariant" >invariant</option>
68 <option value="classic" >classic</option>
69 </param>
70 <param name="maxiter" type="integer" value="100" min="1" label="Maximum number of iterations" />
71 <param name="scale" type="boolean" truevalue="--scale" falsevalue="" checked="true" label="Scale" help="if checked, each block is standardized to zero means and unit variances" />
72 <param name="init" type="select" label="Init">
73 <option value="svd" selected="true">svd</option>
74 <option value="svd.single" >svd.single</option>
75 </param>
76 <param name="tol" type="float" value="1e-06" min="0" label="Convergence stopping value (tol)" />
77 <param name="nearzerovar" type="boolean" truevalue="--nearzerovar" falsevalue="" checked="false" label="Should be set to TRUE in particular for data with many zero values" />
78 </section>
79 </inputs>
80
81 <outputs>
82 <data name="rdata_out" format="rdata" label="${tool.id}_output.rdata" />
83 <data name="sample_metadata_out" format="tabular" label="${tool.id}_${sample_metadata_in.name}" />
84 <collection name="blocks_output" type="list" label="${tool.id}_blocks_output">
85 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="outdir" format="tabular" />
86 </collection>
87 </outputs>
88
89 <tests>
90 <test>
91 <repeat name="blocks">
92 <param name="block_name" value="Block1" />
93 <param name="data_matrix" value="in_block1_data.tabular" />
94 </repeat>
95 <repeat name="blocks">
96 <param name="block_name" value="Block2" />
97 <param name="data_matrix" value="in_block2_data.tabular" />
98 </repeat>
99 <param name="sample_metadata_in" value="in_sample_meta.tabular" />
100 <output name="rdata_out" value="out_rdata.rdata" />
101 <output name="sample_metadata_out" value="out_sample_meta.tabular" />
102 </test>
103 </tests>
104
105 <help>
106 <![CDATA[
107 .. class:: infomark
108
109 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
110
111 ---------------------------------------------------
112
113 .. class:: infomark
114
115 **Please cite**
116
117 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
118 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
119
120 ---------------------------------------------------
121
122 ======================
123 mixOmics blocks.splsda
124 ======================
125
126 -----------
127 Description
128 -----------
129
130 The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets.
131 Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis.
132
133 -----------
134 Input files
135 -----------
136
137 For each block (min 2 blocks):
138 ==============================
139
140 +------------------------------+------------+
141 | Parameter : num + label | Format |
142 +==============================+============+
143 | 1 : Data matrix | tabular |
144 +------------------------------+------------+
145 | 2 : [opt] Variables metadata | tabular |
146 +------------------------------+------------+
147
148 Variables metadata files are optional.
149 If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
150
151 Global input files:
152 ===================
153
154 +-----------------------------+------------+
155 | Parameter : num + label | Format |
156 +=============================+============+
157 | 1 : Samples metadata | tabular |
158 +-----------------------------+------------+
159
160 By default, the last column of the samples metadata matrix will be used as samples description factors.
161 If it's not the case, the column number can be inputed in the `Sample description column number` parameter.
162
163 ----------
164 Parameters
165 ----------
166
167 For each block (min 2 blocks):
168 ==============================
169
170 Block name
171 Name of the block. If not provided, this will default to the input filename
172
173 Number of variables to select for each component
174 If set to 0 (default), all variables will be considered in the model
175
176 Global parameters:
177 ==================
178
179 Sample description column number
180
181 Number of components to include in the model
182
183 Correlation between all blocks
184
185 Advanced options:
186 =================
187
188 Scheme
189
190 Mode
191
192 Maximum number of iterations
193
194 Scale
195
196 Init
197
198 Convergence stopping value (tol)
199
200 Near zero var
201
202 ------------
203 Output files
204 ------------
205
206 mixomics_blocksplsda_output.rdata
207 | rData output
208 | Contains the `mixomics_result` R object containing the result of the block.splsda function
209
210 mixomics_blocksplsda_{input_sample_metadata_name}
211 | tabular output
212 | Identical to the input Sample metadata file with appended columns from the result of block.splsda function
213
214 mixomics_blocksplsda_blocks_output
215 A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block
216
217 ]]>
218 </help>
219
220 <citations>
221 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
222 </citations>
223
224 </tool>