Mercurial > repos > ppericard > mixomics_blocksplsda

annotate mixomics_blocksplsda.xml @ 2:655d1fbcd3e6 draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
author ppericard
date Wed, 12 Jun 2019 11:24:23 -0400
parents 6595c17673cb
children b0ab97ffc2a1
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1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.2.0" profile="16.04" workflow_compatible="true">
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3 <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description>
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4
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5 <requirements>
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6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
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7 <requirement type="package" version="2.0">r-argparse</requirement>
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8 </requirements>
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9
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10 <!-- <stdio>
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11 <exit_code range="1:" level="fatal" />
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12 </stdio> -->
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13
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14 <command detect_errors="aggressive">
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15 <![CDATA[
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16 mkdir outdir
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17 && Rscript
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18 ${__tool_directory__}/mixomics_blocksplsda_script.R
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19 #for $b in $blocks
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20 --block
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21 #if $b.block_name
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22 ${b.block_name}
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23 #else
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24 ${b.data_matrix.name}
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25 #end if
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26 ${b.keep}
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27 ${b.data_matrix}
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28 ${b.variable_metadata}
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29 #end for
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30 --sample_metadata_in ${sample_metadata_in}
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31 --sample_description_col ${sample_description_col}
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32 --ncomp ${ncomp}
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33 ${correlation}
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34 --scheme ${adv.scheme}
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35 --mode ${adv.mode}
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36 --maxiter ${adv.maxiter}
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37 ${adv.scale}
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38 --init ${adv.init}
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39 --tol ${adv.tol}
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40 ${adv.nearzerovar}
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41 --rdata_out ${rdata_out}
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42 --sample_metadata_out ${sample_metadata_out}
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43 --variable_metadata_outdir outdir
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44 ]]>
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45 </command>
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46
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47 <inputs>
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48 <repeat name="blocks" title="Blocks">
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49 <param name="block_name" type="text" label="Block name" />
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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" />
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51 <param name="data_matrix" type="data" format="tabular" label="Data matrix" help="rows = variables, columns = samples" />
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52 <param name="variable_metadata" type="data" format="tabular" optional="true" label="Variables metadata" help="rows = variables" />
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53 </repeat>
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54 <param name="sample_metadata_in" type="data" format="tabular" label="Samples metadata matrix" />
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55 <param name="sample_description_col" type="integer" value="0" min="0" label="Sample description column number" help="Use the last column by default" />
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56 <param name="ncomp" type="integer" value="2" min="1" label="Number of components to include in the model" />
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57 <param name="correlation" type="boolean" truevalue="--correlation" falsevalue="" checked="false" label="Correlation between all blocks"/>
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58 <section name="adv" title="Advanced Options" expanded="false">
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59 <param name="scheme" type="select" label="Scheme">
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60 <option value="horst" selected="true">horst</option>
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61 <option value="factorial" >factorial</option>
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62 <option value="centroid" >centroid</option>
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63 </param>
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64 <param name="mode" type="select" label="Mode">
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65 <option value="regression" selected="true">regression</option>
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66 <option value="canonical" >canonical</option>
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67 <option value="invariant" >invariant</option>
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68 <option value="classic" >classic</option>
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69 </param>
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70 <param name="maxiter" type="integer" value="100" min="1" label="Maximum number of iterations" />
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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" />
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72 <param name="init" type="select" label="Init">
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73 <option value="svd" selected="true">svd</option>
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74 <option value="svd.single" >svd.single</option>
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75 </param>
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76 <param name="tol" type="float" value="1e-06" min="0" label="Convergence stopping value (tol)" />
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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" />
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78 </section>
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79 </inputs>
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80
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81 <outputs>
1
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82 <data name="rdata_out" format="rdata" label="${tool.name}_output.rdata" />
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83 <data name="sample_metadata_out" format="tabular" label="${tool.name}_${sample_metadata_in.name}" />
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84 <collection name="blocks_output" type="list" label="${tool.name}_blocks_output">
0
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85 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="outdir" format="tabular" />
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86 </collection>
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87 </outputs>
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88
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89 <tests>
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90 <test>
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91 <repeat name="blocks">
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92 <param name="block_name" value="Block1" />
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93 <param name="data_matrix" value="in_block1_data.tabular" />
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94 </repeat>
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95 <repeat name="blocks">
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96 <param name="block_name" value="Block2" />
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97 <param name="data_matrix" value="in_block2_data.tabular" />
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98 </repeat>
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99 <param name="sample_metadata_in" value="in_sample_meta.tabular" />
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100 <output name="rdata_out" value="out_rdata.rdata" />
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101 <output name="sample_metadata_out" value="out_sample_meta.tabular" />
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102 </test>
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103 </tests>
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104
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105 <help>
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106 <![CDATA[
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107 .. class:: infomark
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108
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109 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
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110
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111 ---------------------------------------------------
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112
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113 .. class:: infomark
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114
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115 **Please cite**
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116
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117 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
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118 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
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119
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120 ---------------------------------------------------
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121
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122 ======================
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123 mixOmics blocks.splsda
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124 ======================
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125
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126 -----------
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127 Description
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128 -----------
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129
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130 The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets.
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131 Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis.
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132
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133 -----------
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134 Input files
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135 -----------
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136
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137 For each block (min 2 blocks):
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138 ==============================
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139
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140 +------------------------------+------------+
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141 | Parameter : num + label | Format |
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142 +==============================+============+
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143 | 1 : Data matrix | tabular |
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144 +------------------------------+------------+
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145 | 2 : [opt] Variables metadata | tabular |
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146 +------------------------------+------------+
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147
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148 Variables metadata files are optional.
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149 If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
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150
1
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151 1. Data matrix format
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152 * Rows = variables, Columns = samples
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153 * First row = samples name. MUST be the same and in the same order in every block as well as in the sample metadata file (transposed)
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154 * First column = variables name
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155
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156 2. Variables metadata format
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157 * Rows = variables, Columns = metadata
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158 * First row = metadata column names
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159 * First column = variables names. MUST be the same and in the same order than in the associated data matrix
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160
0
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161 Global input files:
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162 ===================
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163
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164 +-----------------------------+------------+
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165 | Parameter : num + label | Format |
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166 +=============================+============+
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167 | 1 : Samples metadata | tabular |
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168 +-----------------------------+------------+
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169
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170 By default, the last column of the samples metadata matrix will be used as samples description factors.
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171 If it's not the case, the column number can be inputed in the `Sample description column number` parameter.
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172
1
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173 1. Samples metadata format
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174 * Rows = samples, Columns = metadata
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175 * First row = metadata column names
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176 * First column = sample names. These names must be identical (transposed) and in the same order than for the blocks data matrices
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177
0
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178 ----------
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179 Parameters
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180 ----------
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181
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182 For each block (min 2 blocks):
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183 ==============================
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184
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185 Block name
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186 Name of the block. If not provided, this will default to the input filename
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187
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188 Number of variables to select for each component
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189 If set to 0 (default), all variables will be considered in the model
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190
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191 Global parameters:
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192 ==================
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193
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194 Sample description column number
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195
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196 Number of components to include in the model
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197
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198 Correlation between all blocks
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199
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200 Advanced options:
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201 =================
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202
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203 Scheme
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204
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205 Mode
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206
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207 Maximum number of iterations
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208
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209 Scale
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210
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211 Init
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212
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213 Convergence stopping value (tol)
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214
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215 Near zero var
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216
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217 ------------
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218 Output files
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219 ------------
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220
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221 mixomics_blocksplsda_output.rdata
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222 | rData output
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223 | Contains the `mixomics_result` R object containing the result of the block.splsda function
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224
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225 mixomics_blocksplsda_{input_sample_metadata_name}
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226 | tabular output
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227 | Identical to the input Sample metadata file with appended columns from the result of block.splsda function
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228
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229 mixomics_blocksplsda_blocks_output
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230 A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block
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231
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232 ]]>
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233 </help>
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234
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235 <citations>
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236 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
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237 </citations>
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238
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239 </tool>