Mercurial > repos > ppericard > mixomics_blocksplsda

comparison mixomics_blocksplsda.xml @ 1:6595c17673cb 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 11:22:33 -0400
parents bea08702ed51
children b0ab97ffc2a1
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0:bea08702ed51 1:6595c17673cb
1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.1.0" profile="16.04" workflow_compatible="true"> 1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.2.0" 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 <requirements>
6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement> 6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
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" /> 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> 78 </section>
79 </inputs> 79 </inputs>
80 80
81 <outputs> 81 <outputs>
82 <data name="rdata_out" format="rdata" label="${tool.id}_output.rdata" /> 82 <data name="rdata_out" format="rdata" label="${tool.name}_output.rdata" />
83 <data name="sample_metadata_out" format="tabular" label="${tool.id}_${sample_metadata_in.name}" /> 83 <data name="sample_metadata_out" format="tabular" label="${tool.name}_${sample_metadata_in.name}" />
84 <collection name="blocks_output" type="list" label="${tool.id}_blocks_output"> 84 <collection name="blocks_output" type="list" label="${tool.name}_blocks_output">
85 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="outdir" format="tabular" /> 85 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="outdir" format="tabular" />
86 </collection> 86 </collection>
87 </outputs> 87 </outputs>
88 88
89 <tests> 89 <tests>
146 +------------------------------+------------+ 146 +------------------------------+------------+
147 147
148 Variables metadata files are optional. 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. 149 If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
150 150
151 1. Data matrix format
152 * Rows = variables, Columns = samples
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)
154 * First column = variables name
155
156 2. Variables metadata format
157 * Rows = variables, Columns = metadata
158 * First row = metadata column names
159 * First column = variables names. MUST be the same and in the same order than in the associated data matrix
160
151 Global input files: 161 Global input files:
152 =================== 162 ===================
153 163
154 +-----------------------------+------------+ 164 +-----------------------------+------------+
155 | Parameter : num + label | Format | 165 | Parameter : num + label | Format |
158 +-----------------------------+------------+ 168 +-----------------------------+------------+
159 169
160 By default, the last column of the samples metadata matrix will be used as samples description factors. 170 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. 171 If it's not the case, the column number can be inputed in the `Sample description column number` parameter.
162 172
173 1. Samples metadata format
174 * Rows = samples, Columns = metadata
175 * First row = metadata column names
176 * First column = sample names. These names must be identical (transposed) and in the same order than for the blocks data matrices
177
163 ---------- 178 ----------
164 Parameters 179 Parameters
165 ---------- 180 ----------
166 181
167 For each block (min 2 blocks): 182 For each block (min 2 blocks):