--- a/mixomics_blocksplsda.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/mixomics_blocksplsda.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
 
     <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description>
 
@@ -33,7 +33,6 @@
         --ncomp ${adv.ncomp}
         ${correlation}
         ##--scheme ${adv.scheme}
-        ##--mode ${adv.mode}
         --maxiter ${adv.maxiter}
         ##${adv.scale}
         --scale ## always activated hidden param
@@ -79,12 +78,6 @@
                 <option value="horst" selected="true">horst</option>
                 <option value="factorial"            >factorial</option>
                 <option value="centroid"             >centroid</option>
-            </param>
-            <param name="mode" type="select" label="Mode">
-                <option value="regression" selected="true">regression</option>
-                <option value="canonical"                 >canonical</option>
-                <option value="invariant"                 >invariant</option>
-                <option value="classic"                   >classic</option>
             </param> -->
             <param name="maxiter" type="integer" value="100" min="1"
                    label="Maximum number of iterations"
@@ -148,8 +141,8 @@
 
 The blocks.splsda function is part of the mixOmics package for exploration and integration of omics datasets.
 This data integration takes as input parameters different omics datasets
-(transcriptomic, metabolomic, metagenomic, ...) and a response variable (e.g. for a sample, the value of the response
-variable is equal to « Treated »  or « Control »). This data integration returns, for each omics dataset, variables
+(transcriptomics, metabolomics, metagenomics, ...) and a response variable (e.g. for a sample, the value of the response
+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
 which are correlated with the variables of the other omic datasets and the response variable. The other functions of
 this pipeline allow visualizing this correlated variables thanks to correlation circles and networks.
 
@@ -198,9 +191,6 @@
 The first row contains the metadata column names.
 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.
 
-Variables metadata files are optional.
-If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
-
 
 Global input files:
 -------------------
@@ -215,47 +205,14 @@
 Samples metadata is in tabular format (.tsv).
 The first column contains the sample names.
 The first row contains the metadata column names.
-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.
+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.
 
 ----------
 Parameters
 ----------
 
-For each block (min 2 blocks):
-------------------------------
-
-Block name
-    Name of the block. If not provided, this will default to the input filename
-
 Number of variables to select for each component
-    If set to 0 (default), all variables will be considered in the model
-
-Global parameters:
-------------------
-
-Sample description column number
-
-Number of components to include in the model
-
-Correlation between all blocks
-
-Advanced options:
------------------
-
-Scheme
-
-Mode
-
-Maximum number of iterations
-
-Scale
-
-Init
-
-Convergence stopping value (tol)
-
-Near zero var
-
+   tune.block.splsda can be used to set the number of variables to select on each component
 
 @HELP_MANUAL@