--- a/mixomics_blocksplsda.xml	Mon Mar 09 11:53:32 2020 -0400
+++ b/mixomics_blocksplsda.xml	Tue Mar 10 06:27:02 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.3.0" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.4.0" 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>
 
@@ -31,13 +31,14 @@
         --sample_description_col ${sample_description_col}
         --ncomp ${ncomp}
         ${correlation}
-        --scheme ${adv.scheme}
-        --mode ${adv.mode}
+        ##--scheme ${adv.scheme}
+        ##--mode ${adv.mode}
         --maxiter ${adv.maxiter}
-        ${adv.scale}
-        --init ${adv.init}
-        --tol ${adv.tol}
-        ${adv.nearzerovar}
+        ##${adv.scale}
+        --scale ## always activated hidden param
+        ##--init ${adv.init}
+        ##--tol ${adv.tol}
+        ##${adv.nearzerovar}
         --rdata_out ${rdata_out}
         --sample_metadata_out ${sample_metadata_out}
         --variable_metadata_outdir outdir
@@ -95,7 +96,7 @@
             <param name="tol" type="float" value="1e-06" min="0"
                    label="Convergence stopping value"
                    help="[tol]" />
-            <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="false"
+            <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="true"
                    label="Should be set to TRUE in particular for data with many zero values" /> -->
         </section>
     </inputs>

--- a/mixomics_blocksplsda_script.R	Mon Mar 09 11:53:32 2020 -0400
+++ b/mixomics_blocksplsda_script.R	Tue Mar 10 06:27:02 2020 -0400
@@ -11,18 +11,28 @@
 
 parser <- ArgumentParser(description='Run the mixOmics block.splsda function')
 
-parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, help="Block name + nb variables to select + data matrix file + variables metadata file")
-parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, help="Samples metadata file")
-parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', required=TRUE, help="Sample description column number")
-parser$add_argument('--ncomp', dest='ncomp', type='integer', required=TRUE, help="Number of components to include in the model")
-parser$add_argument('--correlation', dest='correlation', action="store_true", help="Add correlation between all blocks")
-parser$add_argument('--scheme', dest='scheme', required=TRUE, help="Scheme")
-parser$add_argument('--mode', dest='mode', required=TRUE, help="Mode")
-parser$add_argument('--maxiter', dest='maxiter', type='integer', required=TRUE, help="Maximum number of iterations")
-parser$add_argument('--scale', dest='scale', action="store_true", help="Each block is standardized to zero means and unit variances")
-parser$add_argument('--init', dest='init', required=TRUE, help="Init (svd or svd.single)")
-parser$add_argument('--tol', dest='tol', type='double', required=TRUE, help="Convergence stopping value")
-parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", help="Should be set in particular for data with many zero values")
+parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE,
+                    help="Block name + nb variables to select + data matrix file + variables metadata file")
+parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE,
+                    help="Samples metadata file")
+parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer',
+                    default=0, help="Sample description column number")
+parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2,
+                    help="Number of components to include in the model")
+parser$add_argument('--correlation', dest='correlation', action="store_true",
+                    help="Add correlation between all blocks")
+parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme")
+parser$add_argument('--mode', dest='mode', default="regression", help="Mode")
+parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100,
+                    help="Maximum number of iterations")
+parser$add_argument('--scale', dest='scale', action="store_true",
+                    help="Each block is standardized to zero means and unit variances")
+parser$add_argument('--init', dest='init', default="svd",
+                    help="Init (svd or svd.single)")
+parser$add_argument('--tol', dest='tol', type='double', default=1e-06,
+                    help="Convergence stopping value")
+parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true",
+                    help="Should be set in particular for data with many zero values")
 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
 parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")