--- a/mixomics_blocksplsda.xml	Thu Oct 15 12:22:25 2020 +0000
+++ b/mixomics_blocksplsda.xml	Fri Oct 23 10:15:56 2020 +0000
@@ -1,21 +1,20 @@
-<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="6.12+galaxy0" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy1" 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>
 
-    <requirements>
-        <requirement type="package" version="6.12">bioconductor-mixomics</requirement>
-        <requirement type="package" version="2.0">r-argparse</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_mixomics.xml</import>
+    </macros>
 
-<!--     <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio> -->
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
-    <command detect_errors="aggressive">
-        <![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
+
         mkdir outdir
-        && Rscript
-        ${__tool_directory__}/mixomics_blocksplsda_script.R
+        && @COMMAND_RSCRIPT@/mixomics_blocksplsda.R
+
         #for $b in $blocks
             --block
             #if $b.block_name
@@ -27,8 +26,10 @@
             ${b.data_matrix}
             ${b.variable_metadata}
         #end for
+
         --sample_metadata_in ${sample_metadata_in}
         --sample_description_col ${sample_description_col}
+
         --ncomp ${adv.ncomp}
         ${correlation}
         ##--scheme ${adv.scheme}
@@ -40,11 +41,14 @@
         ##--init ${adv.init}
         ##--tol ${adv.tol}
         ##${adv.nearzerovar}
+
         --rdata_out ${rdata_out}
         ##--sample_metadata_out ${sample_metadata_out}
         --variable_metadata_outdir outdir
-        ]]>
-    </command>
+
+        @COMMAND_LOG_EXIT@
+
+    ]]></command>
 
     <inputs>
         <repeat name="blocks" title="Blocks">
@@ -73,7 +77,7 @@
             <param name="ncomp" type="integer" value="2" min="1"
                    label="Number of components to include in the model"
                    help="[ncomp] Number of new variables (components) computed by the data integration." />
-<!--             <param name="scheme" type="select" label="Scheme">
+            <!-- <param name="scheme" type="select" label="Scheme">
                 <option value="horst" selected="true">horst</option>
                 <option value="factorial"            >factorial</option>
                 <option value="centroid"             >centroid</option>
@@ -87,13 +91,13 @@
             <param name="maxiter" type="integer" value="100" min="1"
                    label="Maximum number of iterations"
                    help="[max.iter] Maximum number of iterations performed by block.splsda." />
-<!--            <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true"
+            <!-- <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" /> -->
             <param name="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true"
                    label="Check for missing values"
                    help="will raise an error if missing values are found in data matrices" />
-<!--             <param name="init" type="select" label="Init">
+            <!-- <param name="init" type="select" label="Init">
                 <option value="svd" selected="true">svd</option>
                 <option value="svd.single"         >svd.single</option>
             </param>
@@ -106,7 +110,7 @@
     </inputs>
 
     <outputs>
-        <data name="rdata_out" format="rdata" label="${tool.name}_output.rdata" />
+        <data name="rdata_out" format="rdata" label="${tool.name}_output.RData" />
         <!-- <data name="sample_metadata_out" format="tabular"
               label="${tool.name}_${sample_metadata_in.name}" /> -->
         <collection name="blocks_output" type="list" label="${tool.name}_blocks_output">
@@ -127,26 +131,13 @@
             </repeat>
             <param name="sample_metadata_in" value="in_sample_meta.tabular" />
             <output name="rdata_out" value="out_rdata.rdata" />
-            <output name="sample_metadata_out" value="out_sample_meta.tabular" />
+            <!-- <output name="sample_metadata_out" value="out_sample_meta.tabular" /> -->
         </test>
     </tests>
 
-    <help>
-        <![CDATA[
-.. class:: infomark
-
-**Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
-
----------------------------------------------------
+    <help><![CDATA[
 
-.. class:: infomark
-
-**Please cite**
-
-Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
-PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
-
----------------------------------------------------
+@HELP_AUTHORS@
 
 ======================
 mixOmics blocks.splsda
@@ -159,12 +150,30 @@
 The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets.
 Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis.
 
+-----------------
+Workflow position
+-----------------
+
+**Downstream tools**
+
+======================= ================================== ==========
+Name                               Output file               Format
+======================= ================================== ==========
+mixOmics.plotIndiv      mixomics_blocksplsda_output.RData  rdata
+----------------------- ---------------------------------- ----------
+mixOmics.plotVar        mixomics_blocksplsda_output.RData  rdata
+----------------------- ---------------------------------- ----------
+visCorVar.matCorAddVar  mixomics_blocksplsda_output.RData  rdata
+======================= ================================== ==========
+
+---------------------------------------------------
+
 -----------
 Input files
 -----------
 
 For each block (min 2 blocks):
-==============================
+------------------------------
 
 +------------------------------+------------+
 | Parameter : num + label      |   Format   |
@@ -188,7 +197,7 @@
     * First column = variables names. MUST be the same and in the same order than in the associated data matrix
 
 Global input files:
-===================
+-------------------
 
 +-----------------------------+------------+
 | Parameter : num + label     |   Format   |
@@ -209,7 +218,7 @@
 ----------
 
 For each block (min 2 blocks):
-==============================
+------------------------------
 
 Block name
     Name of the block. If not provided, this will default to the input filename
@@ -218,7 +227,7 @@
     If set to 0 (default), all variables will be considered in the model
 
 Global parameters:
-==================
+------------------
 
 Sample description column number
 
@@ -227,7 +236,7 @@
 Correlation between all blocks
 
 Advanced options:
-=================
+-----------------
 
 Scheme
 
@@ -243,26 +252,22 @@
 
 Near zero var
 
+
+@HELP_MANUAL@
+
 ------------
 Output files
 ------------
 
-mixomics_blocksplsda_output.rdata
-    | rData output
+mixomics_blocksplsda_output.RData
+    | RData output
     | Contains the `mixomics_result` R object containing the result of the block.splsda function
 
-mixomics_blocksplsda_{input_sample_metadata_name}
-    | tabular output
-    | Identical to the input Sample metadata file with appended columns from the result of block.splsda function
-
 mixomics_blocksplsda_blocks_output
     A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block
 
-        ]]>
-    </help>
+    ]]></help>
 
-    <citations>
-        <citation type="doi">10.1371/journal.pcbi.1005752</citation>
-    </citations>
+    <expand macro="citations" />
 
 </tool>
\ No newline at end of file