--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/viscorvar_matcoraddvar.xml	Fri Oct 23 10:15:56 2020 +0000
@@ -0,0 +1,136 @@
+<tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
+
+    <description>determine the correlation circles that can be overlaid and compute the correlations</description>
+
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_viscorvar.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command detect_errors="aggressive"><![CDATA[
+
+        @COMMAND_RSCRIPT@/viscorvar_matcoraddvar.R
+
+        --input_rdata ${input_rdata}
+        --block_Y_file ${block_Y}
+
+        ##--cutoff_comp ${cutoff_comp}
+        --cutoff_comp 0.75
+        #if str($var_of_interest_file) !='':
+            --interest_var_file ${var_of_interest_file}
+        #end if
+
+        --output_rdata ${output_rdata}
+        --output_response_var ${output_response_var}
+        --output_blocks_comb ${output_blocks_comb}
+
+        @COMMAND_LOG_EXIT@
+
+    ]]></command>
+
+    <inputs>
+        <param name="input_rdata" type="data" format="rdata"
+               label="Input RData file from block.SPLSDA"
+               help="This is the RData output file from the block.splsda function." />
+        <param name="block_Y" type="data" format="tabular"
+               label="Block Y"
+               help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
+        <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
+        <param name="var_of_interest_file" type="data" format="txt" optional="true"
+               label="Variables of interest (Optional)"
+               help="variables not belonging to any block will not be considered"/>
+        <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
+               label="Cutoff comp"
+               help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> -->
+    </inputs>
+
+    <outputs>
+        <data name="output_rdata" format="rdata" label="${tool.name}_output.RData" />
+        <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" />
+        <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+
+@HELP_AUTHORS@
+
+======================
+visCorVar matCorAddVar
+======================
+
+-----------
+Description
+-----------
+
+Bla bla...
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+======================= =================================== ========
+Name                    Output file                         Format
+======================= =================================== ========
+mixOmics.block.splsda   mixomics_blocksplsda_output.RData   rdata
+======================= =================================== ========
+
+**Downstream tools**
+
+================================ ========================================= ========
+Name                             Output file                               Format
+================================ ========================================= ========
+visCorVar.circleCor              viscorvar_matcoraddvar_output.RData       rdata
+-------------------------------- ----------------------------------------- --------
+visCorVar.computeMatSimilarity   viscorvar_matcoraddvar_output.RData       rdata
+-------------------------------- ----------------------------------------- --------
+visCorVar.networkVar             viscorvar_matcoraddvar_response_var.tsv   tabular
+================================ ========================================= ========
+
+---------------------------------------------------
+
+-----------
+Input files
+-----------
+
++---------------------------------+------------+
+| Parameter : num + label         |   Format   |
++=================================+============+
+| 1 : Rdata block.splsda output   |   Rdata    |
++---------------------------------+------------+
+| 2 : Block Y                     |   tabular  |
++---------------------------------+------------+
+| 3 : [opt] Variables of interest |   txt      |
++---------------------------------+------------+
+
+----------
+Parameters
+----------
+
+@HELP_MANUAL@
+
+------------
+Output files
+------------
+
+viscorvar_matcoraddvar_output.RData
+    RData output
+
+viscorvar_matcoraddvar_response_var.tsv
+
+
+viscorvar_matcoraddvar_blocks_comb.tsv
+
+
+    ]]></help>
+
+    <expand macro="citations" />
+
+</tool>
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