--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/matCorAddVar.xml	Tue Jun 23 19:57:35 2020 -0400
@@ -0,0 +1,60 @@
+<tool id="matCorAddVar" name="matCorAddVar" version="1.0" profile="16.04" workflow_compatible="true">
+
+    <description>determine the correlation circles that can be overlaid and compute the correlations</description>
+
+    <requirements>
+        <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda -->
+        <requirement type="package" version="2.0">r-argparse</requirement>
+        <!-- <requirement type="package" version="0.3">viscorvar</requirement> -->
+    </requirements>
+
+    <stdio>
+        <!-- <exit_code range="1:" level="fatal" /> -->
+    </stdio>
+ 
+    <command detect_errors="aggressive">
+        <![CDATA[
+        Rscript
+        ${__tool_directory__}/matCorAddVar_wrapper.R
+        --input_rdata ${input_rdata}
+        ##--cutoff_comp ${cutoff_comp}
+        --cutoff_comp 0.775
+        #if str($var_of_interest_file) !='':
+            --interest_var_file ${var_of_interest_file}
+        #end if
+        --block_Y_file ${block_Y}
+        --output_rdata ${output_rdata}
+        --output_response_var ${output_response_var}
+        --output_blocks_comb ${output_blocks_comb}
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="input_rdata" type="data" format="rdata"
+               label="Input RData file from block.SPLSDA"
+               help="This is the RData output file from the block.splsda function." />
+        <param name="block_Y" type="data" format="tabular"
+               label="Block Y"
+               help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
+        <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
+        <param name="var_of_interest_file" type="data" format="txt" optional="true"
+               label="Variables of interest (Optional)"
+               help="these variables have to belong to datasets that can be superimposed"/>
+<!--         <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
+               label="Cutoff comp"
+               help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> -->
+    </inputs>
+
+    <outputs>
+        <data name="output_rdata" format="rdata" label="${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>
+    </help>
+
+</tool>
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