diff networkVar.xml @ 3:0a3c83f2197a draft

planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/networkVar.xml	Fri Oct 25 07:10:59 2019 -0400
@@ -0,0 +1,62 @@
+<tool id="networkVar" name="networkVar" version="0.2.0" profile="16.04" workflow_compatible="true">
+
+    <description></description>
+    
+    <requirements>
+        <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
+        <requirement type="package" version="1.2">r-igraph</requirement>
+        <requirement type="package" version="2.0">r-argparse</requirement>
+    </requirements>
+    
+    <stdio>
+        <!-- <exit_code range="1:" level="fatal" /> -->
+    </stdio>
+
+    <command detect_errors="aggressive">
+        <![CDATA[
+        Rscript
+        ${__tool_directory__}/networkVar_wrapper.R
+        --mat_similarity_rdata ${mat_similarity_rdata}
+        --block_splsda_rdata ${block_splsda_rdata}
+        --var_list_file ${var_list_file}
+
+        #if str($var_of_interest_file) !='':
+            --interest_var_file ${var_of_interest_file}
+        #end if
+        
+        --responses_var ${select_responses_var}
+
+        --output_graph ${output_graph}
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="mat_similarity_rdata" type="data" format="rdata" label="Input RData file from computeMatSimilarity"/>
+        <param name="block_splsda_rdata" type="data" format="rdata" label="Input RData file from block.SPLSDA"/>
+        <param name="var_list_file" type="data" format="tabular" label="Variables list file" />
+        
+        <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
+        <param name="var_of_interest_file" type="data" format="tabular" optional="true" label="Variables of interest (Optional)" />
+
+        <param name="responses_var_list" type="data" format="tabular" label="List of response variables"/>
+        <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables">
+        <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
+            <options from_dataset="responses_var_list">
+                <column name="value" index="0"/>
+                <filter type="unique_value" column="0"/>
+                <filter type="sort_by" name="sorted_value" column="0"/>
+            </options>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help>
+    </help>
+
+</tool>
\ No newline at end of file