diff networkVar.xml @ 0:d0b77b926863 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/networkVar.xml	Tue Jun 23 19:57:35 2020 -0400
@@ -0,0 +1,64 @@
+<tool id="networkVar" name="networkVar" version="1.0" profile="16.04" workflow_compatible="true">
+
+    <description>creates a network between selected variables of datasets and the response variables. In the network, the similarity between two variables is associated with the link between these two variables.</description>
+
+    <requirements>
+        <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda -->
+        <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}
+        --var_list_file ${var_list_file}
+        --response_var ${select_response_var}
+        --output_graph ${output_graph}
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="mat_similarity_rdata" type="data" format="rdata"
+               label="Input computeMatSimilarity RData file"
+               help="output RData file from computeMatSimilarity"/>
+        <param name="var_list_file" type="data" format="tabular"
+               label="Variables list file"
+               help="selected variables output tabular file from circleCor"/>
+
+        <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
+        <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
+               label="Variables of interest (Optional)"
+               help="these variables have to belong to datasets that can be superimposed"/> -->
+
+        <param name="response_var_list" type="data" format="tabular"
+               label="List of response variables"
+               help="output *_response_var.tsv file from matCorAddVar"/>
+        <param name="select_response_var" type="select" display="checkboxes" multiple="true"
+               label="Response variables"
+               help="response variables that will be plotted in the network">
+        <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
+            <options from_dataset="response_var_list">
+                <column name="value" index="0"/>
+                <filter type="unique_value" column="0"/>
+                <filter type="sort_by" name="sorted_value" column="0"/>
+            </options>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help>
+    </help>
+
+</tool>
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