diff viscorvar_networkvar.xml @ 2:c8533e9298e5 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/viscorvar_networkvar.xml	Fri Oct 23 10:15:56 2020 +0000
@@ -0,0 +1,125 @@
+<tool id="viscorvar_networkvar" name="visCorVar networkVar" version="@TOOL_VERSION@+galaxy1" 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>
+
+    <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_networkvar.R
+
+        --mat_similarity_rdata ${mat_similarity_rdata}
+        --var_list_file ${var_list_file}
+        --response_var ${select_response_var}
+
+        --output_graph ${output_graph}
+
+        @COMMAND_LOG_EXIT@
+
+    ]]></command>
+
+    <inputs>
+        <param name="mat_similarity_rdata" type="data" format="rdata"
+               label="Input computeMatSimilarity RData file"
+               help="output RData file from computeMatSimilarity"/>
+        <param name="var_list_file" type="data" format="tabular"
+               label="Variables list file"
+               help="selected variables output tabular file from circleCor"/>
+
+        <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
+        <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
+               label="Variables of interest (Optional)"
+               help="these variables have to belong to datasets that can be superimposed"/> -->
+
+        <param name="response_var_list" type="data" format="tabular"
+               label="List of response variables"
+               help="output *_response_var.tsv file from matCorAddVar"/>
+        <param name="select_response_var" type="select" display="checkboxes" multiple="true"
+               label="Response variables"
+               help="response variables that will be plotted in the network">
+        <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
+            <options from_dataset="response_var_list">
+                <column name="value" index="0"/>
+                <filter type="unique_value" column="0"/>
+                <filter type="sort_by" name="sorted_value" column="0"/>
+            </options>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+
+@HELP_AUTHORS@
+
+====================
+visCorVar networkVar
+====================
+
+-----------
+Description
+-----------
+
+Bla bla...
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+================================ ============================================= =========
+Name                             Output file                                   Format
+================================ ============================================= =========
+visCorVar.computeMatSimilarity   viscorvar_computematsimilarity_output.RData   rdata
+-------------------------------- --------------------------------------------- ---------
+visCorVar.circleCor              viscorvar_circlecor_selected_var.tsv          tabular
+-------------------------------- --------------------------------------------- ---------
+visCorVar.matCorAddVar           viscorvar_matcoraddvar_response_var.tsv       tabular
+================================ ============================================= =========
+
+---------------------------------------------------
+
+-----------
+Input files
+-----------
+
++-------------------------------------------------------+------------+
+| Parameter : num + label                               |   Format   |
++=======================================================+============+
+| 1 : Rdata visCorVar.computeMatSimilarity output       |   rdata    |
++-------------------------------------------------------+------------+
+| 2 : *_selected_var.tsv visCorVar.circleCor output     |   tabular  |
++-------------------------------------------------------+------------+
+| 3 : *_response_var.tsv visCorVar.matCorAddVar output  |   tabular  |
++-------------------------------------------------------+------------+
+
+----------
+Parameters
+----------
+
+@HELP_MANUAL@
+
+------------
+Output files
+------------
+
+viscorvar_networkvar_graph.graphml
+	GraphML file
+
+    ]]></help>
+
+    <expand macro="citations" />
+
+</tool>
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