diff rpviz.xml @ 19:dbc40b306014 draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty
author pablocarb
date Thu, 13 Jun 2019 08:56:51 -0400
parents 612a2f94522f
children b30e3e5ee8f8
line wrap: on
line diff
--- a/rpviz.xml	Tue Jun 11 12:09:38 2019 -0400
+++ b/rpviz.xml	Thu Jun 13 08:56:51 2019 -0400
@@ -1,25 +1,19 @@
-<tool id="rpviz" name="rpVisualizer" version="0.1.0" python_template_version="3.5">
+<tool id="rpviz" name="rpviz" version="0.1.0" python_template_version="3.5">
     <description>Pathway visualizer</description>
     <requirements>
-        <requirement type="package">python-libsbml</requirement>
-        <requirement type="package">networkx</requirement>
-        <requirement type="package">beautifulsoup4</requirement>
-        <requirement type="package">rdkit</requirement>
+        <requirement type="package">requests</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-     git clone https://github.com/pablocarb/rpviz.git $__tool_directory__/rpviz;
-     cd $__tool_directory__/rpviz; git pull; cd ..;
-     cd $__tool_directory__;
-     echo `which python` > $__tool_directory__/info.log;
-     PYTHONPATH="$__tool_directory__" python $__tool_directory__/toolVisualizer.py $input1 $output1
+     python $__tool_directory__/toolRPViz.py $input1 $output1 -server $server
    ]]></command>
     <inputs>
         <param type="data" name="input1" format="xml" />
+    	<param name="server" type="text" label="RPViz RES server" value="http://rpviz.synbiochem.co.uk/REST" help="RPviz REST server" />
     </inputs>
     <outputs>
         <data name="output1" format="html" from_work_dir="out.html" />
     </outputs>
     <help><![CDATA[
-        python3 toolVisualizer.py inputfile outputfile
+        python3 toolRPViz.py [server SERVER] inputfile outputfile
     ]]></help>
 </tool>