Mercurial > repos > pablocarb > synbiodesign
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 |
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--- 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>