comparison rpviz.xml @ 19:dbc40b306014 draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty

18:612a2f94522f

<tool id="rpviz" name="rpVisualizer" 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>
    </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
   ]]></command>
    <inputs>
        <param type="data" name="input1" format="xml" />
    </inputs>
    <outputs>
        <data name="output1" format="html" from_work_dir="out.html" />
    </outputs>
    <help><![CDATA[
        python3 toolVisualizer.py inputfile outputfile
    ]]></help>
</tool>

19:dbc40b306014

<tool id="rpviz" name="rpviz" version="0.1.0" python_template_version="3.5">
    <description>Pathway visualizer</description>
    <requirements>
        <requirement type="package">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
     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 toolRPViz.py [server SERVER] inputfile outputfile
    ]]></help>
</tool>