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<tool id="optbiodes2" name="OptSynBioDes" version="0.1.0">
    <description>Optimal synbio design: from genetic parts to SBOL-compliant constructs description</description>
    <requirements>
        <requirement type="package" version="2">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/toolOptBioDes.py $input1 -partsfile $input2 -genesfile $input3 $output1 $output2 -sbolOut $output3 -server $server
    ]]></command>
    <inputs>
        <param type="integer" name="input1" value="48" label="Library size" help="Library size" />
        <param type="data" name="input2" label="Regulatory parts list" format="csv" />
        <param type="data" name="input3" label="Genes list" format="csv" />
    	<param name="server" type="text" label="OptBioDes RES server" value="http://optbiodes.synbiochem.co.uk/REST" help="OptBioDes REST server" />
    </inputs>
    <outputs>
        <data name="output1" format="csv" from_work_dir="out1.csv" />
        <data name="output2" format="csv" from_work_dir="out2.csv" />
        <data name="output3" format="csv" from_work_dir="out3.csv" />
    </outputs>
    <help><![CDATA[
        usage: toolOptBioDes.py [-h] [-server SERVER] infile outfile diagfile

toolOptBioDes: Optimal SynBio Design. Pablo Carbonell, SYNBIOCHEM, 2019

arguments:
  size            Library size
  partsfile       Input genetic parts csv file.
  genesfile       Input gene list csv file.
  outfile         Output csv design file.
  diagfile        Output csv diagnostics file.
  sbolfile        Output SBOL combinatorial genetic library

optional arguments:
  -h, --help      show this help message and exit
  -server SERVER  OptBioDes server.

    ]]></help>
</tool>