annotate optbiodes.xml @ 4:6dbb43bdf2f4 draft

planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty

<tool id="optbiodes" name="OptBioDes" version="0.1.0">
    <description>optimal synbio design</description>
    <requirements>
        <requirement type="package" version="2">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/toolOptBioDes.py $input1 $input2 $output1 $output2 -server $server
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="xlsx" />
        <param type="integer" name="input2" format="xlsx" />
    	<param name="server" type="text" label="OptBioDes RES server" value="http://doe.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" />
    </outputs>
    <help><![CDATA[
        usage: toolOptBioDes.py [-h] [-server SERVER] infile outfile diagfile

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

positional arguments:
  infile          Input xlsx file (DoE specificiations).
  outfile         Output csv design file.
  diagfile        Output csv diagnostics file.

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

    ]]></help>
</tool>