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annotate optbiodes.xml @ 19:dbc40b306014 draft

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author pablocarb
date Thu, 13 Jun 2019 08:56:51 -0400
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1 <tool id="optbiodes" name="OptBioDes" version="0.1.0">
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2 <description>optimal synbio design</description>
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3 <requirements>
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4 <requirement type="package" version="2">requests</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python $__tool_directory__/toolOptBioDes.py $input1 $input2 $output1 $output2 -server $server
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="input1" format="csv" />
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11 <param type="integer" name="input2" value="48" label="Library size" help="Library size" />
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12 <param name="server" type="text" label="OptBioDes RES server" value="http://optbiodes.synbiochem.co.uk/REST" help="OptBioDes REST server" />
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13 </inputs>
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14 <outputs>
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15 <data name="output1" format="csv" from_work_dir="out1.csv" />
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16 <data name="output2" format="csv" from_work_dir="out2.csv" />
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17 </outputs>
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18 <help><![CDATA[
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19 usage: toolOptBioDes.py [-h] [-server SERVER] infile outfile diagfile
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21 toolOptBioDes: Optimal SynBio Design. Pablo Carbonell, SYNBIOCHEM, 2019
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23 positional arguments:
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24 infile Input xlsx file (DoE specificiations).
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25 outfile Output csv design file.
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26 diagfile Output csv diagnostics file.
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28 optional arguments:
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29 -h, --help show this help message and exit
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30 -server SERVER OptBioDes server.
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32 ]]></help>
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33 </tool>