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optbiodes2.xml
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optbiodes2.xml
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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>