annotate optbiodes2.xml @ 25:2f8af738e139 draft

planemo upload commit c74b3ff2329f69ac7b309cc7d9bdf7b9d78106fb-dirty

<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" format="csv" />
        <param type="data" name="input3" 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>