Mercurial > repos > pablocarb > synbiodesign

view selenzyme.xml @ 14:ff6c33d3a9d5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5
author pablocarb
date Tue, 11 Jun 2019 09:38:55 -0400
parents 856bd14e6e96
children
line wrap: on
line source

<tool id="selenzyme" name="Selenzyme" version="0.1.0">
    <description>enzyme sequence selection from reaction template</description>
    <requirements>
        <requirement type="package" version="2">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/toolSelenzyme.py $input1 $output1 -server $server
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="csv" />
    	<param name="server" type="text" label="Selenzyme RES server" value="http://selenzyme.synbiochem.co.uk/REST" help="Selenzyme REST server" />
    </inputs>
    <outputs>
        <data name="output1" format="csv" from_work_dir="out.csv" />
    </outputs>
    <help><![CDATA[
        usage: toolSelenzyme.py [-h] [-server SERVER] infile outfile

toolSelenzyme: Enzyme sequence selection. Pablo Carbonell, SYNBIOCHEM, 2019

positional arguments:
  infile          Input csv file.
  outfile         Input csv file.

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

    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/bty065</citation>
    </citations>
</tool>