annotate lcrgenie.xml @ 1:afbbecdcc0e3 draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

<tool id="LCRGenie" name="LCR Genie" version="@TOOL_VERSION@" profile="19.09">
    <description>Ligase Chain Reaction</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">lcr_genie</requirement>
    </requirements>
    <stdio>
        <regex match="WARNING:" level="warning" />
        <regex match="ERROR:" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m lcr_genie
            '$LCR_input'
            out.xlsx
            --melting_temp '$adv.melting_temp'
        && cp out.xlsx '$LCR_output'
    ]]></command>
    <inputs>
        <param name="LCR_input" type="data" format="xml" label="Constructs" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="melting_temp" value="60.0" type="float" label="Target melting temperature for the bridging oligos" />
        </section>
    </inputs>
    <outputs>
        <data name="LCR_output" format="xlsx" label="LCR Genie: Assembly Plan" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="LCR_input" value="LCR_input_lycopene.xml" />
            <output name="LCR_output" >
                <assert_contents>
                    <has_size value="58196" delta="100" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
LCRGenie
========

LCR Genie is a web-based tool for supporting the design of bridging oligos, which are required for annealing together individual synthetic DNA parts (designed by PartsGenie) into multi-gene plasmid assemblies, designed by OptDoE. 


Input
-----

* **input**\ : (string) is the path to an .xml SBOL file containing constructs designs and sequences
* **melting_temp**\ : (float) is the target melting temperature for the bridging oligos (default=60.0)

Output
------

* **output**\ : (string) is the path to the output spreadsheet

Project Links
---------------------

* `GitHub <https://github.com/neilswainston/LCRGenie/>`_

Version
----------

1.0.2

Authors
-------

* **Neil Swainston**
* **Joan Hérisson**

License
-------

`MIT <https://github.com/neilswainston/LCRGenie/blob/master/LICENSE>`_


    ]]></help>
</tool>