annotate rp2biosensor.xml @ 3:4b2318e9b097 draft

"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"

<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09">
    <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python -m rp2biosensor
        '$rp2_results'
        '$sink_file'
        --opath '$html_file'
        #if str($adv.json_graph) == "true"
            --ojson '$json_file'
        #end if
    ]]></command>
    <inputs>
        <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/>
        <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
        </section>
    </inputs>
    <outputs>
        <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
        <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
            <filter> adv['json_graph'] </filter>
        </data>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced -->
        <param name="rp2_results" value="rp2-results-lactate.csv" />
        <param name="sink_file" value="sink-h2o2.csv" />
        <output name="html_file" md5="88ba7cd2501c4d671b9eac396e7b4af9"/>
        </test>
    </tests>
    <help><![CDATA[
rp2biosensor
================

Generate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results.

Input
-----

Required:

* **rp2_results**\ : (string) RetroPath2.0 results.
* **sink_file**\ : (string) Sink file used for RetroPath2.0.

Output
------

* **opath**\ : (string) Output path. Default: biosensor.html.

* **otype**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file.

* **ojson**\ : (string) Output the graph as json file if the path is not None. Default: None

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

* `GitHub <https://github.com/brsynth/rp2biosensor>`_

Version
----------

3.1.0

Authors
-------

* **Thomas Duigou**

License
-------

* `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_

    ]]></help>
</tool>