annotate rpscore.xml @ 2:f29ff80bab42 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 387d0dd233c1d9948152a2d4af9e69ad10fe1b6a

<tool id="rptools_rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Computes a global score for a heterologous pathway</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python -m rptools.rpscore '$pathway' '$scored_pathway'
        --no_of_rxns_thres '$adv.no_of_rxns_thres'
        --log "error"
    ]]></command>
    <inputs>
        <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
        </section>
    </inputs>
    <outputs>
        <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" />
    </outputs>
    <tests>
        <test>
        <!-- check if identical outputs are produced with default parameters  -->
            <param name="pathway" value="pathway.xml" />
            <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/>
        </test>
    </tests>
    <help><![CDATA[
Score Pathway
==============

Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.

Input
-----

Required:

* **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...).
* **Scored pathway**\ : pathway file (rpSBML) with global score.

Advanced options:

* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1038/s41467-022-32661-x</citation>
    </citations>
</tool>