annotate rpthermo.xml @ 5:cec1e919d24f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 162ee89a8e36033f32973d72dfc1b11ca27da61f

<tool id="rptools_rpthermo" name="Thermo" version="@TOOL_VERSION@" profile="21.09">
    <description>Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <regex match="WARNING:" level="warning" />
        <regex match="ERROR:" level="fatal" />
        <regex match="ERROR:root:ChemAxon" level="warning" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        export XDG_CACHE_HOME="\${TMPDIR:-.}" ;
        python -m rptools.rpthermo
        '$input'
        '$pathway_with_thermo'
        --pH '$adv.ph'
        --ionic_strength '$adv.ionic_strength'
        --pMg '$adv.pMg'
    ]]></command>
    <!-- <environment_variables>
        <environment_variable name="XDG_CACHE_HOME">\$TMPDIR</environment_variable>
    </environment_variables> -->
    <inputs>
        <param name="input" type="data" format="sbml" label="SBML Input File" help="Pathways in SBML format" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="ph" type="float" value="7.5" min="0" max="14" label="Compartment pH of the pathway" />
            <param name="ionic_strength" type="float" value="0.25" min="0" max="500" label="Compartment ionic strength of the pathway" />
            <param name="pMg" type="float" value="3.0" label="Compartment pMg (Magnesium vapor pressure) of the pathway" />
        </section>
    </inputs>
    <outputs>
        <data name="pathway_with_thermo" format="sbml" label="${tool.name} - ${input.name}" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="input" value="rp_013_0001.xml" />
            <output name="pathway_with_thermo">
                <assert_contents>
                    <is_valid_xml />
                    <!--check thermo_dG0_prime value-->
                    <has_text text="-2308.11630" />
                    <!--check thermo_dG value-->
                    <has_text text="-2151.84763" />
                    <has_n_lines n="522" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Thermodynamics
==============
Calculate the formation energy of chemical species either using an internal database or estimate it by decomposing them using the `component contribution <https://gitlab.com/elad.noor/component-contribution>`_ method. Thereafter this tool predicts the Gibbs free energy of reactions and of the whole heterologous pathway by combining the formation energy of each individual compound.

The goal of the thermodynamic analysis is to estimate the feasibility of the predicted pathways toward target production, in physiological conditions (PH, ionic strength).

.. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpThermo/standalone/galaxy/img/rpThermo.png
	:width: 80 %
	:align: center


|


Above is an illustration of the Gibbs free energy calculation using the component contribution package. The color-coded arrows from red (best) to blue (worst) show the best and worst-performing reactions.

Required:

Inputs
------

* **SBML Input File**\ : Pathways in SBML format

Advanced Options:

* **PH**\ :(float) Compartment PH of the pathway
* **Ionic strength**\ :(float) Compartment ionic strength of the pathway
* **pMg**\ :(float) Compartment pMg (Magnesium vapor pressure) of the pathway

Output
------

* **Pathway with thermo**\ : annotated pathways (with thermodynamics information for each reaction) in SBML(Systems Biology Markup Language) format.
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1003098</citation>
        <citation type="doi">10.1038/s41467-022-32661-x</citation>
    </citations>
</tool>