comparison rpextractsink.xml @ 2:caf2b5731a5e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690

1:e40480dbe95d

<tool id="rptools_rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Generate the RetroPath2.0 sink file from an SBML input</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">5.13.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
    </requirements>
    <stdio>
        <regex match="Could not retreive any species in the compartment" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rptools.rpextractsink

    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with iCN718 model input  -->
            <param name="input" value="iCN718.xml.gz" />
            <output name="sink" file="sink.csv" ftype="csv" compare="diff"/>
        </test>
    </tests>
    <help><![CDATA[

Sink from SBML
=================

Sink refers to the collection of chemical species used by the restrosynthesis algorithm of `RetroPath2.0 <https://doi.org/10.1016/j.ymben.2017.12.002>`_ to finish metabolic route exploration. This tool uses an SBML (Systems Biology Markup Language) file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytosol, Golgi apparatus, nucleus, etc) and uses its MIRIAM (Minimal Information Requested In the Annotation of Models) annotation to find their InChI (International Chemical Identifier) structures. In *Advanced Options*, You can use *Remove dead-end metabolites using FVA evaluation?* to conduct Flux Variability Analysis to remove metabolites that lack the requisite flux that would account for their production or consumption within the metabolic network.

Output
------

* **Sink**\ : CSV file containing a collection of chemical species used by the restrosynthesis algorithm of `RetroPath2.0 <https://doi.org/10.1016/j.ymben.2017.12.002>`_.

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

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

License
-------

`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_

Acknowledgments
---------------

* Thomas Duigou

    ]]></help>
    <creator>
        <person givenName="Joan" familyName="Hérisson" email="[e-mail]" identifier="https://orcid.org/0000-0001-9741-0847" />
        <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" />
    </creator>
    <citations>
        <citation type="doi">10.1038/nbt1156</citation>
        <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
        <citation type="doi">10.1186/1752-0509-7-74</citation>
        <citation type="doi">10.1093/bioinformatics/btn051</citation>
    </citations>
</tool>

2:caf2b5731a5e

<tool id="rptools_rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Generate the RetroPath2.0 sink file from an SBML input</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <regex match="Could not retreive any species in the compartment" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rptools.rpextractsink

    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with iCN718 model input  -->
            <param name="input" value="iCN718.xml.gz" />
            <output name="sink" md5="0a7438b90704bf1ba88e123e6bb54df2" />
        </test>
    </tests>
    <help><![CDATA[
Sink from SBML
=================

Sink refers to the collection of chemical species used by the restrosynthesis algorithm of `RetroPath2.0 <https://doi.org/10.1016/j.ymben.2017.12.002>`_ to finish metabolic route exploration. This tool uses an SBML (Systems Biology Markup Language) file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytosol, Golgi apparatus, nucleus, etc) and uses its MIRIAM (Minimal Information Requested In the Annotation of Models) annotation to find their InChI (International Chemical Identifier) structures. In *Advanced Options*, You can use *Remove dead-end metabolites using FVA evaluation?* to conduct Flux Variability Analysis to remove metabolites that lack the requisite flux that would account for their production or consumption within the metabolic network.

Output
------

* **Sink**\ : CSV file containing a collection of chemical species used by the restrosynthesis algorithm of `RetroPath2.0 <https://doi.org/10.1016/j.ymben.2017.12.002>`_.
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1038/nbt1156</citation>
        <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
        <citation type="doi">10.1186/1752-0509-7-74</citation>
        <citation type="doi">10.1093/bioinformatics/btn051</citation>
        <citation type="doi">10.1038/s41467-022-32661-x</citation>
    </citations>
</tool>