comparison rpextractsink.xml @ 3:d9287c69a7f4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 044274b46d50a1d0e3708e80e0dfecf1de653c65

2:caf2b5731a5e

    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rptools.rpextractsink
            '$input'
            '$sink'
            --compartment_id '$compartment_id'
            $adv.remove_dead_end
            --cache-dir "\${TMPDIR:-.}"
    ]]></command>
    <inputs>
        <param name="input" type="data" format="sbml" optional="false" label="Strain" help="The structure of metabolites present in the chosen chassis strain in SBML format" />
        <param name="compartment_id" type="text" value="c" label="SBML compartment ID" help="Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol)" >
            <validator type="empty_field" message="SBML compartment ID is required"/>
        </param>
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="--remove_dead_end" type="boolean" truevalue="--remove_dead_end" falsevalue="" checked="true" label="Remove dead-end metabolites using FVA evaluation?" help="Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites" />
        </section>
    </inputs>
    <outputs>
        <data name="sink" format="csv" metadata_source="input" label="Sink - ${input.name}" />
    </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
=================

* **SBML compartment ID**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol).

Advanced options:

* **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites.

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>`_.

3:d9287c69a7f4

    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rptools.rpextractsink
            '$input'
            '$sink'
            --compartment-id '$compartment_id'
            $adv.remove_dead_end
            $adv.standalone
            --cache-dir "\${TMPDIR:-.}"
    ]]></command>
    <inputs>
        <param name="input" type="data" format="sbml" optional="false" label="Strain" help="The structure of metabolites present in the chosen chassis strain in SBML format" />
        <param name="compartment_id" type="text" value="c" label="SBML compartment ID" help="Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol)" >
            <validator type="empty_field" message="SBML compartment ID is required"/>
        </param>
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="--remove_dead_end" type="boolean" truevalue="--remove-dead-end" falsevalue="" checked="true" label="Remove dead-end metabolites using FVA evaluation?" help="Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites" />
            <param argument="--standalone" type="boolean" truevalue="--standalone" falsevalue="" checked="true" label="Do not connect to Internet" help="If True, do not retrieve InChI from Internet" />
        </section>
    </inputs>
    <outputs>
        <data name="sink" format="csv" metadata_source="input" label="Sink - ${input.name}" />
    </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="5ff3987609142e828ec8e3c97b8dab12" />
        </test>
    </tests>
    <help><![CDATA[
Sink from SBML
=================

* **SBML compartment ID**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol).

Advanced options:

* **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites.
* **Do not connect to Internet**: (boolean, default: False) If True, do not retrieve InChI from Internet

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>`_.