comparison rpfba.xml @ 2:6f0d786299ca draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty

1:c554f15279fe

<tool id="rpfba" name="FBA" version="@TOOL_VERSION@" profile="19.09">
    <description>Perform FBA for the RetroPath2.0 heterologous pathways</description>
    <macros>
        <token name="@TOOL_VERSION@">5.12.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
    </requirements>
    <stdio>

        <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
        <param name="model" type="data" format="sbml" label="Model (SBML)" />
        <param name="compartment_id" type="text" label="SBML compartment ID" value="c" >
            <validator type="empty_field" message="A compartment ID is required"/>
        </param>
        <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" >
            <validator type="empty_field" message="Reaction ID is required"/>
        </param>
        <param name="biomass_rxn_id" type="text" label="biomass reaction ID" value="" >
            <validator type="empty_field" message="Biomass reaction ID is required"/>
        </param>
        <conditional name="input_sim_type">
            <param name="sim_type" type="select" label="Constraint based simulation type">
                <option value="fraction" selected="true">Fraction of Reaction</option>

        <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718)  -->
            <param name="pathway" value="rp_001_0001.xml" />
            <param name="model" value="iCN718.xml.gz" />
            <param name="biomass_rxn_id" value="R_BIOMASS__3" />
            <output name="pathway_with_fba" >
                <assert_contents>
                    <is_valid_xml />

                </assert_contents>
            </output>
        </test>
        <test>
        <!-- test 2: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718)  and sim_type=fba-->
            <param name="pathway" value="rp_001_0001.xml" />
            <param name="model" value="iCN718.xml.gz" />
            <param name="biomass_rxn_id" value="R_BIOMASS__3" />
            <conditional name="input_sim_type">
                <param name="sim_type" value="fba"/>
            </conditional>

                </assert_contents>
            </output>
        </test>
        <test>
        <!-- test 3: check if identical outputs are produced with R_DM_biomass_c biomass name ID and BiGG model (iCN718)  and sim_type=pfba-->
            <param name="pathway" value="rp_001_0001.xml" />
            <param name="model" value="iCN718.xml.gz" />
            <param name="biomass_rxn_id" value="R_DM_biomass_c" />
            <conditional name="input_sim_type">
                <param name="sim_type" value="pfba"/>
            </conditional>

Input
-----

Required:


* **pathway_file**\ : (string) SBML file that contains an heterologous pathway
* **model_filel**\ : (string) Path to the GEM SBML model
* **compartment_id**\ : (string) Model compartment id (e.g. 'c' or 'MNXC3')
* **outfile**\ : (string) Path to the output file

Advanced options:


* **--sim**\ : (string, default=fraction) Valid options include: fraction, fba, pfba. The type of constraint based modelling method
* **--biomass_rxn_id**\ : (string, default=biomass) biomass reaction ID that will be restricted in the "fraction" simulation type. This parameter is ignored for "fba" and "pfba"
* **--objective_rxn_id**\ : (string, default=rxn_target) reaction ID to optimise. This parameters is required in all simulation type
* **--fraction_of**\ : (float, default=0.75) Portion of the maximal flux used to set the maximal and minimal bounds for the source reaction of the "fraction" simulation type
* **--merge**\ : (boolean, default=False) output the full merged model instead of heterologous pathway only
* **--ignore_orphan_species**\ : (boolean, default=True) ignore metabolites that are only consumed or produced
* **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical'


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

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

Version
----------

5.12.1

Authors
-------

* **Melchior du Lac**
* **Joan Hérisson**

License
-------

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

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

* Thomas Duigou
    ]]></help>
    <citations>
        <citation type="doi">10.1186/1752-0509-7-74</citation>
        <citation type="doi">10.1515/jib-2016-290 </citation>    
    </citations>
</tool>

2:6f0d786299ca

<tool id="rpfba" name="Flux balance analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>for the RetroPath2.0 heterologous pathways</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">6.0.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
    </requirements>
    <stdio>

        <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
        <param name="model" type="data" format="sbml" label="Model (SBML)" />
        <param name="compartment_id" type="text" label="SBML compartment ID" value="c" >
            <validator type="empty_field" message="A compartment ID is required"/>
        </param>
        <param name="objective_rxn_id" type="text" value="rxn_target" label="Reaction ID to optimise" >
            <validator type="empty_field" message="Reaction ID is required"/>
        </param>
        <param name="biomass_rxn_id" type="text" label="Biomass reaction ID" value="" >
            <validator type="empty_field" message="Biomass reaction ID is required"/>
        </param>
        <conditional name="input_sim_type">
            <param name="sim_type" type="select" label="Constraint based simulation type">
                <option value="fraction" selected="true">Fraction of Reaction</option>

        <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718)  -->
            <param name="pathway" value="rp_001_0001_rpfba_in.xml" />
            <param name="model" value="iCN718.xml.gz" />
            <param name="biomass_rxn_id" value="R_BIOMASS__3" />
            <output name="pathway_with_fba" >
                <assert_contents>
                    <is_valid_xml />

                </assert_contents>
            </output>
        </test>
        <test>
        <!-- test 2: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718)  and sim_type=fba-->
            <param name="pathway" value="rp_001_0001_rpfba_in.xml" />
            <param name="model" value="iCN718.xml.gz" />
            <param name="biomass_rxn_id" value="R_BIOMASS__3" />
            <conditional name="input_sim_type">
                <param name="sim_type" value="fba"/>
            </conditional>

                </assert_contents>
            </output>
        </test>
        <test>
        <!-- test 3: check if identical outputs are produced with R_DM_biomass_c biomass name ID and BiGG model (iCN718)  and sim_type=pfba-->
            <param name="pathway" value="rp_001_0001_rpfba_in.xml" />
            <param name="model" value="iCN718.xml.gz" />
            <param name="biomass_rxn_id" value="R_DM_biomass_c" />
            <conditional name="input_sim_type">
                <param name="sim_type" value="pfba"/>
            </conditional>

Input
-----

Required:

* **Pathway (rpSBML)**\ : SBML file that contains an heterologous pathway
* **Model (SBML)**\ : GEM SBML model file
* **Biomass reaction ID**\ : (string) biomass reaction ID that will be restricted in the "fraction" simulation type. This parameter is ignored for "fba" and "pfba"

Optional:

* **SBML compartment ID**\ : (string, default='c') Model compartment id (e.g. 'c' or 'MNXC3')
* **reaction ID to optimise**\ : (string, default=rxn_target) reaction ID to optimise. This parameters is required in all simulation type
* **Constraint based simulation type**\ : (string, default=Fraction of Reaction) The type of constraint based modelling method. Valid options include: Fraction of Reaction, FBA, Parsimonious FBA.
* **Fraction of the optimum**\ : (float, default=0.75) Portion of the maximal flux used to set the maximal and minimal bounds for the source reaction of the "fraction" simulation type.

Advanced options:

* **Output the merged model?**\ : (boolean, default=False) output the full merged model instead of heterologous pathway only
* **Ignore Orphan Species?**\ : (boolean, default=True) ignore metabolites that are only consumed or produced


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

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

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">10.1186/1752-0509-7-74</citation>
        <citation type="doi">10.1515/jib-2016-290 </citation>    
    </citations>
</tool>