comparison rpfba.xml @ 5:beabdc945670 draft default tip

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

4:f297590100c8

            #if str($adv.merge) == "true":
                --merge '$output_merge'
            #end if
                --objective_rxn_id '$objective_rxn_id'
                --sim '$input_sim_type.sim_type'
            #if str($adv.ignore_orphan_species) == "true":
                --ignore_orphan_species
            #end if
                --log "error"
            #if str($input_sim_type.sim_type)=="fba"
                --fraction_of 0.0
            #else

            <when value="fba">
            </when>
        </conditional>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="merge" type="boolean" label="Output the merged model?" checked="false" display="checkboxes" />
            <param name="ignore_orphan_species" type="boolean" label="Ignore metabolites that are only consumed or produced?" checked="true" />
        </section>
    </inputs>
    <outputs>
        <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" />
        <data name="output_merge" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name} - merge">

* **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
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1186/1752-0509-7-74</citation>
        <citation type="doi">10.1515/jib-2016-290</citation>

5:beabdc945670

            #if str($adv.merge) == "true":
                --merge '$output_merge'
            #end if
                --objective_rxn_id '$objective_rxn_id'
                --sim '$input_sim_type.sim_type'
            #if str($adv.with_orphan_species) == "true":
                --with_orphan_species
            #end if
                --log "error"
            #if str($input_sim_type.sim_type)=="fba"
                --fraction_of 0.0
            #else

            <when value="fba">
            </when>
        </conditional>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="merge" type="boolean" label="Output the merged model?" checked="false" display="checkboxes" />
            <param name="with_orphan_species" type="boolean" label="Add metabolites that are only consumed or produced?" checked="false" />
        </section>
    </inputs>
    <outputs>
        <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" />
        <data name="output_merge" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name} - merge">

* **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
* **With Orphan Species?**\ : (boolean, default=False) add metabolites that are only consumed or produced
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1186/1752-0509-7-74</citation>
        <citation type="doi">10.1515/jib-2016-290</citation>