Mercurial > repos > tduigou > rpfba
changeset 2:6f0d786299ca draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
| author | tduigou |
|---|---|
| date | Fri, 18 Nov 2022 16:14:30 +0000 |
| parents | c554f15279fe |
| children | |
| files | rpfba.xml |
| diffstat | 1 files changed, 25 insertions(+), 32 deletions(-) [+] |
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--- a/rpfba.xml Thu Feb 10 11:36:24 2022 +0000 +++ b/rpfba.xml Fri Nov 18 16:14:30 2022 +0000 @@ -1,7 +1,8 @@ -<tool id="rpfba" name="FBA" version="@TOOL_VERSION@" profile="19.09"> - <description>Perform FBA for the RetroPath2.0 heterologous pathways</description> +<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="@TOOL_VERSION@">5.12.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">6.0.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> @@ -34,10 +35,10 @@ <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" > + <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="" > + <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"> @@ -66,7 +67,7 @@ <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="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" > @@ -82,7 +83,7 @@ </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="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"> @@ -100,7 +101,7 @@ </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="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"> @@ -150,22 +151,21 @@ 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" -* **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 +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: - -* **--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' +* **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 @@ -173,27 +173,20 @@ * `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>`_ +* `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ Acknowledgments --------------- * Thomas Duigou ]]></help> + <creator> + <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" 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>