From 53b6c3fe090fccd4a8d0b2c695280b7f7b3b4302 Mon Sep 17 00:00:00 2001 From: guillaume-gricourt Date: Fri, 1 Dec 2023 14:50:13 +0100 Subject: [PATCH 1/3] feat(tools): rptools, update rptools --- tools/rptools/macros.xml | 2 +- tools/rptools/rpfba.xml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/rptools/macros.xml b/tools/rptools/macros.xml index 9ac9d279..36127303 100644 --- a/tools/rptools/macros.xml +++ b/tools/rptools/macros.xml @@ -1,5 +1,5 @@ - 6.4.1 + 6.5.0 0 diff --git a/tools/rptools/rpfba.xml b/tools/rptools/rpfba.xml index 93a86921..47902894 100644 --- a/tools/rptools/rpfba.xml +++ b/tools/rptools/rpfba.xml @@ -15,8 +15,8 @@ #end if --objective_rxn_id '$objective_rxn_id' --sim '$input_sim_type.sim_type' - #if str($adv.ignore_orphan_species) == "true": - --ignore_orphan_species + #if str($adv.with_orphan_species) == "true": + --with_orphan_species #end if --log "error" #if str($input_sim_type.sim_type)=="fba" @@ -55,7 +55,7 @@
- +
From fe5cc8d00cb0865e5651b7f9b54f3ca543fb9150 Mon Sep 17 00:00:00 2001 From: guillaume-gricourt Date: Fri, 1 Dec 2023 14:52:25 +0100 Subject: [PATCH 2/3] docs(tools): rptools, update rpfba --- tools/rptools/rpfba.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/rptools/rpfba.xml b/tools/rptools/rpfba.xml index 47902894..17493460 100644 --- a/tools/rptools/rpfba.xml +++ b/tools/rptools/rpfba.xml @@ -55,7 +55,7 @@
- +
@@ -165,7 +165,7 @@ Optional: 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 +* **With Orphan Species?**\ : (boolean, default=False) add metabolites that are only consumed or produced ]]> From b3e90f3aa78f0acc001eeadc5ed22004e93f1f6c Mon Sep 17 00:00:00 2001 From: guillaume-gricourt Date: Thu, 15 Feb 2024 21:51:14 +0100 Subject: [PATCH 3/3] fix(tools): rptools, rm unused files --- tools/rptools/rpcompletion.xml | 37 +++++++++++----------- tools/rptools/rpextractsink.xml | 4 +-- tools/rptools/rpfba.xml | 4 +-- tools/rptools/rpranker.xml | 4 +-- tools/rptools/rpreport.xml | 13 +++----- tools/rptools/rpscore.xml | 4 +-- tools/rptools/rpthermo.xml | 5 +-- tools/rptools/rpviz.xml | 6 ++-- tools/rptools/test-data/medium.fmt.a.csv | 3 -- tools/rptools/test-data/minimal_medium.csv | 1 - 10 files changed, 36 insertions(+), 45 deletions(-) delete mode 100644 tools/rptools/test-data/medium.fmt.a.csv delete mode 100644 tools/rptools/test-data/minimal_medium.csv diff --git a/tools/rptools/rpcompletion.xml b/tools/rptools/rpcompletion.xml index b0ddc496..52697a99 100644 --- a/tools/rptools/rpcompletion.xml +++ b/tools/rptools/rpcompletion.xml @@ -4,21 +4,20 @@ macros.xml - - - - @@ -39,18 +38,18 @@ - - - + + + `_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data. +Completes mono-component reactions output by RetroPath2.0 (10.1016/j.ymben.2017.12.002) with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data. Input ----- diff --git a/tools/rptools/rpextractsink.xml b/tools/rptools/rpextractsink.xml index 2f09798f..7e4d424a 100644 --- a/tools/rptools/rpextractsink.xml +++ b/tools/rptools/rpextractsink.xml @@ -37,8 +37,8 @@ `_ 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. diff --git a/tools/rptools/rpfba.xml b/tools/rptools/rpfba.xml index 17493460..278217dd 100644 --- a/tools/rptools/rpfba.xml +++ b/tools/rptools/rpfba.xml @@ -119,8 +119,8 @@ `_. +rpReport - Report for RetroPath +=============================== +Generates HTML pages to explore the main characteristics (thermodynamics, fluxes, number of metabolic steps, reaction rule score) of pathways predicted with RetroPath suite (10.1016/j.ymben.2017.12.002). Input ----- -Required: - * **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite. Output ------ -* **Pathways HTML Report**: Pathways HTML Report +* **Pathways HTML Report**: Pathways HTML Report. ]]> diff --git a/tools/rptools/rpscore.xml b/tools/rptools/rpscore.xml index b07ab288..1442e03e 100644 --- a/tools/rptools/rpscore.xml +++ b/tools/rptools/rpscore.xml @@ -26,8 +26,8 @@ `_ method. Thereafter this tool predicts the Gibbs free energy of reactions and of the whole heterologous pathway by combining the formation energy of each individual compound. The goal of the thermodynamic analysis is to estimate the feasibility of the predicted pathways toward target production, in physiological conditions (PH, ionic strength). diff --git a/tools/rptools/rpviz.xml b/tools/rptools/rpviz.xml index 690ec81d..e93b77bc 100644 --- a/tools/rptools/rpviz.xml +++ b/tools/rptools/rpviz.xml @@ -76,10 +76,10 @@ `_. +Visualize pathways from the RetroPath Suite (10.1016/j.ymben.2017.12.002). Input ----- diff --git a/tools/rptools/test-data/medium.fmt.a.csv b/tools/rptools/test-data/medium.fmt.a.csv deleted file mode 100644 index 253cf0a0..00000000 --- a/tools/rptools/test-data/medium.fmt.a.csv +++ /dev/null @@ -1,3 +0,0 @@ -compound_id,compound_annotation,compound_group,upper_bound,medium_name -MNXM9,pi,ion,1000,m9 -MNXM196,fe3,ion,1000,m9 diff --git a/tools/rptools/test-data/minimal_medium.csv b/tools/rptools/test-data/minimal_medium.csv deleted file mode 100644 index 0b44af73..00000000 --- a/tools/rptools/test-data/minimal_medium.csv +++ /dev/null @@ -1 +0,0 @@ -,minimize_flux,minimize_component