Mercurial > repos > bimib > cobraxy
changeset 460:6a7010997b32 draft
Uploaded
| author | luca_milaz |
|---|---|
| date | Mon, 22 Sep 2025 13:42:03 +0000 |
| parents | f8c3d9f28f64 |
| children | 73f02860f7d7 |
| files | COBRAxy/flux_simulation_beta.xml |
| diffstat | 1 files changed, 49 insertions(+), 29 deletions(-) [+] |
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--- a/COBRAxy/flux_simulation_beta.xml Wed Sep 17 14:52:40 2025 +0000 +++ b/COBRAxy/flux_simulation_beta.xml Mon Sep 22 13:42:03 2025 +0000 @@ -36,15 +36,24 @@ --name $names #end if - --thinning 0 - #if $algorithm_param.algorithm == 'OPTGP': - --thinning $algorithm_param.thinning + #if $sampling_params.enable_sampling == 'True': + --thinning 0 + #if $sampling_params.algorithm_param.algorithm == 'OPTGP': + --thinning $sampling_params.algorithm_param.thinning + #end if + --algorithm $sampling_params.algorithm_param.algorithm + --n_batches $sampling_params.n_batches + --n_samples $sampling_params.n_samples + --output_type "${",".join(map(str, $sampling_params.output_types))}" + #else: + --thinning 0 + --algorithm CBS + --n_batches 1 + --n_samples 0 + --output_type "mean" #end if - --algorithm $algorithm_param.algorithm - --n_batches $n_batches - --n_samples $n_samples + --seed $seed - --output_type "${",".join(map(str, $output_types))}" --output_type_analysis "${",".join(map(str, $output_types_analysis))}" #if 'FVA' in str($output_types_analysis): @@ -79,30 +88,40 @@ </when> </conditional> - <conditional name="algorithm_param"> - <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:"> - <option value="CBS" selected="true">CBS</option> - <option value="OPTGP">OPTGP</option> + <conditional name="sampling_params"> + <param name="enable_sampling" type="select" label="Enable sampling:" help="Choose whether to perform flux sampling."> + <option value="False" selected="true">No sampling (optimization only)</option> + <option value="True">Enable sampling</option> </param> - <when value="OPTGP"> - <param name="thinning" argument="--thinning" type="integer" label="Thinning:" value="100" help="Number of iterations to wait before taking a sample."/> + + <when value="True"> + <conditional name="algorithm_param"> + <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:"> + <option value="CBS" selected="true">CBS</option> + <option value="OPTGP">OPTGP</option> + </param> + <when value="OPTGP"> + <param name="thinning" argument="--thinning" type="integer" label="Thinning:" value="100" help="Number of iterations to wait before taking a sample."/> + </when> + </conditional> + + <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="1000" help="Number of samples to generate."/> + <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="1" help="This is useful for computational performances."/> + + <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs from sampling"> + <option value="mean" selected="true">Mean</option> + <option value="median" selected="false">Median</option> + <option value="quantiles" selected="false">Quantiles</option> + <option value="fluxes" selected="false">All fluxes</option> + </param> </when> </conditional> - <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="0" help="Select 0 Set to 0 if you don’t want to perform sampling but only optimization."/> - <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="1" help="This is useful for computational performances."/> <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" help="Random seed."/> - <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs from sampling"> - <option value="mean" selected="true">Mean</option> - <option value="median" selected="false">Median</option> - <option value="quantiles" selected="false">Quantiles</option> - <option value="fluxes" selected="false">All fluxes</option> - </param> - <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from optimization"> - <option value="pFBA" selected="true">pFBA</option> - <option value="FVA" selected="false">FVA</option> + <option value="pFBA" selected="false">pFBA</option> + <option value="FVA" selected="true">FVA</option> <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option> </param> @@ -132,18 +151,20 @@ ------------- This tool generates flux distributions for each samples using: -1. a sampling-based strategy: CBS (Corner-based sampling) or OPTGP (Improved Artificial Centering Hit-and-Run sampler) algorithms. -2. an optimization-based strategy: parsimonious-FBA (optimized by Biomass), FVA (with configurable optimality percentage), Biomass sensitivity analysis (single reaction knock-out) +1. a sampling-based strategy (optional): CBS (Corner-based sampling) or OPTGP (Improved Artificial Centering Hit-and-Run sampler) algorithms. +2. an optimization-based strategy: parsimonious-FBA (optimized by Biomass), FVA (with configurable optimality percentage), Biomass sensitivity analysis (single reaction knock-out) Two upload modes are supported: 1. **Model + bounds**: Upload one base model (tabular file) and multiple bound files (one per context/cell type) 2. **Multiple complete models**: Upload multiple complete model files, each with integrated bounds -It can return sampled fluxes by applying summary statistics: +**Sampling (optional)**: When enabled, it can return sampled fluxes by applying summary statistics: - mean - median - quantiles (0.25, 0.50, 0.75) +**Optimization**: Always available with FVA as the default analysis method. + Output: ------------- @@ -158,5 +179,4 @@ </help> <expand macro="citations_fluxes" /> -</tool> - +</tool> \ No newline at end of file