Mercurial > repos > bimib > cobraxy
changeset 443:3d4e10546917 draft
Uploaded
| author | francesco_lapi |
|---|---|
| date | Wed, 10 Sep 2025 16:50:16 +0000 |
| parents | 37cb70ff98b1 |
| children | 06564187fba3 |
| files | COBRAxy/flux_simulation_beta.xml flux_simulation_beta.xml |
| diffstat | 2 files changed, 5 insertions(+), 155 deletions(-) [+] |
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--- a/COBRAxy/flux_simulation_beta.xml Wed Sep 10 16:45:58 2025 +0000 +++ b/COBRAxy/flux_simulation_beta.xml Wed Sep 10 16:50:16 2025 +0000 @@ -95,16 +95,11 @@ <option value="fluxes" selected="false">All fluxes</option> </param> - <conditional name="cond_output_types_analysis"> - <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from flux analysis"> - <option value="pFBA" selected="false">pFBA</option> - <option value="FVA" selected="false">FVA</option> - <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option> - </param> - <when value="FVA"> - <param name="perc_opt" argument="--perc_opt" type="float" label="Fraction of optimality for FVA (0-1):" value="0.9" help="Choose the fraction of optimality for FVA (0-1). Default is 0.9."/> - </when> - </conditional> + <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from flux analysis"> + <option value="pFBA" selected="false">pFBA</option> + <option value="FVA" selected="false">FVA</option> + <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option> + </param> </inputs> <outputs>
--- a/flux_simulation_beta.xml Wed Sep 10 16:45:58 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -<tool id="fluxSimulation - Beta" name="Flux Simulation - BETA" version="2.0.0"> - - <macros> - <import>marea_macros.xml</import> - </macros> - - <requirements> - <requirement type="package" version="1.24.4">numpy</requirement> - <requirement type="package" version="2.0.3">pandas</requirement> - <requirement type="package" version="0.29.0">cobra</requirement> - <requirement type="package" version="5.2.2">lxml</requirement> - <requirement type="package" version="1.4.2">joblib</requirement> - <requirement type="package" version="1.11">scipy</requirement> - </requirements> - - <command detect_errors="exit_code"> - <![CDATA[ - python $__tool_directory__/flux_simulation_beta.py - --tool_dir $__tool_directory__ - --model_and_bounds $model_and_bounds.model_and_bounds - - #if $model_and_bounds.model_and_bounds == 'True': - --model_upload $model_and_bounds.model_upload - --input "${",".join(map(str, $model_and_bounds.inputs))}" - #set $names = "" - #for $input_temp in $model_and_bounds.inputs: - #set $names = $names + $input_temp.element_identifier + "," - #end for - --name $names - #else: - --input "${",".join(map(str, $model_and_bounds.model_files))}" - #set $names = "" - #for $input_temp in $model_and_bounds.model_files: - #set $names = $names + $input_temp.element_identifier + "," - #end for - --name $names - #end if - - --thinning 0 - #if $algorithm_param.algorithm == 'OPTGP': - --thinning $algorithm_param.thinning - #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))}" - --out_log $log - ]]> - </command> - - <inputs> - <conditional name="model_and_bounds"> - <param name="model_and_bounds" argument="--model_and_bounds" type="select" label="Upload mode:" help="Choose whether to upload the model and bounds in separate files or to upload multiple complete model files."> - <option value="True" selected="true">Model + bounds (separate files)</option> - <option value="False">Multiple complete models</option> - </param> - - <when value="True"> - <param name="model_upload" argument="--model_upload" type="data" format="csv,tsv,tabular" - label="Model (rules) file:" - help="Upload a CSV/TSV file that contains the model reaction rules. Recommended columns: ReactionID, Reaction (formula), Rule (GPR). Optional columns: name, lower_bound, upper_bound, InMedium. If bounds are present here they may be overridden by separate bound files." /> - - <param name="inputs" argument="--inputs" multiple="true" type="data" format="tabular,csv,tsv" - label="Bound file(s):" - help="Upload one or more CSV/TSV files containing reaction bounds. Each file must include at least: ReactionID, lower_bound, upper_bound. Files are applied in the order provided; later files override earlier ones for the same ReactionID." /> - </when> - - <when value="False"> - <param name="model_files" argument="--model_files" multiple="true" type="data" format="csv,tsv,tabular" - label="Complete model files:" - help="Upload one or more CSV/TSV files, each containing both model rules and reaction bounds for different contexts/cells. Required columns: ReactionID, Reaction, Rule, lower_bound, upper_bound." /> - </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> - </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"/> - <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="true">Median</option> - <option value="quantiles" selected="true">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 flux analysis"> - <option value="pFBA" selected="false">pFBA</option> - <option value="FVA" selected="false">FVA</option> - <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option> - </param> - </inputs> - - <outputs> - <data format="txt" name="log" label="Flux Simulation - Log" /> - <data name="output" format="tabular" label="Flux Simulation - Output"> - <discover_datasets pattern="__name_and_ext__" directory="flux_simulation" visible="true" /> - </data> - </outputs> - - <help> - <![CDATA[ -What it does -------------- - -This tool generates flux samples starting from metabolic models using CBS (Corner-based sampling) or OPTGP (Improved Artificial Centering Hit-and-Run sampler) algorithms. - -Two upload modes are supported: -1. **Model + bounds**: Upload one base model 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: - - mean - - median - - quantiles (0.25, 0.50, 0.75) - -Flux analysis can be performed over the metabolic model: - - parsimonious-FBA (optimized by Biomass) - - FVA - - Biomass sensitivity analysis (single reaction knock-out) - -Output: -------------- - -The tool generates: - - Samples: reporting the sampled fluxes for each reaction (reaction names on the rows and sample names on the columns). Format: tab-separated. - - a log file (.txt). - -**TIP**: The Batches parameter helps maintain memory efficiency. For 10,000 samples, use n_samples=1,000 and n_batches=10. -**TIP**: The Thinning parameter for OPTGP helps converge to stationary distribution. -]]> - </help> - <expand macro="citations_fluxes" /> -</tool> \ No newline at end of file