Mercurial > repos > bimib > marea_2
changeset 363:985cd6f42be4 draft
Uploaded
author | luca_milaz |
---|---|
date | Wed, 18 Sep 2024 09:13:24 +0000 |
parents | cee894a3e41c |
children | 95cda56f01a9 |
files | marea_2/flux_simulation.xml |
diffstat | 1 files changed, 129 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/marea_2/flux_simulation.xml Wed Sep 18 09:13:24 2024 +0000 @@ -0,0 +1,129 @@ +<tool id="fluxSimulation" name="Flux Simulation" 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="1.10.1">scipy</requirement> + </requirements> + + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/flux_simulation.py + --tool_dir $__tool_directory__ + --model_selector $cond_model.model_selector + #if $cond_model.model_selector == 'Custom' + --model $model + --model_name $model.element_identifier + #end if + --input "${",".join(map(str, $inputs))}" + #set $names = "" + #for $input_temp in $inputs: + #set $names = $names + $input_temp.element_identifier + "," + #end for + --name $names + --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="cond_model"> + <expand macro="options_ras_to_bounds_model"/> + <when value="Custom"> + <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" /> + </when> + </conditional> + + <param name="inputs" argument="--inputs" multiple="true" type="data" format="tabular, csv, tsv" label="Bound(s):" /> + + + <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="10" help="This is useful for computational perfomances."/> + + <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" helph="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="fluxSimulation - Log" /> + <collection name="results" type="list" label="${tool.name} - Samples"> + <discover_datasets pattern="__name_and_ext__" directory="flux_simulation"/> + </collection> + </outputs> + + + <help> + <![CDATA[ +What it does +------------- + +This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms. +It can return sampled fluxes by appliying summary statistics: + - mean + - median + - quantiles (0.25, 0.50, 0.75). +Moreover, flux analysis can be perfomed over the metabolic model: + - parsimoniuos-FBA (optimized by Biomass) + - FVA + - Biomass sensitivity analysis (single reaction knock-out). It the ratio between the optimal FBA coefficients of the Biomass reaction after knocking-out a reaction and the same over the complete model. + +Accepted files: + - A model: JSON or XML file reporting reactions and rules contained in the model. It can be a single model, multiple models or a collection of models. + - Cell-specific bounds: generated by RAS to Bounds tool. + +Output: +------------- + +The tool generates: + - Samples: reporting the sampled fluxes for each reaction. Format: csv. + - a log file (.txt). + +**TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10. + + +]]> + </help> + <expand macro="citations" /> +</tool> \ No newline at end of file