diff COBRAxy/src/flux_simulation.xml @ 539:2fb97466e404 draft

Uploaded

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+++ b/COBRAxy/src/flux_simulation.xml	Sat Oct 25 14:55:13 2025 +0000
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+<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="1.11">scipy</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code">
+        <![CDATA[
+        python $__tool_directory__/flux_simulation.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_list = []
+            #for $input_temp in $model_and_bounds.inputs:
+                #silent $names_list.append(str($input_temp.element_identifier))
+            #end for
+            --name "${",".join($names_list)}"
+        #else:
+            --input "${",".join(map(str, $model_and_bounds.model_files))}"
+            #set $names_list = []
+            #for $input_temp in $model_and_bounds.model_files:
+                #silent $names_list.append(str($input_temp.element_identifier))
+            #end for
+            --name "${",".join($names_list)}"
+        #end if
+        
+        --sampling_enabled $sampling_params.sampling_enabled
+        
+        #if $sampling_params.sampling_enabled == '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
+            --seed $sampling_params.seed
+            --output_type "${",".join(map(str, $sampling_params.output_types))}"
+        #else:
+            --thinning 0
+            --algorithm 'CBS'
+            --n_batches 1
+            --n_samples 1
+            --seed 0
+            --output_type 'mean'
+        #end if
+        
+        #if $output_types_analysis:
+            --output_type_analysis "${",".join(map(str, $output_types_analysis))}"
+        #end if
+        
+        #if 'FVA' in str($output_types_analysis):
+            --perc_opt $fva_params.optimality_fraction
+        #end if
+        
+        --out_log $log
+
+        #if $sampling_params.sampling_enabled == 'true':
+            #if 'mean' in str($sampling_params.output_types):
+                --out_mean $mean_results
+            #end if
+            #if 'median' in str($sampling_params.output_types):
+                --out_median $median_results
+            #end if
+            #if 'quantiles' in str($sampling_params.output_types):
+                --out_quantiles $quantile_results
+            #end if
+        #end if
+        
+        #if 'FVA' in str($output_types_analysis):
+            --out_fva $fva_results
+        #end if
+        #if 'pFBA' in str($output_types_analysis):
+            --out_pfba $pFBA_results
+        #end if
+        #if 'sensitivity' in str($output_types_analysis):
+            --out_sensitivity $sensitivity_results
+        #end if
+        ]]>
+    </command>
+
+    <inputs>
+        <conditional name="model_and_bounds">
+            <param name="model_and_bounds" argument="--model_and_bounds" type="select" label="Input format:" 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 tabular:"
+                    help="Upload a CSV/TSV file that contains the model reaction rules generated by the Import Metabolic Model tool. 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 generated by the Ras2Bounds tool. 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 tabular:"
+                    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="sampling_params">
+            <param name="sampling_enabled" argument="--sampling_enabled" type="boolean" display="checkboxes" checked="false" label="Enable sampling" help="Enable flux sampling"/>
+            
+            <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" min="1" max="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="Choose 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>
+            </when>
+            
+            <when value="false">
+                <!-- Hidden parameters when sampling is disabled -->
+                <param name="algorithm" type="hidden" value="CBS"/>
+                <param name="n_samples" type="hidden" value="1000"/>
+                <param name="n_batches" type="hidden" value="1"/>
+                <param name="seed" type="hidden" value="0"/>
+                <param name="output_types" type="hidden" value="mean"/>
+            </when>
+        </conditional>
+
+        <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Choose outputs from optimization">
+            <option value="FVA" selected="true">FVA</option>
+            <option value="pFBA" selected="false">pFBA</option>
+            <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>
+        </param>
+
+        <conditional name="fva_params">
+            <param name="show_fva_options" type="boolean" display="checkboxes" checked="false" label="Configure FVA parameters" help="Show additional FVA configuration options"/>
+            <when value="true">
+                <param name="optimality_fraction" argument="--fva_optimality" type="float" label="FVA Optimality (fraction):" value="0.90" min="0.0" max="1.0" 
+                    help="Fraction of optimality for FVA analysis. 1.0 means the flux must be optimal, lower values allow suboptimal solutions."/>
+            </when>
+            <when value="false">
+                <param name="optimality_fraction" argument="--fva_optimality" type="hidden" value="1.0"/>
+            </when>
+        </conditional>
+
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="log" label="Flux Simulation - Log" />
+        
+        <collection name="fluxes_results" type="list" label="Fluxes">
+            <filter>sampling_params['sampling_enabled'] and 'fluxes' in sampling_params['output_types']</filter>
+            <discover_datasets name="collection" pattern="__name_and_ext__" directory="flux_simulation"/>
+        </collection>
+        
+        <data format="tabular" name="mean_results" label="Mean">
+            <filter>sampling_params['sampling_enabled'] and 'mean' in sampling_params['output_types']</filter>
+        </data>
+        
+        <data format="tabular" name="median_results" label="Median">
+            <filter>sampling_params['sampling_enabled'] and 'median' in sampling_params['output_types']</filter>
+        </data>
+        
+        <data format="tabular" name="quantile_results" label="Quantiles">
+            <filter>sampling_params['sampling_enabled'] and 'quantiles' in sampling_params['output_types']</filter>
+        </data>
+        
+        <data format="tabular" name="fva_results" label="FVA">
+            <filter>output_types_analysis and 'FVA' in output_types_analysis</filter>
+        </data>
+        
+        <data format="tabular" name="pFBA_results" label="pFBA">
+            <filter>output_types_analysis and 'pFBA' in output_types_analysis</filter>
+        </data>
+        
+        <data format="tabular" name="sensitivity_results" label="Sensitivity">
+            <filter>output_types_analysis and 'sensitivity' in output_types_analysis</filter>
+        </data>
+    </outputs>
+
+    <help>
+    <![CDATA[
+Overview
+-------------
+
+This tool generates flux samples from a set of metabolic models. It supports two input modes:
+    - Model + bounds: upload a single base model and multiple bound files (one per context/cell type)
+    - Multiple complete models: upload multiple model files, each already containing its own bounds.
+
+In the first mode:
+    - the base model must be in tabular format as produced by the Import Metabolic Model tool.
+    - the bound files should come from the RAStoBounds tool.
+
+In the second mode, provide a separate tabular file for each complete model.
+
+Available analyses
+------------- 
+
+Two types of analysis are available:
+    - flux optimization
+    - flux sampling
+
+For flux optimization, one of the following methods can be performed:
+    - parsimonious-FBA
+    - Flux Variability Analysis
+    - Biomass sensitivity analysis (single reaction knock-out)
+The objective function — a linear combination of fluxes weighted by specific coefficients — depends on the provided metabolic network.
+
+For flux sampling, one of the following methods can be performed: 
+    - CBS (Corner-based sampling)
+    - OPTGP (Improved Artificial Centering Hit-and-Run sampler) algorithms.
+
+
+Output:
+-------------
+
+The tool produces:
+   - 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).
+
+The sampled fluxes can be reported as full datasets or summarized using descriptive statistics such as mean, median, and quantiles (0.25, 0.50, 0.75), computed for each model.
+
+**TIP**: Bounds generated by RAStoBound are grouped in a collection. You can select collections by clicking on "Dataset Collection" option in the "Bound file(s):" input parameter.
+
+**TIP**: The Batches parameter helps maintain memory efficiency. For example, for 10,000 samples, use n_samples=1,000 and n_batches=10.
+
+**TIP**: Adjust the Thinning parameter to improve convergence toward the stationary distribution. 
+Common thinning values are 100 or 1000.Note that if you set thinning = 100 and request 100 samples, the total number of generated flux samples will be 100 * 100.
+
+**TIP**: FVA optimality percentage allows you to explore suboptimal flux ranges. 100% restricts to optimal solutions, while lower values (e.g., 90%) allow broader flux ranges.
+]]>
+    </help>
+    <expand macro="citations_fluxes" />
+</tool>
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