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+++ b/flux_simulation_beta.xml	Wed Sep 10 16:45:58 2025 +0000
@@ -0,0 +1,145 @@
+<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>
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