# HG changeset patch
# User francesco_lapi
# Date 1757523016 0
# Node ID 3d4e10546917e77fbbe1b1f24074131ae68fdc9b
# Parent  37cb70ff98b159b886422e649417cd25e03db472
Uploaded

diff -r 37cb70ff98b1 -r 3d4e10546917 COBRAxy/flux_simulation_beta.xml
--- 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>
diff -r 37cb70ff98b1 -r 3d4e10546917 flux_simulation_beta.xml
--- 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