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+++ b/COBRAxy/flux_simulation.xml	Sun Oct 13 11:41:34 2024 +0000
@@ -0,0 +1,134 @@
+<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="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 a model in JSON or XML format by using CBS (Corner-based sampling) or OPTGP (Improved 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). 
+
+Flux analysis can be perfomed over the metabolic model:
+   - parsimoniuos-FBA (optimized by Biomass)
+   - FVA
+   - Biomass sensitivity analysis (single reaction knock-out). It is the ratio between the optimal of the Biomass reaction computed by FBA 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 ENGRO2 or a custom model. 
+   - Context-specific bounds: generated by RAS to Bounds tool. This can be a collection of bounds too (one bounds file per context).
+
+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 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.
+**TIP**: The Thinning parameter of the OPTGP algorithm is useful to converge to a stationary distribution (see cited articles by Galuzzi, Milazzo and Damiani).
+
+]]>
+    </help>
+    <expand macro="citations_fluxes" />
+ 
+</tool>
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