changeset 104:bf759eb48bf2 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flux_sampling.xml	Thu Jun 27 12:07:50 2024 +0000
@@ -0,0 +1,80 @@
+<tool id="fluxSampling" name="COBRAxy Model sampling" version="2.0.0">
+    
+    <macros>
+        <import>marea_macros.xml</import>
+    </macros>
+
+	<requirements>
+        <requirement type="package" version="0.29.0">cobra</requirement>
+        <requirement type="package" version="4.9.3">lxml</requirement>
+	</requirements>
+
+    <command detect_errors="exit_code">
+        <![CDATA[
+      	python $__tool_directory__/flux_sampling.py
+        --input $input
+        --name $input.element_identifier
+        #if $algorithm_param.algorithm == 'OPTGP':
+        	--thinning $thinning
+        --n_batches $n_batches
+        --n_samples $n_samples
+        --seed $seed
+        --output_format $output_format
+        --out_log $log
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" argument="--input" type="data" format="xml, json" label="Model:" />
+
+        <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:" />
+        	</when>
+
+		</conditional>
+
+        <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" default="1"/>
+
+        <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" default="1000"/>
+
+        <param name="seed" argument="--seed" type="integer" label="Seed:" default="0"/>
+        
+        <param name="output_format" argument="--output_format" type="select" label="Output files format:">
+            <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
+            <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="log" label="fluxSampling - $name - Log" />
+        
+        <collection name="results" type="list" label="Model sampling result ($output_format)">
+            <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
+        </collection>
+    </outputs>
+
+    <help>
+    <![CDATA[
+What it does
+-------------
+
+This tool generates feasible 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.
+
+Accepted files:
+    - A model: JSON or XML file reporting reactions and rules contained in the model.   
+
+
+Output:
+-------------
+
+The tool generates:
+    - Samples: reporting the sampled fluxes for each reaction in the custom model given. Format: csv or pickle.
+    - a log file (.txt).
+    ]]>
+    </help>
+    <expand macro="citations" />
+</tool>
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