changeset 221:c3f2be2334bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/marea_2_0/utils/model_generator.xml	Sat Jul 06 09:54:41 2024 +0000
@@ -0,0 +1,83 @@
+<tool id="modelGenerator" name="COBRAxy Model generator" 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>
+        <requirement type="package" version="1.4.2">joblib</requirement>
+	</requirements>
+
+    <command detect_errors="exit_code">
+        <![CDATA[
+        python $__tool_directory__/model_generator.py
+        --model_selector $cond_model.model_selector
+        --tool_dir $__tool_directory__
+        --input_medium $input_medium
+        --input_ras $input_ras
+        --output_type "${",".join(map(str, $output_types))}"
+        --out_log $log
+        #if $cond_model.model_selector == 'Custom'
+            --model $model
+            --model_name $model.element_identifier
+        #end if
+        ]]>
+    </command>
+
+    <inputs>
+
+        <conditional name="cond_model">
+            <expand macro="options"/>
+            <when value="Custom">
+                <param name="model" argument="--model" type="data" format="json, xml" label="Custom modellll" />
+            </when>
+        </conditional>
+
+        <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
+
+        <param name="input_medium" argument="--input_medium" multiple="false" type="data" format="tabular, csv, tsv" label="Medium:"/>
+
+        <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs">
+            <option value="FBA" selected="false">FBA</option>
+            <option value="pFBA" selected="false">pFBA</option>
+            <option value="FVA" selected="false">FVA</option>
+            <option value="sensitivity" selected="false">Sensitivity knock-out</option>
+        </param>
+        
+    </inputs>
+
+        		
+    <outputs>
+        <data format="txt" name="log" label="modelGenerator - Log" />
+        <collection name="results" type="list" label="${tool.name} - Results">
+            <discover_datasets pattern="__name_and_ext__" directory="model_generator"/>
+        </collection>
+    </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) 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. It can be a single model, multiple models or a collection of models. 
+
+Output:
+-------------
+
+The tool generates:
+    - Samples: reporting the sampled fluxes for each reaction. Format: csv or pickle.
+    - 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.
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
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