changeset 344:eff58e727e4b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/custom_data_generator.xml	Thu Sep 04 22:10:03 2025 +0000
@@ -0,0 +1,87 @@
+<tool id="CustomDataGenerator" name="Custom Data Generator" 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>
+	</requirements>
+
+    <command detect_errors="exit_code">
+        <![CDATA[
+      	python $__tool_directory__/custom_data_generator.py
+        --medium_selector $cond_medium.medium_selector
+        --output_format $output_format
+        #if $cond_model.model_selector == 'Custom_model'
+            --input $cond_model.input
+            --name $cond_model.name
+        #else
+            --model $cond_model.model_selector
+            --name $cond_model.model_selector
+        #end if
+        #if $cond_medium.medium_selector == 'Custom'
+            --medium $cond_medium.medium
+        #end if
+        --out_log $log
+        --out_data $out_data
+        ]]>
+    </command>
+    <inputs>
+        <!-- modello -->
+        <conditional name="cond_model">
+            <expand macro="options_model"/>
+            <when value="Custom_model">
+                <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
+                <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" help="Default: CustomModel. Do not use spaces or special symbols." />
+            </when>
+        </conditional>
+
+        <!-- formato output -->
+        <param name="output_format" argument="--output_format" type="select" label="Output format:">
+            <option value="tabular" selected="true">CSV (tabular)</option>
+            <option value="xlsx">Excel (.xlsx)</option>
+        </param>
+
+        <!-- medium -->
+        <conditional name="cond_medium">
+            <expand macro="options_ras_to_bounds_medium"/>
+            <when value="Custom">
+                <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
+            </when>
+        </conditional> 
+    </inputs>
+
+    <outputs>
+        <data name="log" format="txt" label="CustomDataGenerator - Log" />
+        <data name="out_data" format="$output_format" label="${cond_model.model_selector}_data" />
+    </outputs>
+
+    <help>
+    <![CDATA[
+What it does
+-------------
+
+This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
+Reactions and rules can be used as inputs for the RAS and RPS generator tools.
+
+Accepted files:
+    - A model: JSON or XML file reporting reactions and rules contained in the model. Supported compressed formats: .zip, .gz and .bz2 - Filename must end with .json.zip (.xml.zip), .json.gz (.xml.gz) or .json.bz2 (.xml.bz2) for JSON (XML) files.   
+
+
+Output:
+-------------
+
+The tool generates:
+    - rules: reporting the rules for each reaction in the custom model given. Format: csv (tab separated).
+    - reactions: reporting the reactions in the custom model given. Format: csv (tab separated).
+    - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated).
+    - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated).
+    - a log file (.txt).
+    ]]>
+    </help>
+    <expand macro="citations" />
+</tool>
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