changeset 89:5ea689ae9eac draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/marea_2/ras_to_bounds.xml	Sat Jul 20 16:07:22 2024 +0000
@@ -0,0 +1,79 @@
+<tool id="MaREA RAS to bounds" name="RAStoBounds" 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__/ras_to_bounds.py
+        --model_selector $cond_model.model_selector
+        #if $cond_model.model_selector == 'Custom'
+            --model $model
+            --model_name $model.element_identifier
+        #end if
+        --medium_selector $cond_medium.medium_selector
+        #if $cond_medium.medium_selector == 'Custom'
+            --medium $medium
+            --medium_name $medium.element_identifier
+        #end if
+        --input_ras $input_ras
+        --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="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
+        
+        <conditional name="cond_medium">
+            <expand macro="options_ras_to_bounds_medium"/>
+            <when value="Custom">
+                <param name="medium" argument="--medium" type="data" format="csv" label="Custom medium" />
+            </when>
+        </conditional> 
+
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="log" label="RAStoBounds - $name - Log" />
+        
+        <collection name="results" type="list" label="Ras to Bounds ($output_format)">
+            <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
+        </collection>
+    </outputs>
+
+    <help>
+    <![CDATA[
+What it does
+-------------
+
+This tool generates two files containing reactions and rules respectively, starting from a custom model in JSON or XML format, that can be used as inputs for the RAS and RPS generator modules.
+
+Accepted files:
+    - A model: JSON or XML file reporting reactions and rules contained in the model.   
+
+
+Output:
+-------------
+
+The tool generates:
+    - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
+    - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
+    - a log file (.txt).
+    ]]>
+    </help>
+    <expand macro="citations" />
+</tool>
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