--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpreport.xml	Mon Feb 14 14:23:00 2022 +0000
@@ -0,0 +1,97 @@
+<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@" profile="19.09">
+    <description>Generates HTML report to explore the main characteristics of pathways
+predicted with RetroPath suite</description>
+    <macros>
+        <token name="@TOOL_VERSION@">5.12.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if str($input_type_conditional.input_type) == "sbml":
+            cd /tmp &&
+            #set input_folder="tmp_folder"
+            mkdir -p '$input_folder' &&
+            #for $input in $input_type_conditional.input_sbml.keys():
+                ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input';
+            #end for
+            python -m rptools.rpreport -d '$input_folder'
+        #elif str($input_type_conditional.input_type) == "tar":
+            python -m rptools.rpreport '${input_type_conditional.input_tar}'
+        #end if
+        '$html_file.files_path'
+        && cp '$html_file.files_path'/index.html '$html_file'
+    ]]></command>
+    <inputs>
+        <conditional name="input_type_conditional">
+            <param name="input_type" type="select" label="Source SBML format">
+                <option value="tar" selected="True">TAR</option>
+                <option value="sbml">Collection</option>
+            </param>
+            <when value="tar">
+                <param name="input_tar" type="data" format="tar" label="Source SBML" />
+            </when>
+            <when value="sbml">
+                <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="html_file" format="html" label="Pathways HTML Report"/>
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 2: check if identical html output is produced (tar input) --> 
+            <conditional name="input_type_conditional">
+                <param name="input_type" value="tar"/>
+                <param name="input_tar" value="input_rpSBML.tar" />
+            </conditional>
+            <output name="html_file" file="rpreport_output.html" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+rpReport
+=========
+
+Generates HTML pages to explore the main characteristics (thermodynamics,
+fluxes, number of metabolic steps, reaction rule score) of pathways predicted
+with RetroPath suite
+
+
+Input
+-----
+
+Required:
+
+* **source_path**: (string) Path to a tar archive (default) or folder (using '-d' option) containing rpSBML file(s).
+
+Output
+------
+* **output_folder**: (string) Output folder where report file(s) will be generated.
+
+Project Links
+---------------------
+* `GitHub <https://github.com/brsynth/rptools>`_
+
+Version
+----------
+
+5.12.1
+
+Authors
+-------
+
+* **Olivier Telle**
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+* Joan Hérisson
+
+Licence
+-------
+
+`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
+    ]]></help>
+</tool>
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