--- a/rpreport.xml	Fri Nov 18 16:18:02 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
-    <description>Explore the main characteristics of pathways predicted with RetroPath suite</description>
-    <macros>
-        <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@TOOL_VERSION@">6.0.1</token>
-    </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        #if str($input_type_conditional.input_type) == "sbml":
-            #set input_folder="tmp_folder"
-            mkdir -p '$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" help="rpSBML file(s) containing pathways predicted with RetroPath suite in TAR format"/>
-            </when>
-            <when value="sbml">
-                <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" help="Collection of rpSBML files containing pathways predicted with RetroPath suite"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="html_file" format="html" label="Pathways HTML Report"/>
-    </outputs>
-    <tests>
-        <test>
-        <!-- test 1: 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 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
-
-
-Input
------
-
-Required:
-
-* **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite.
-
-Output
-------
-
-* **Pathways HTML Report**: Pathways HTML Report
-
-Project Links
----------------------
-
-* `GitHub <https://github.com/brsynth/rptools>`_
-
-Acknowledgments
----------------
-
-* Thomas Duigou
-* Joan Hérisson
-
-Licence
--------
-
-`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
-    ]]></help>
-    <creator>
-        <person givenName="Olivier" familyName="Telle" email="olivier.telle@inrae.fr" />
-    </creator>
-</tool>
\ No newline at end of file