diff rpreport.xml @ 0:a1764894d6ca draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpreport.xml	Wed Nov 16 11:11:58 2022 +0000
@@ -0,0 +1,91 @@
+<tool id="rptools_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@">5.13.1</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="[e-mail]" />
+    </creator>
+</tool>