--- a/rp2paths.xml	Tue Feb 22 11:31:06 2022 +0000
+++ b/rp2paths.xml	Mon Apr 03 08:15:46 2023 +0000
@@ -1,106 +1,84 @@
-<tool id="rp2paths" name="RP2paths" version="1.5.0">
+<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" licence="@LICENSE@">
     <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.5.0</token>
+        <token name="@LICENSE@">MIT</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.5.0">rp2paths</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
     </requirements>
-	<stdio>
+    <stdio>
         <regex match="TIMEOUT:" level="fatal" />
         <regex match="ERROR:"   level="fatal" />
-		<regex match="WARNING:" level="warning" />
-	</stdio>
+        <regex match="WARNING:" level="warning" />
+    </stdio>
     <command detect_errors="exit_code"><![CDATA[
         mkdir out &&
         python -m rp2paths all
         '$rp2_pathways'
         --outdir out
         --timeout '$adv.timeout' &&
-        if test -f "out/compounds.txt"; then
-          cp out/compounds.txt '$compounds';
-          cp out/out_paths.csv '$master_pathways';
+        cp out/compounds.txt '$compounds' &&
+        if test -f 'out/out_paths.csv'; then
+            cp out/out_paths.csv '$master_pathways';
         fi
     ]]></command>
     <inputs>
-        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" />
+        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/>
         <section name="adv" title="Advanced Options" expanded="false">
-			<param name="timeout" type="integer" value="1800" label="Time Out" />
+            <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
         </section>
     </inputs>
     <outputs>
-        <data name="master_pathways" format="csv" label="${tool.name} (Pathways)" />
-        <data name="compounds" format="tsv" label="${tool.name} (Compounds)" />
+        <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
+        <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
     </outputs>
     <tests>
         <test>
             <!-- test 1: check if identical outputs are produced with default parameters  -->
             <param name="rp2_pathways" value="retropath2_pathways.csv" />
             <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
-            <output name="compounds" file="rp2paths_compounds.tsv" ftype="tsv" compare="diff"/>
+            <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
         </test>
     </tests>
     <help><![CDATA[
-rp2paths
+RP2paths
 ========
 
 
-RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. Source code may be found at the following location: `GitHub <https://github.com/brsynth/rp2paths>`_.
+**RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the `RetroPath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_ into individual pathways and enumerate them. This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , and outputs the enumerated pathways (using `EC numbers <https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme-commission-number>`_ ) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.
+
+
+An example of **enumerated pathways** is illustred in the figure below for the production of a target molecule: `Styrene <https://www.sciencedirect.com/topics/chemical-engineering/styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme-commission-number>`_.
+
+
+.. image:: ${static_path}/images/enumerated_pathways.png
+    :width: 40 %
+    :align: center
+
+|
 
 Input
 -----
 
 Required information:
 
-
-* **rp_results**\ : (string) Path to the ReatroPath2.0 pathways file
+* **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
 
 Advanced options:
 
-
-* **timeout**\ : (string, default: 30 minutes) Time out time of the tool
-* **server_url**\ : (string) IP address of the rp2paths REST service
+* **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
 
 Output
 ------
 
-
-* **out_paths**\ : (string) Path to the RP2paths pathways. Describes all the indiviudal enumerated pathways that produce the compound of interest.
-* **out_compounds**\ : (string) Path to the RP2paths Compounds. Describes the structure of all the chemical species involved in all pathways.
-
-Versioning
-----------
-
-v1.4.3
-
-Authors
--------
-
-
-* **Melchior du Lac**
-* Thomas Duigou
-* Baudoin Delépine
-* Pablo Carbonell
-
-License
--------
-
-`MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
-
-Acknowledgments
----------------
-
-
-* Joan Hérisson
-
+* **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
+* **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
     ]]></help>
+    <creator>
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+    </creator>
     <citations>
-        <citation type="bibtex">
-@article{delepine2018retropath2,
-  title={RetroPath2.0: a retrosynthesis workflow for metabolic engineers},
-  author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
-  journal={Metabolic engineering},
-  volume={45},
-  pages={158--170},
-  year={2018},
-  publisher={Elsevier}}
-        </citation>
+        <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>