--- a/rp2paths.xml	Tue May 30 21:09:26 2023 +0000
+++ b/rp2paths.xml	Wed Jul 24 08:44:12 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
     <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.5.0</token>
+        <token name="@TOOL_VERSION@">1.5.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
@@ -17,7 +17,8 @@
         '$rp2_pathways'
         --outdir out
         --timeout '$adv.timeout' &&
-        cp out/compounds.txt '$compounds' &&
+        mv out/compounds.txt out/compounds.tsv &&
+        cp out/compounds.tsv '$compounds' &&
         if test -f 'out/out_paths.csv'; then
             cp out/out_paths.csv '$master_pathways';
         fi
@@ -45,10 +46,7 @@
 ========
 
 
-**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>`_.
+**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) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.
 
 
 .. image:: ${static_path}/images/enumerated_pathways.png