From 96a30e92eab3144b924fdba7b63be10b218160a7 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Wed, 24 Jul 2024 10:38:10 +0200
Subject: [PATCH] `rpcompletion` input extension (#192)

* fix(tools): rptools rpcompletion, mv input extension

* fix(tools): rptools, rm bad urls

* fix(tools): rptools rpcompletion, mv test case

* fix(tools): rptools rpcompletion, mv test case
---
 tools/rptools/rpcompletion.xml  | 6 +++---
 tools/rptools/rpextractsink.xml | 1 -
 tools/rptools/rpreport.xml      | 2 +-
 tools/rptools/rpviz.xml         | 2 +-
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/tools/rptools/rpcompletion.xml b/tools/rptools/rpcompletion.xml
index b0ddc496..6cf126a9 100644
--- a/tools/rptools/rpcompletion.xml
+++ b/tools/rptools/rpcompletion.xml
@@ -22,7 +22,7 @@
     ]]></command>
     <inputs>
         <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
-        <param name="rp2paths_compounds" type="data" format="csv" label="RP2paths compounds" />
+        <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
         <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
         <param name="sink" type="data" format="csv" label="Sink from SBML" />
         <section name="adv" title="Advanced Options" expanded="false">
@@ -43,14 +43,14 @@
             <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
             <param name="rp2_pathways" value="1-rp2_metnet.csv" />
             <param name="sink" value="2-sink.csv" />
-            <output_collection name="pathways" type="list" count="9"/>
+            <output_collection name="pathways" type="list" count="10"/>
         </test>
     </tests>
     <help><![CDATA[
 rpCompletion
 ============
 
-Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
+Completes mono-component reactions output by `RetroPath2.0 <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
 
 Input
 -----
diff --git a/tools/rptools/rpextractsink.xml b/tools/rptools/rpextractsink.xml
index 2f09798f..539da1b2 100644
--- a/tools/rptools/rpextractsink.xml
+++ b/tools/rptools/rpextractsink.xml
@@ -69,7 +69,6 @@ Output
         <citation type="doi">10.1038/nbt1156</citation>
         <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
         <citation type="doi">10.1186/1752-0509-7-74</citation>
-        <citation type="doi">10.1093/bioinformatics/btn051</citation>
         <citation type="doi">10.1038/s41467-022-32661-x</citation>
     </citations>
 </tool>
diff --git a/tools/rptools/rpreport.xml b/tools/rptools/rpreport.xml
index 39b16029..58d88850 100644
--- a/tools/rptools/rpreport.xml
+++ b/tools/rptools/rpreport.xml
@@ -51,7 +51,7 @@ 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>`_.
+with `RetroPath suite <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_.
 
 
 Input
diff --git a/tools/rptools/rpviz.xml b/tools/rptools/rpviz.xml
index 690ec81d..ba4ee87b 100644
--- a/tools/rptools/rpviz.xml
+++ b/tools/rptools/rpviz.xml
@@ -79,7 +79,7 @@
 RPVIZ
 =====
 
-Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
+Visualize pathways from the `RetroPath Suite <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_.
 
 Input
 -----