From 6c9b6792931c52c21d4f889dcfa15a088912e435 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 25 Dec 2023 10:59:40 +0100
Subject: [PATCH 1/2] Update tool_conf.xml.j2 try to reorganize ecology tools
 and add geometric mean tools

Looking at earth-system work so ecology tools can be better organized
---
 templates/galaxy/config/tool_conf.xml.j2 | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/templates/galaxy/config/tool_conf.xml.j2 b/templates/galaxy/config/tool_conf.xml.j2
index e9549b145..2b5617462 100644
--- a/templates/galaxy/config/tool_conf.xml.j2
+++ b/templates/galaxy/config/tool_conf.xml.j2
@@ -525,13 +525,7 @@
     <tool file="/opt/galaxy/custom-tools/test/imaging/coordinates_of_roi/coordinates_of_roi.xml" />
     <tool file="/opt/galaxy/custom-tools/test/imaging/projective_transformation_points/projective_transformation_points.xml" /-->
   </section>
-
-  <section id="gis_data_handling" name="GIS Data Handling" />
-  <section id="animal_detection_on_acoustic_recordings" name="Animal Detection on Acoustic Recordings" />
-  <section id="compute_indicators_for_satellite_remote_sensing" name="Compute indicators for satellite remote sensing" />
   
-  <section id="regional_variation" name="Regional Variation" >
-  </section>
   <section id="genome_diversity" name="Genome Diversity" >
   </section>
 
@@ -551,9 +545,6 @@
   <section id="climate_analysis" name="Climate Analysis" />
   <section id="apollo" name="Apollo" />
   <section id="imaging" name="Imaging" />
-  <section id="species_abundance" name="Species abundance" />
-  <section id="compute_indicators_for_turnover_boulders_fields" name="Compute indicators for turnover boulders fields" />
-  <section id="ecoregionalization" name="Ecoregionalization" />
   <section id="astronomy" name="Astronomy" />
   <section id="interactivetools" name="Interactive tools">
         <tool file="interactive/interactivetool_source.xml" />
@@ -643,4 +634,16 @@
     <tool file="interactive/interactivetool_mgnify_notebook.xml" />
     <tool file="interactive/interactivetool_mgnify_notebook_1.2.2.xml" />
   </section>
+
+<!-- Ecology subdomain -->
+<label id="ecology-data-management" text="Data management" />
+  <section id="gis_data_handling" name="GIS Data Handling" />
+<label id="ecology-indicators" text="Biodiversity indicators" />
+  <section id="compute_indicators_for_turnover_boulders_fields" name="Compute indicators for turnover boulders fields" />
+  <section id="ecoregionalization" name="Ecoregionalization" />
+  <section id="geom_mean" name="Indicators from geometric mean" />
+  <section id="animal_detection_on_acoustic_recordings" name="Animal Detection on Acoustic Recordings" />
+  <section id="compute_indicators_for_satellite_remote_sensing" name="Compute indicators for satellite remote sensing" />
+  <section id="regional_variation" name="Regional Variation" />
+  <section id="species_abundance" name="Species abundance" />
 </toolbox>

From bd7f21b67382bf555d8298d18664eff4b824c8d4 Mon Sep 17 00:00:00 2001
From: Yvan Le Bras <yvan.le-bras@mnhn.fr>
Date: Mon, 25 Dec 2023 12:28:41 +0100
Subject: [PATCH 2/2] Update templates/galaxy/config/tool_conf.xml.j2
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 templates/galaxy/config/tool_conf.xml.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/galaxy/config/tool_conf.xml.j2 b/templates/galaxy/config/tool_conf.xml.j2
index 2b5617462..cc32a2869 100644
--- a/templates/galaxy/config/tool_conf.xml.j2
+++ b/templates/galaxy/config/tool_conf.xml.j2
@@ -636,7 +636,7 @@
   </section>
 
 <!-- Ecology subdomain -->
-<label id="ecology-data-management" text="Data management" />
+<label id="ecology-data-management" text="Ecology Data Management" />
   <section id="gis_data_handling" name="GIS Data Handling" />
 <label id="ecology-indicators" text="Biodiversity indicators" />
   <section id="compute_indicators_for_turnover_boulders_fields" name="Compute indicators for turnover boulders fields" />