Merge pull request #958 from Marie59/tools

Modify tools section for earth-system

templates/galaxy/config/global_host_filters.py.j2

@@ -22,7 +22,11 @@ def per_host_tool_labels( context, label ):
     # hide genomics label in the single cell subdomain
     if label.id == "genomics_label" and subdomain == "singlecell":
         return False
-
+
+    # show earth-system labels only in that subdomain
+    if label.id.startswith("earth-system-label"):
+        return subdomain == "earth-system"
+
     # Core tools used by all virtual hosts.
     valid_labels = [ "file_meta_label", "general_text_label"]
     general_ngs_labels = [ "genomics_label" ]
@@ -131,7 +135,14 @@ DOMAIN_SECTIONS = {
     'annotation': GENERAL_NGS_SECTIONS + ['annotation', 'apollo', 'ncbi_blast', 'assembly', 'variant_calling', 'fetch_sequences___alignments', 'ontology', 'emboss', 'evolution', 'genome_diversity', 'multiple_alignments', 'graph_display_data'],
     'materials': ['muon_spectroscopy'],
     'aqua': ["climate_analysis", "gis_data_handling", "graph_display_data", "interactivetools", "machine_learning"],
-    'earth-system': ["interactivetools"],
+    'earth-system': [
+        "earth-system-section-watercoastal", 
+        "earth-system-section-earthcritical", 
+        "earth-system-section-volcano", 
+        "earth-system-section-biogeo", 
+        "earth-system-section-marineomics", 
+        "earth-system-section-interactivetools"
+    ],
 }
 
 
@@ -160,6 +171,10 @@ def per_host_tool_sections( context, section ):
     if section.id.startswith("single-cell-section"):
         return subdomain == "singlecell"
 
+    # show earth-system tools only in that subdomain
+    if section.id.startswith("earth-system-section"):
+        return subdomain == "earth-system"
+
     # Core tools used by all virtual hosts.
     # HiCtools mode: published in NAR 2018
     if host == "usegalaxy.eu":

templates/galaxy/config/tool_conf.xml.j2

@@ -603,4 +603,38 @@
 	<tool file="interactive/interactivetool_metashark.xml" />
 	<tool file="interactive/interactivetool_audiolabeler.xml" />
   </section>
+
+<!-- Earth-system subdomain -->
+<label id="earth-system-label-interactive-tools" text="General interactive tools" />  
+  <section id="earth-system-section-interactivetools" name="Interactive tools">
+    <tool file="interactive/interactivetool_jupyter_notebook.xml" />
+    <tool file="interactive/interactivetool_jupyter_notebook_1.0.0.xml" />
+    <tool file="interactive/interactivetool_rstudio.xml" />
+    <tool file="interactive/interactivetool_rstudio_0_3.xml" />
+    <tool file="interactive/interactivetool_climate_notebook.xml" />
+    <tool file="interactive/interactivetool_pangeo_notebook.xml" />
+    <tool file="interactive/interactivetool_pangeo_ml_notebook.xml" />
+  </section>
+  <label id="earth-system-label-dynamics" text="Earth & Environmental dynamics" />
+  <section id="earth-system-section-watercoastal" name="Water Coastal Dynamics">
+    <tool file="interactive/interactivetool_divand.xml" />
+    <tool file="interactive/interactivetool_source.xml" />
+    <tool file="interactive/interactivetool_odv.xml" />
+  </section>
+  <section id="earth-system-section-earthcritical" name="Earth Critical Zone">
+    <tool file="interactive/interactivetool_qgis.xml" />
+  </section>
+  <section id="earth-system-section-volcano" name="Volcano">
+    <tool file="interactive/interactivetool_hdfview.xml" />
+  </section>
+  <label id="earth-system-label-biogeo" text="Environmental Bio-geochemical assets" />
+  <section id="earth-system-section-biogeo" name="Bio-geochemical">
+    <tool file="interactive/interactivetool_scoop3.xml" />
+  </section>
+  <label id="earth-system-label-biodiv" text="Biodiversity observation" />
+  <section id="earth-system-section-marineomics" name="Marine Omics">
+    <tool file="interactive/interactivetool_pampa.xml" />
+    <tool file="interactive/interactivetool_mgnify_notebook.xml" />
+    <tool file="interactive/interactivetool_mgnify_notebook_1.2.2.xml" />
+  </section>
 </toolbox>