From 29750cac246a2cf8a943180a89c670417fb13353 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Manuel=20Dom=C3=ADnguez?=
 <dominguj@informatik.uni-freiburg.de>
Date: Fri, 6 Oct 2023 12:20:46 +0200
Subject: [PATCH] Reorganize single cell subdomain

- Modify sections displayed on the subdomain.
- Create sections specific to the single cell subdomain.
---
 .../galaxy/config/global_host_filters.py.j2   | 26 +++++++++++++++--
 templates/galaxy/config/tool_conf.xml.j2      | 29 ++++++++++++++++++-
 2 files changed, 52 insertions(+), 3 deletions(-)

diff --git a/templates/galaxy/config/global_host_filters.py.j2 b/templates/galaxy/config/global_host_filters.py.j2
index 5ca29d6c9..572075ff0 100644
--- a/templates/galaxy/config/global_host_filters.py.j2
+++ b/templates/galaxy/config/global_host_filters.py.j2
@@ -77,8 +77,26 @@ DOMAIN_SECTIONS = {
         "biom_manipulation"],
     'rna': GENERAL_NGS_SECTIONS + ["rna_seq", "annotation", "rna_analysis",
         "graph_display_data"],
-    'singlecell': GENERAL_NGS_SECTIONS + ["rna_seq", "annotation", "rna_analysis",
-        "graph_display_data", "single-cell", "interactivetools"],
+    'singlecell': [
+        "sam_bam",
+        "fasta_fastq_manipulation",
+        "fasta_fastq",
+        "fastq_quality_control",
+        "sam_bam_manipulation",
+        "graph_display_data",
+        "single-cell",
+        "single-cell-section-scdata",
+        "single-cell-section-scanpy",
+        "single-cell-section-seurat",
+        "single-cell-section-raceid",
+        "single-cell-section-cell-annotation",
+        "single-cell-section-cell-multiomics",
+        "single-cell-section-cell-inference",
+        "single-cell-section-cell-spatial",
+        "single-cell-section-hca-scanpy",
+        "single-cell-section-hca-seurat",
+        "single-cell-section-interactivetools"
+    ],
     'humancellatlas': GENERAL_NGS_SECTIONS + ["rna_seq", "annotation", "rna_analysis",
         "graph_display_data", "single-cell", "interactivetools"] + human_cell_atlas_sections,
     'clipseq': GENERAL_NGS_SECTIONS + ["rna_seq", "peak_calling", "rna_analysis",
@@ -118,6 +136,10 @@ def per_host_tool_sections( context, section ):
         else:
             return False
 
+    # show single cell interactive tools only in that subdomain
+    if section.id.startswith("single-cell-section") and subdomain != "singlecell":
+        return False
+
     # Core tools used by all virtual hosts.
     # HiCtools mode: published in NAR 2018
     if host == "usegalaxy.eu":
diff --git a/templates/galaxy/config/tool_conf.xml.j2 b/templates/galaxy/config/tool_conf.xml.j2
index a267a5680..97fa7ab3b 100644
--- a/templates/galaxy/config/tool_conf.xml.j2
+++ b/templates/galaxy/config/tool_conf.xml.j2
@@ -273,6 +273,26 @@
     </section>
   <section id="single-cell" name="Single-cell">
   </section>
+  <section id="single-cell-section-scdata" name="Import/manipulate sc data">
+  </section>
+  <section id="single-cell-section-scanpy" name="Scanpy">
+  </section>
+  <section id="single-cell-section-seurat" name="Seurat">
+  </section>
+  <section id="single-cell-section-raceid" name="RaceID">
+  </section>
+  <section id="single-cell-section-cell-annotation" name="Automated cell annotation">
+  </section>
+  <section id="single-cell-section-cell-multiomics" name="Multiomics">
+  </section>
+  <section id="single-cell-section-cell-inference" name="Inference">
+  </section>
+  <section id="single-cell-section-cell-spatial" name="Spatial">
+  </section>
+  <section id="single-cell-section-hca-scanpy" name="HCA-Scanpy">
+  </section>
+  <section id="single-cell-section-hca-seurat" name="HCA-Seurat">
+  </section>
   <section id="spatial_omics" name="Spatial Omics" />  
   <!-- HCA Single Cell tools -->
   <section id="hca_sc_get-scrna" name="Get scRNAseq data">
@@ -578,5 +598,12 @@
 	<tool file="interactive/interactivetool_metashark.xml" />
 	<tool file="interactive/interactivetool_audiolabeler.xml" />
   </section>
-
+  <section id="single-cell-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_cellxgene.xml" />
+    <tool file="interactive/interactivetool_cellxgene_1.1.1.xml" />
+  </section>
 </toolbox>