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Reorganize single cell subdomain #925

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Oct 6, 2023
Merged

Reorganize single cell subdomain #925

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26 changes: 24 additions & 2 deletions templates/galaxy/config/global_host_filters.py.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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":
Expand Down
29 changes: 28 additions & 1 deletion templates/galaxy/config/tool_conf.xml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down Expand Up @@ -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>
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