From ea90041a7925825ba585e1217569c7e27638dc42 Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Mon, 29 Jul 2024 07:23:00 +1000
Subject: [PATCH] Parse tools for usegalaxy.org.au

---
 .../parse_tools_to_produce_yml_files.py       |   4 +
 subdomains/scripts/tools_au.py                |  49 +
 .../tool_panel/usegalaxy.org.au.yml           | 964 ++++++++++++++++++
 3 files changed, 1017 insertions(+)
 create mode 100644 subdomains/scripts/tools_au.py
 create mode 100644 subdomains/singlecell/tool_panel/usegalaxy.org.au.yml

diff --git a/subdomains/scripts/parse_tools_to_produce_yml_files.py b/subdomains/scripts/parse_tools_to_produce_yml_files.py
index 57b48a6a..2651d926 100644
--- a/subdomains/scripts/parse_tools_to_produce_yml_files.py
+++ b/subdomains/scripts/parse_tools_to_produce_yml_files.py
@@ -5,6 +5,8 @@
 import re 
 import argparse
 
+import tools_au
+
 parser = argparse.ArgumentParser(description='Create installation yaml files from a Yaml file containing the panel_view/Toolkit data')
 parser.add_argument('--tk', action="store", dest='toolkit', help='Path of the toolkit.yaml file') # Toolkit.yaml file
 parser.add_argument('--yml-folder', action="store", dest='dest', help='Folder containing the yml files with tool installed in the target instance') # Folder containing the .yml and yml.lock containing the tools installed in the target instance
@@ -33,3 +35,5 @@
                 f.write("- name: "+tool+"\n")
                 f.write("  owner: "+owner+"\n")
     f.close()
+
+tools_au.parse()
diff --git a/subdomains/scripts/tools_au.py b/subdomains/scripts/tools_au.py
new file mode 100644
index 00000000..87edb7e9
--- /dev/null
+++ b/subdomains/scripts/tools_au.py
@@ -0,0 +1,49 @@
+"""Convert YAML files for install on AU.
+
+Assumes that wdir contains tool yaml files.
+"""
+
+import yaml
+from pathlib import Path
+
+WDIR = Path(__file__).parent
+EXCLUDE_KEYS = [
+    'install_repository_dependencies',
+    'tool_panel_section_label',
+]
+OUTPUT_FILE = WDIR / 'usegalaxy.org.au.yml'
+
+
+def parse():
+    data = {'tools': []}
+    for f in WDIR.glob('*.yml.lock'):
+        if not f.name.endswith('.yml.lock'):
+            continue
+        print(f"Extracting data from {f}...")
+        with open(f, 'r') as handle:
+            section_data = yaml.safe_load(handle)
+        section_data['tools'] = [
+            _transcribe_to_au(x) for x in section_data['tools']
+        ]
+        for key in EXCLUDE_KEYS:
+            section_data.pop(key)
+        data['tools'] += section_data['tools']
+    for key in ('install_resolver_dependencies', 'install_tool_dependencies'):
+        data[key] = section_data[key]
+    write_data(data)
+    print(f'Data transcribed and written to {OUTPUT_FILE}')
+
+
+def _transcribe_to_au(tool):
+    tool['tool_panel_section_label'] = 'Single-Cell'
+    tool.pop('tool_panel_section_id')
+    return tool
+
+
+def write_data(data):
+    with open(OUTPUT_FILE, 'w') as handle:
+        yaml.dump(data, handle, default_flow_style=False)
+
+
+if __name__ == '__main__':
+    parse()
diff --git a/subdomains/singlecell/tool_panel/usegalaxy.org.au.yml b/subdomains/singlecell/tool_panel/usegalaxy.org.au.yml
new file mode 100644
index 00000000..fd7d9bd5
--- /dev/null
+++ b/subdomains/singlecell/tool_panel/usegalaxy.org.au.yml
@@ -0,0 +1,964 @@
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: scanpy_plot
+  owner: iuc
+  revisions:
+  - 6adf98e782f3
+  - 6f5349dd5c49
+  - 7647e5cd1b8b
+  - 95777145cb92
+  - 9a169729c9f9
+  - 9b0cdb8cf6be
+  - aa0c474463c2
+  - f7446fd8d5e7
+  tool_panel_section_label: Single-Cell
+- name: scanpy_inspect
+  owner: iuc
+  revisions:
+  - 3081ff5c84a3
+  - 5c3ebe2adc77
+  - 6bd82ed14acd
+  - 6c145a6868cc
+  - 9d33775ec67d
+  - c5d3684f7c4c
+  - e4c99c83dfbf
+  - f54f0f0598ad
+  tool_panel_section_label: Single-Cell
+- name: scanpy_filter
+  owner: iuc
+  revisions:
+  - 277313130da5
+  - 2d02d9702d3a
+  - 3c86f71498bc
+  - 5511647110ff
+  - a03ff8633507
+  - b409c2486353
+  - d636ce5cde16
+  - f87ed6503715
+  tool_panel_section_label: Single-Cell
+- name: scanpy_normalize
+  owner: iuc
+  revisions:
+  - 51d945eab1e1
+  - 5342ce58cd1e
+  - 7b9fafe32c86
+  - 94c19fb1281c
+  - a407e7f8bdc1
+  - ab55fe8030b6
+  - c9cb76cf8d6c
+  - d844935c906c
+  tool_panel_section_label: Single-Cell
+- name: scanpy_cluster_reduce_dimension
+  owner: iuc
+  revisions:
+  - 35bc2eb568ed
+  - 3e4e1cf73d98
+  - 4d8f983cd751
+  - 6acb08931836
+  - 6f83f8fd381f
+  - aaa5da8e73a9
+  - b2df381a6004
+  - edec35114f72
+  tool_panel_section_label: Single-Cell
+- name: scanpy_remove_confounders
+  owner: iuc
+  revisions:
+  - 215733a383f2
+  - 458e8f43a775
+  - 73ab2ac53d06
+  - 80d4e2cac903
+  - bf2017df9837
+  - c2ef03559dc6
+  - c65fce500915
+  - d18e7a6e5cd4
+  tool_panel_section_label: Single-Cell
+- name: anndata_export
+  owner: iuc
+  revisions:
+  - 0cb889db0910
+  - 32c5c85cbc12
+  - c0b037b12765
+  - c5ac926c838f
+  - e1c3c2f2a834
+  tool_panel_section_label: Single-Cell
+- name: anndata_import
+  owner: iuc
+  revisions:
+  - 00712416fdaa
+  - '499059586799'
+  - 93dd15e13e6a
+  - ae1e5d9d8972
+  - cfc3f5a57dc6
+  - fb9e030ffae4
+  tool_panel_section_label: Single-Cell
+- name: anndata_inspect
+  owner: iuc
+  revisions:
+  - 038e32885fec
+  - 383dcb0500f9
+  - 39e945f0b2c1
+  - 6f0d0c784f09
+  - ee98d611afc6
+  tool_panel_section_label: Single-Cell
+- name: anndata_manipulate
+  owner: iuc
+  revisions:
+  - 3d748954434b
+  - 43cb7b5a6fe7
+  - 8db95f488f0f
+  - ed4996a16f7f
+  tool_panel_section_label: Single-Cell
+- name: modify_loom
+  owner: iuc
+  revisions:
+  - 4b0adaa31c95
+  - 59be31ac9dc3
+  - 7784821452ac
+  - e98619de2776
+  - eeab712b0b99
+  tool_panel_section_label: Single-Cell
+- name: dropletutils
+  owner: iuc
+  revisions:
+  - 2c1200fba922
+  - a9caad671439
+  - cdf4443d5625
+  - cfe1e6c28d95
+  tool_panel_section_label: Single-Cell
+- name: raceid_clustering
+  owner: iuc
+  revisions:
+  - 0bff0ee0683a
+  - 7e014059a88d
+  - a4b734cd253b
+  - c4f39bf4a068
+  tool_panel_section_label: Single-Cell
+- name: raceid_filtnormconf
+  owner: iuc
+  revisions:
+  - 43c146e25a43
+  - 7608d5faee41
+  - b83fbc90161e
+  - d45f092caf24
+  tool_panel_section_label: Single-Cell
+- name: raceid_inspectclusters
+  owner: iuc
+  revisions:
+  - 37a47c4fd84d
+  - 41f34e925bd5
+  - be4646256624
+  - f3eb2291da05
+  tool_panel_section_label: Single-Cell
+- name: raceid_inspecttrajectory
+  owner: iuc
+  revisions:
+  - 3478133d0f6f
+  - 69018f285aa3
+  - a6821f856a1e
+  - c8434a623268
+  tool_panel_section_label: Single-Cell
+- name: raceid_trajectory
+  owner: iuc
+  revisions:
+  - 2af7c5086a96
+  - 44b935f2271b
+  - 72979cac22b2
+  - e93b008c637a
+  tool_panel_section_label: Single-Cell
+- name: scanpy_filter_cells
+  owner: ebi-gxa
+  revisions:
+  - 7fd39eb52f38
+  - 8ed4e80e8799
+  - ba64b91ed2b9
+  - bf1e0bdec1db
+  - e9283529cba1
+  tool_panel_section_label: Single-Cell
+- name: scanpy_filter_genes
+  owner: ebi-gxa
+  revisions:
+  - 474a69c47184
+  - 7143938df06e
+  - a1698b43abeb
+  - cc64914b0cf4
+  - d82d999fa716
+  tool_panel_section_label: Single-Cell
+- name: scanpy_normalise_data
+  owner: ebi-gxa
+  revisions:
+  - 1e9616772e16
+  - 3027cb62adbd
+  - 3a4564b9d685
+  - 6b97ffba31da
+  tool_panel_section_label: Single-Cell
+- name: scanpy_find_variable_genes
+  owner: ebi-gxa
+  revisions:
+  - 2861ca3bfe4d
+  - 5c62f39aab8f
+  - 64dd8bb151e1
+  - 82bd7bf93454
+  - ae467daae2f7
+  tool_panel_section_label: Single-Cell
+- name: scanpy_scale_data
+  owner: ebi-gxa
+  revisions:
+  - 22f2957da902
+  - 2b6913c840bf
+  - 4cc9362782b4
+  - f86b2c3bc459
+  tool_panel_section_label: Single-Cell
+- name: scanpy_run_pca
+  owner: ebi-gxa
+  revisions:
+  - 04bdc69f00d7
+  - 4428dba93375
+  - 59028945c857
+  - 988edd5fa902
+  - c4f7fb2b1f70
+  tool_panel_section_label: Single-Cell
+- name: scanpy_compute_graph
+  owner: ebi-gxa
+  revisions:
+  - 22bd5861706d
+  - 3cf0177ed87e
+  - 5ec3b715809c
+  - 6417cccad133
+  - fcaa9048cdaf
+  tool_panel_section_label: Single-Cell
+- name: scanpy_run_tsne
+  owner: ebi-gxa
+  revisions:
+  - 181d61d2f3cd
+  - 384cacc40611
+  - a147dce191e9
+  - abdb61e4afa3
+  - fe727a9496ea
+  tool_panel_section_label: Single-Cell
+- name: scanpy_run_umap
+  owner: ebi-gxa
+  revisions:
+  - abae3d11d920
+  - ad70b3552c99
+  - bd4a244faeb8
+  - e31937baa330
+  - ea91cfd0444e
+  tool_panel_section_label: Single-Cell
+- name: scanpy_find_cluster
+  owner: ebi-gxa
+  revisions:
+  - 15e8a4c60418
+  - 2ccd9f9e2cd0
+  - 36735850e461
+  - 621d7d7a605f
+  - 8dc3d8941217
+  tool_panel_section_label: Single-Cell
+- name: scanpy_find_markers
+  owner: ebi-gxa
+  revisions:
+  - 615a46c220f0
+  - 7042ce140caa
+  - 81c34e67f262
+  - a57c0538e56b
+  - d8f5224005bb
+  tool_panel_section_label: Single-Cell
+- name: scanpy_plot_embed
+  owner: ebi-gxa
+  revisions:
+  - 35f6611fb8c3
+  - 7d5c97823f8b
+  - 9fafbfcdee0d
+  - a71086d2e55f
+  tool_panel_section_label: Single-Cell
+- name: anndata_ops
+  owner: ebi-gxa
+  revisions:
+  - 31e5e6d606ef
+  - 53a251c6d991
+  - 825dfd66e3fb
+  - a4774b7b2e85
+  tool_panel_section_label: Single-Cell
+- name: scanpy_parameter_iterator
+  owner: ebi-gxa
+  revisions:
+  - 4e4420ed5292
+  - 73d43034c860
+  - a8c73996ac50
+  - b9dd12ab0550
+  tool_panel_section_label: Single-Cell
+- name: scanpy_read_10x
+  owner: ebi-gxa
+  revisions:
+  - 078aa23c9374
+  - 4d13979de6ee
+  - 9afcfcd1d215
+  - c8391a25dee3
+  tool_panel_section_label: Single-Cell
+- name: scanpy_integrate_harmony
+  owner: ebi-gxa
+  revisions:
+  - 2cef3539f420
+  - 3111bcf039dd
+  - 5bea4f3c4edf
+  - c354af93f567
+  tool_panel_section_label: Single-Cell
+- name: gtf2gene_list
+  owner: ebi-gxa
+  revisions:
+  - 14b3f2a4523b
+  - 1a642de6db01
+  tool_panel_section_label: Single-Cell
+- name: scanpy_run_fdg
+  owner: ebi-gxa
+  revisions:
+  - be019b069e31
+  tool_panel_section_label: Single-Cell
+- name: scanpy_run_diffmap
+  owner: ebi-gxa
+  revisions:
+  - 79cc06a557b0
+  tool_panel_section_label: Single-Cell
+- name: scanpy_run_paga
+  owner: ebi-gxa
+  revisions:
+  - b2768cae00a1
+  tool_panel_section_label: Single-Cell
+- name: scanpy_run_dpt
+  owner: ebi-gxa
+  revisions:
+  - 03921aa8b29c
+  tool_panel_section_label: Single-Cell
+- name: scanpy_plot_trajectory
+  owner: ebi-gxa
+  revisions:
+  - cb1992d1804b
+  tool_panel_section_label: Single-Cell
+- name: alevin
+  owner: bgruening
+  revisions:
+  - 04b494623f8e
+  - c9944a2600f1
+  - e32b215b7c04
+  - e4c01dcece8b
+  - f2000bc73102
+  tool_panel_section_label: Single-Cell
+- name: droplet_barcode_plot
+  owner: ebi-gxa
+  revisions:
+  - 8f605643ccfd
+  tool_panel_section_label: Single-Cell
+- name: salmon_kallisto_mtx_to_10x
+  owner: ebi-gxa
+  revisions:
+  - 88f5a0a6a818
+  - e42c217a450f
+  tool_panel_section_label: Single-Cell
+- name: dropletutils_read_10x
+  owner: ebi-gxa
+  revisions:
+  - ca62f52e0d7f
+  tool_panel_section_label: Single-Cell
+- name: dropletutils_empty_drops
+  owner: ebi-gxa
+  revisions:
+  - fa662ca7ae7f
+  tool_panel_section_label: Single-Cell
+- name: sceasy_convert
+  owner: ebi-gxa
+  revisions:
+  - f62bc418173f
+  tool_panel_section_label: Single-Cell
+- name: retrieve_scxa
+  owner: ebi-gxa
+  revisions:
+  - 72b6e1747e37
+  tool_panel_section_label: Single-Cell
+- name: scanpy_regress_variable
+  owner: ebi-gxa
+  revisions:
+  - 0bab2ae44e7a
+  - 1200b55768ce
+  tool_panel_section_label: Single-Cell
+- name: music_construct_eset
+  owner: bgruening
+  revisions:
+  - 282819d09a4f
+  - 2cfd0db49bbc
+  - 7ffaa0968da3
+  tool_panel_section_label: Single-Cell
+- name: music_inspect_eset
+  owner: bgruening
+  revisions:
+  - 7705cc75ac18
+  - 8c64a2da3869
+  tool_panel_section_label: Single-Cell
+- name: music_manipulate_eset
+  owner: bgruening
+  revisions:
+  - 22232092be53
+  tool_panel_section_label: Single-Cell
+- name: music_deconvolution
+  owner: bgruening
+  revisions:
+  - 2ba99a52bd44
+  - 56371b5a2da9
+  tool_panel_section_label: Single-Cell
+- name: music_compare
+  owner: bgruening
+  revisions:
+  - 4447ed460308
+  tool_panel_section_label: Single-Cell
+- name: episcanpy_build_matrix
+  owner: iuc
+  revisions:
+  - 31a21ba2c5ea
+  tool_panel_section_label: Single-Cell
+- name: episcanpy_preprocess
+  owner: iuc
+  revisions:
+  - 29f5f25b9935
+  tool_panel_section_label: Single-Cell
+- name: sinto_barcode
+  owner: iuc
+  revisions:
+  - d1b34ac42b8f
+  tool_panel_section_label: Single-Cell
+- name: sinto_fragments
+  owner: iuc
+  revisions:
+  - 29e6bfb2cf49
+  tool_panel_section_label: Single-Cell
+- name: baredsc_1d
+  owner: iuc
+  revisions:
+  - 02b1fe7aed76
+  - 0e70b2dfe4be
+  - 4fff5a293013
+  - 769d815e4b0d
+  tool_panel_section_label: Single-Cell
+- name: baredsc_2d
+  owner: iuc
+  revisions:
+  - 344c2af50552
+  - a90f8efe08b4
+  - aa4a6f0916b4
+  - c29e7bb492bf
+  tool_panel_section_label: Single-Cell
+- name: baredsc_combine_1d
+  owner: iuc
+  revisions:
+  - 050cf43887d3
+  - 5b7c81b35b89
+  - b13d3e4c48e1
+  - c32347702e12
+  tool_panel_section_label: Single-Cell
+- name: baredsc_combine_2d
+  owner: iuc
+  revisions:
+  - 02fc39c8610d
+  - 1d77986f9ddc
+  - 239193b96d72
+  - ae969fdb8442
+  tool_panel_section_label: Single-Cell
+- name: cite_seq_count
+  owner: iuc
+  revisions:
+  - 3df3d1b51110
+  tool_panel_section_label: Single-Cell
+- name: velocyto_cli
+  owner: iuc
+  revisions:
+  - 883c33ef3372
+  - 90e95e9ee190
+  tool_panel_section_label: Single-Cell
+- name: gsc_scran_normalize
+  owner: artbio
+  revisions:
+  - 6864acb21714
+  tool_panel_section_label: Single-Cell
+- name: snapatac2_clustering
+  owner: iuc
+  revisions:
+  - 8f8bef61fd0b
+  tool_panel_section_label: Single-Cell
+- name: snapatac2_peaks_and_motif
+  owner: iuc
+  revisions:
+  - 588c811fdd48
+  tool_panel_section_label: Single-Cell
+- name: snapatac2_plotting
+  owner: iuc
+  revisions:
+  - fecf9664c885
+  tool_panel_section_label: Single-Cell
+- name: snapatac2_preprocessing
+  owner: iuc
+  revisions:
+  - cec3e76eaf05
+  tool_panel_section_label: Single-Cell
+- name: seurat_plot
+  owner: ebi-gxa
+  revisions:
+  - 95d79f1134f0
+  tool_panel_section_label: Single-Cell
+- name: scanpy_integrate_bbknn
+  owner: ebi-gxa
+  revisions:
+  - c9da9192eee5
+  tool_panel_section_label: Single-Cell
+- name: scanpy_integrate_combat
+  owner: ebi-gxa
+  revisions:
+  - 3c47bc560688
+  tool_panel_section_label: Single-Cell
+- name: scanpy_integrate_mnn
+  owner: ebi-gxa
+  revisions:
+  - ff6decc0f432
+  tool_panel_section_label: Single-Cell
+- name: scanpy_plot_scrublet
+  owner: ebi-gxa
+  revisions:
+  - 6f5509cf3176
+  tool_panel_section_label: Single-Cell
+- name: scanpy_multiplet_scrublet
+  owner: ebi-gxa
+  revisions:
+  - 53ce0e336840
+  tool_panel_section_label: Single-Cell
+- name: seurat_run_umap
+  owner: ebi-gxa
+  revisions:
+  - b9424c715a0d
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicaggregatestatistic
+  owner: bgruening
+  revisions:
+  - 01c37e54e86e
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicdifferentialtest
+  owner: bgruening
+  revisions:
+  - 9d42a6133690
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicexportdata
+  owner: bgruening
+  revisions:
+  - 23b8d6b8960c
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicplotviewpoint
+  owner: bgruening
+  revisions:
+  - 013e53ccc7ac
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicqualitycontrol
+  owner: bgruening
+  revisions:
+  - b892fa1fcaec
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicsignificantinteractions
+  owner: bgruening
+  revisions:
+  - 640e0e45518a
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicviewpoint
+  owner: bgruening
+  revisions:
+  - f881c94fb3b3
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicqualitycontrol
+  owner: bgruening
+  revisions:
+  - b892fa1fcaec
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicsignificantinteractions
+  owner: bgruening
+  revisions:
+  - 640e0e45518a
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicviewpoint
+  owner: bgruening
+  revisions:
+  - f881c94fb3b3
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_chicviewpointbackgroundmodel
+  owner: bgruening
+  revisions:
+  - 9d02f1819e81
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_hicadjustmatrix
+  owner: bgruening
+  revisions:
+  - 2dccb6bb0add
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_hicaggregatecontacts
+  owner: bgruening
+  revisions:
+  - f0216498a666
+  tool_panel_section_label: Single-Cell
+- name: hicexplorer_hicaverageregions
+  owner: bgruening
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