Merge branch 'usegalaxy-eu:master' into master

Makefile

@@ -53,6 +53,8 @@ update_trusted: $(UPDATE_TRUSTED_IUC) ## Run the update script
 	python3 scripts/update-tool.py goeckslab.yaml
 	python3 scripts/update-tool.py eirene.yaml
 	python3 scripts/update-tool.py lldelisle.yaml
+	python3 scripts/update-tool.py tools_q2d2.yaml
+	python3 scripts/update-tool.py ufz.yaml
 
 update_all: $(UPDATED_YAMLS)
 

asaim.yaml.lock

@@ -18,6 +18,7 @@ tools:
   - 734abc7ac21d
   - 751a694ec620
   - 83c7d564b128
+  - 8848455c0270
   - aad3885b3216
   - b723c120161a
   - ba931a59dd59
@@ -84,6 +85,7 @@ tools:
   - c19b16e5729c
   - e4574a4d09d8
   - f7985e0479b9
+  - f7e2f1eb3a16
   tool_panel_section_label: Quality Control
 - name: format_cd_hit_output
   owner: bebatut

bgruening.yaml

@@ -37,6 +37,10 @@ tools:
     owner: bgruening
     tool_panel_section_label: "Convert Formats"
 
+  - name: uniprot_rest_interface
+    owner: bgruening
+    tool_panel_section_label: Convert Formats
+
 # SAM/BAM
 
   - name: sambamba_flagstat
@@ -184,6 +188,10 @@ tools:
     owner: bgruening
     tool_panel_section_label: Imaging
 
+  - name: bioimage_inference
+    owner: bgruening
+    tool_panel_section_label: Imaging
+
   - name: woundhealing_scratch_assay
     owner: bgruening
     tool_panel_section_label: Imaging
@@ -322,6 +330,13 @@ tools:
     owner: bgruening
     tool_panel_section_label: Machine Learning
 
+  - name: flexynesis
+    owner: bgruening
+    tool_panel_section_label: Machine Learning
+
+  - name: chatgpt_openai_api
+    owner: bgruening
+    tool_panel_section_label: Machine Learning
 
 # MAPPING
 
@@ -355,7 +370,11 @@ tools:
   - name: itsx
     owner: bgruening
     tool_panel_section_label: Metagenomic Analysis
-
+
+  - name: motus
+    owner: bgruening
+    tool_panel_section_label: Metagenomic Analysis
+
   - name: tiara
     owner: bgruening
     tool_panel_section_label: Metagenomic Analysis

bgruening.yaml.lock

@@ -21,6 +21,7 @@ tools:
   owner: bgruening
   revisions:
   - 04bfb8ee7e23
+  - 3ae9331790a6
   - 4e9a3745dce4
   - 5376a7767fb3
   - 57e2503e6039
@@ -39,6 +40,7 @@ tools:
   - 31dfed0f0eed
   - 391a19477a12
   - 39881709807e
+  - 3e81299dfce3
   - 4dada93ef525
   - 7e2ee5f43778
   - 8dbc700cb940
@@ -49,6 +51,7 @@ tools:
   revisions:
   - 2a5a0b61a84e
   - bb871fbe177f
+  - cfe1d6e23237
   - fd0e8bda0154
   tool_panel_section_label: Convert Formats
 - name: hictk
@@ -59,6 +62,11 @@ tools:
   - a2e75bad2872
   - d36215791ad3
   tool_panel_section_label: Convert Formats
+- name: uniprot_rest_interface
+  owner: bgruening
+  revisions:
+  - 95fb5712344f
+  tool_panel_section_label: Convert Formats
 - name: sambamba_flagstat
   owner: bgruening
   revisions:
@@ -92,6 +100,7 @@ tools:
   - a6318f87f2cd
   - abba05ead5d7
   - e009d8260be2
+  - e7449b2c14bf
   tool_panel_section_label: Annotation
 - name: cpat
   owner: bgruening
@@ -138,8 +147,10 @@ tools:
   owner: bgruening
   revisions:
   - 1ce9b1d72ec3
+  - 1f0769f0b56b
   - 276f5d8712d5
   - 291923e6f276
+  - 3e4f8642c77e
   - 3ee0ef312022
   - 8d4f03b5fe9d
   - cb8dfd28c16f
@@ -202,6 +213,7 @@ tools:
   owner: bgruening
   revisions:
   - 8c99976de71e
+  - a34826ae0a73
   - b61022e1b807
   tool_panel_section_label: Assembly
 - name: split_file_to_collection
@@ -224,6 +236,7 @@ tools:
   - 5127a713de83
   - 5799092ffdff
   - 690c2caa367e
+  - 6ec1b853c8fd
   - 8ccbf07a5433
   - ad1149b4f795
   tool_panel_section_label: FASTA/FASTQ
@@ -245,9 +258,17 @@ tools:
 - name: jbrowse2
   owner: fubar
   revisions:
+  - 137e08517410
+  - 2fff478aca4b
+  - 4aec47f872b3
   - 56f9a6e0fe80
+  - 69c6ea16c148
+  - 878c27dfea9d
+  - af482048ca1a
   - b1260bca5fdc
+  - b55199c56abd
   - c017111e976a
+  - c4b77883c0a7
   - dc3fe98e7b37
   tool_panel_section_label: Graph/Display Data
 - name: plotly_ml_performance_plots
@@ -257,6 +278,7 @@ tools:
   - 4fac53da862f
   - 62e3a4e8c54c
   - 85da91bbdbfb
+  - f234e2e59d76
   tool_panel_section_label: Graph/Display Data
 - name: plotly_regression_performance_plots
   owner: bgruening
@@ -268,8 +290,15 @@ tools:
   owner: bgruening
   revisions:
   - 030bfe6065d9
+  - 9186100e75b5
   - eda6dfae9617
   tool_panel_section_label: Imaging
+- name: bioimage_inference
+  owner: bgruening
+  revisions:
+  - b0f2d3b4a278
+  - caea9ee1ffac
+  tool_panel_section_label: Imaging
 - name: woundhealing_scratch_assay
   owner: bgruening
   revisions:
@@ -995,6 +1024,18 @@ tools:
   revisions:
   - 02fa7b2245e6
   tool_panel_section_label: Machine Learning
+- name: flexynesis
+  owner: bgruening
+  revisions:
+  - bd808d1c4e0c
+  tool_panel_section_label: Machine Learning
+- name: chatgpt_openai_api
+  owner: bgruening
+  revisions:
+  - 08c658e9aa9e
+  - 7770a4bd42e2
+  - dab494dce303
+  tool_panel_section_label: Machine Learning
 - name: graphmap_align
   owner: bgruening
   revisions:
@@ -1036,6 +1077,11 @@ tools:
   revisions:
   - 2cbd0d66aa08
   tool_panel_section_label: Metagenomic Analysis
+- name: motus
+  owner: bgruening
+  revisions:
+  - d20f3b9a59a2
+  tool_panel_section_label: Metagenomic Analysis
 - name: tiara
   owner: bgruening
   revisions:
@@ -1045,6 +1091,7 @@ tools:
   owner: rnateam
   revisions:
   - 6f28e90db932
+  - 8e649f27aa0d
   - a65296ffb4a0
   - bcfce5aac49c
   - bf28a8cff401

cheminformatics.yaml.lock

@@ -198,6 +198,7 @@ tools:
   - 2c5c7da26e08
   - 49242402887b
   - 4c9d6b47045c
+  - 8302ab092300
   - c066b5accacf
   - f0502d809c4b
   tool_panel_section_label: ChemicalToolBox
@@ -728,12 +729,14 @@ tools:
   - a5f4b80e6769
   - b8838a9aa31a
   - de4c80d17527
+  - fac2c28b4c55
   tool_panel_section_label: ChemicalToolBox
 - name: openbabel_remsmall
   owner: bgruening
   revisions:
   - 0c95b0f51114
   - 11952f619e90
+  - 81836d586797
   - ac9567d307a2
   - aebc671bae78
   - c8d8caa9a54d
@@ -752,6 +755,7 @@ tools:
   - 50dc8ca09a50
   - 78640d0127ce
   - 8b23033ff72c
+  - 985ab0acd514
   - 99517f9b780d
   - f27e2eaffb5f
   tool_panel_section_label: ChemicalToolBox
@@ -765,6 +769,7 @@ tools:
   - 49d21d05f77c
   - 5b66a1684f18
   - 9c15e92bed39
+  - a638d8d13bb3
   - a84187d7bda6
   - eed751918a20
   - f924a1728291
@@ -773,6 +778,7 @@ tools:
   owner: bgruening
   revisions:
   - 417845394cdf
+  - 50eaae9df8d3
   - 53cf744d1c6f
   - a26f96c1f061
   - a72ae2711a97
@@ -794,6 +800,7 @@ tools:
   - 9249b0e0e6bd
   - abceed0106cd
   - cc8ca507174f
+  - f70b83b730ac
   tool_panel_section_label: ChemicalToolBox
 - name: openbabel_multi_obgrep
   owner: bgruening
@@ -806,6 +813,7 @@ tools:
   - 136ceea822f5
   - 3ec5e9a716ac
   - 672b3365ddbc
+  - 75ee9c410951
   - 7672039a0bb0
   - a66827fc370d
   - ba2d56f16904
@@ -824,13 +832,15 @@ tools:
   - aedce3959676
   - afd14e10a318
   - d92ada24e4ad
+  - f5d7ffbb2d33
   - f93f3e01abe8
   tool_panel_section_label: ChemicalToolBox
 - name: openbabel_remove_protonation_state
   owner: bgruening
   revisions:
   - 00263ca6ffb8
   - 0bf5331f62ef
+  - 22a866858b81
   - 44488fa95d1d
   - 5dc2a6cd6da1
   - 612c134546a2
@@ -845,6 +855,7 @@ tools:
   - 1400d1977e7b
   - 1c66bf08f687
   - 37f6668ce540
+  - 4242b4d68e9c
   - a072cb207571
   - a9df9aae60bb
   - b59c91adeac1
@@ -859,6 +870,7 @@ tools:
   - 202e3a64859b
   - 80d78559a5a3
   - 9a83f24376b0
+  - 9adf3fae2771
   - ab2b9d87b067
   - bd678d7db2ae
   - c19608db6b15
@@ -873,6 +885,7 @@ tools:
   - 69e02cf88856
   - 72d13f75b67c
   - 8ee975c49a3d
+  - 988085c7a0ea
   - a9ea2eac7300
   - da0059ee548a
   - da03b00048b1
@@ -886,6 +899,7 @@ tools:
   - 43167f164076
   - 6e4b7e0c61a6
   - 716dcb5bbb71
+  - 7b6fd1c273cd
   - 883fe4f7f1b2
   - 976a5975b952
   - bfb8555f0003
@@ -902,6 +916,7 @@ tools:
   - 65254472e5b4
   - 854a7a169623
   - b2569e22b40c
+  - c5de6c19eb06
   - d751e92477ea
   - e289f65f6b91
   tool_panel_section_label: ChemicalToolBox