Merge pull request galaxyproject#857 from galaxyproject/create-pull-r…

…equest/patch Update all repos 2024-10-05
natefoo · Oct 7, 2024 · cf39e04 · cf39e04
2 parents 6d5bcc7 + aadca77
commit cf39e04
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diff --git a/usegalaxy.org/annotation.yml.lock b/usegalaxy.org/annotation.yml.lock
@@ -25,6 +25,7 @@ tools:
   revisions:
   - 09855551d713
   - 28433faa6e42
+  - bd0e53f3a891
   - ca6d970d931c
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
@@ -34,6 +35,7 @@ tools:
   - 6519ebe25019
   - 7be22100e5e1
   - dc027fa56d55
+  - f1e653756174
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
 - name: bp_genbank2gff3

diff --git a/usegalaxy.org/assembly.yml b/usegalaxy.org/assembly.yml
@@ -94,3 +94,5 @@ tools:
   owner: iuc
 - name: refseq_masher
   owner: nml
+- name: nextdenovo
+  owner: bgruening
diff --git a/usegalaxy.org/assembly.yml.lock b/usegalaxy.org/assembly.yml.lock
@@ -444,3 +444,9 @@ tools:
   - 1ec42f033bb4
   tool_panel_section_id: assembly
   tool_panel_section_label: Assembly
+- name: nextdenovo
+  owner: bgruening
+  revisions:
+  - 733eab97b979
+  tool_panel_section_id: assembly
+  tool_panel_section_label: Assembly
diff --git a/usegalaxy.org/chip_seq.yml.lock b/usegalaxy.org/chip_seq.yml.lock
@@ -68,6 +68,7 @@ tools:
 - name: pe_histogram
   owner: iuc
   revisions:
+  - 594b85e4237a
   - bd1416eea1f0
   tool_panel_section_id: chip_seq
   tool_panel_section_label: ChIP-seq

diff --git a/usegalaxy.org/convert_formats.yml.lock b/usegalaxy.org/convert_formats.yml.lock
@@ -61,6 +61,7 @@ tools:
   revisions:
   - 2dcfbbf9071a
   - 68f57cc8fad0
+  - 78fb18899c99
   - b8cdc0507586
   tool_panel_section_id: convert_formats
   tool_panel_section_label: Convert Formats
@@ -70,11 +71,13 @@ tools:
   - 297962e79f39
   - 4844c1810c16
   - a64c24430f5e
+  - ac3fed111eb6
   tool_panel_section_id: convert_formats
   tool_panel_section_label: Convert Formats
 - name: fastq_to_tabular
   owner: devteam
   revisions:
+  - 43807a65369f
   - 4b347702c4aa
   - 614a63f14adf
   - ccf4e1d1fcbe

diff --git a/usegalaxy.org/fasta_fastq.yml.lock b/usegalaxy.org/fasta_fastq.yml.lock
@@ -125,6 +125,7 @@ tools:
   revisions:
   - 09a2199cd356
   - 822cc1e6274e
+  - 8d958759cf2a
   - c885369b207b
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
@@ -133,13 +134,15 @@ tools:
   revisions:
   - 2ccb8dcabddc
   - 3e396e702cea
+  - b41c2c1bcfbf
   - ef49268ee579
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_paired_end_deinterlacer
   owner: devteam
   revisions:
   - 03d57fea6482
+  - 523c2aff0376
   - b7ce72b00e62
   - f3936d0632cb
   tool_panel_section_id: fasta_fastq
@@ -155,13 +158,15 @@ tools:
   revisions:
   - 249c8393f2d4
   - 35e38452bb3f
+  - 397dc333436b
   - 9bbe5b7ffa12
   - e39cc71d3ed6
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_masker_by_quality
   owner: devteam
   revisions:
+  - 4e1d64e6385f
   - 9282652e7234
   - 9dfda4e310ed
   - eb592e9ec47a
@@ -173,6 +178,7 @@ tools:
   - 4ac14b275aca
   - 5b87038565bb
   - 7861f3b10c68
+  - e30352e889fe
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_groomer
@@ -181,20 +187,23 @@ tools:
   - 47e5dbc3e790
   - 71e5fa25b8a2
   - 8611b80a14d6
+  - e9f8633db0a2
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_filter
   owner: devteam
   revisions:
   - 06934412f56d
   - 10b75444feae
+  - '144275714590'
   - 81a9090d6df3
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_combiner
   owner: devteam
   revisions:
   - 56389130cb63
+  - 9115b978ce10
   - b05e39b9c170
   - f1dc2a761c30
   tool_panel_section_id: fasta_fastq
@@ -232,6 +241,7 @@ tools:
   - 2d0d13b0b0f1
   - 33794bdb7fe0
   - b63b2bfb3ea3
+  - f0b18efb97f1
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastq_trimmer_by_quality
@@ -276,6 +286,7 @@ tools:
   owner: devteam
   revisions:
   - 2051602a5f97
+  - 5cbde03c1103
   - 7d37cfda8e00
   - e12f68d2cc4e
   tool_panel_section_id: fasta_fastq

diff --git a/usegalaxy.org/fastq_quality_control.yml.lock b/usegalaxy.org/fastq_quality_control.yml.lock
@@ -43,6 +43,7 @@ tools:
   - b1cea1b2fcd0
   - e2cf940128d5
   - f0e7deab6518
+  - f86c27295151
   tool_panel_section_id: fastq_quality_control
   tool_panel_section_label: FASTQ Quality Control
 - name: fastx_quality_statistics

diff --git a/usegalaxy.org/graph_display_data.yml.lock b/usegalaxy.org/graph_display_data.yml.lock
@@ -271,6 +271,7 @@ tools:
 - name: pe_histogram
   owner: iuc
   revisions:
+  - 594b85e4237a
   - bd1416eea1f0
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
@@ -324,6 +325,7 @@ tools:
   owner: fubar
   revisions:
   - 0e592dcaeb7f
+  - 137e08517410
   - 2fff478aca4b
   - 4aec47f872b3
   - 56f9a6e0fe80

diff --git a/usegalaxy.org/metagenomic_analysis.yml.lock b/usegalaxy.org/metagenomic_analysis.yml.lock
@@ -333,13 +333,15 @@ tools:
   owner: iuc
   revisions:
   - 5a0fa29951ae
+  - 8388fe31d604
   - b7429b53be2a
   - e562293ee5ec
   tool_panel_section_id: metagenomic_analysis
   tool_panel_section_label: Metagenomic Analysis
 - name: khmer_extract_partitions
   owner: iuc
   revisions:
+  - 1061711538c6
   - 2c763fb18010
   - 98b53d46e851
   - adb3dd5a899f
@@ -349,13 +351,15 @@ tools:
   owner: iuc
   revisions:
   - 06d1d91c67e5
+  - 570505540a7b
   - 77410799e8e9
   - b3d513c7093e
   tool_panel_section_id: metagenomic_analysis
   tool_panel_section_label: Metagenomic Analysis
 - name: khmer_filter_below_abundance_cutoff
   owner: iuc
   revisions:
+  - 00f7064c564b
   - 19607c740d19
   - 569001af897d
   - b469ab47b490
@@ -364,6 +368,7 @@ tools:
 - name: khmer_normalize_by_median
   owner: iuc
   revisions:
+  - 4d23ab83ea29
   - 557cc16931f4
   - b1fe2ef3d244
   - e84073b420a8
@@ -374,12 +379,14 @@ tools:
   revisions:
   - 385a965c6f87
   - 55109291a355
+  - 65b382bf9b7c
   - c018a72b523e
   tool_panel_section_id: metagenomic_analysis
   tool_panel_section_label: Metagenomic Analysis
 - name: khmer_filter_abundance
   owner: iuc
   revisions:
+  - 29a4d6e2ae9c
   - 8c6433857aa8
   - 97f65399e30d
   - b86562b4f3fd
@@ -391,6 +398,7 @@ tools:
   - 7624945cacd3
   - c0caca5af183
   - e0de12ae3fc2
+  - e699e2747356
   tool_panel_section_id: metagenomic_analysis
   tool_panel_section_label: Metagenomic Analysis
 - name: maxbin2

diff --git a/usegalaxy.org/presto.yml.lock b/usegalaxy.org/presto.yml.lock
@@ -17,6 +17,7 @@ tools:
   revisions:
   - 097b44ff88db
   - 967b96c6005a
+  - aa3554e51549
   - ef917c03493c
   - faba8f53524e
   tool_panel_section_id: presto
@@ -25,6 +26,7 @@ tools:
   owner: iuc
   revisions:
   - 0b103d43a2c7
+  - 1f3ae16f3655
   - 620f3b0a1430
   - 824d24bfe8dd
   tool_panel_section_id: presto
@@ -33,6 +35,7 @@ tools:
   owner: iuc
   revisions:
   - 488cd05be723
+  - 7f93403bc705
   - fc1fd003bc80
   - fd8f1ac582bd
   tool_panel_section_id: presto
@@ -43,13 +46,15 @@ tools:
   - 1ed5b0772f98
   - 4049467b8bb8
   - 90315cb06d06
+  - de864d852bce
   tool_panel_section_id: presto
   tool_panel_section_label: pRESTO
 - name: presto_pairseq
   owner: iuc
   revisions:
   - 49e7407445c3
   - 7bdff30820bf
+  - eed465eb14a3
   - f47efbc66fad
   tool_panel_section_id: presto
   tool_panel_section_label: pRESTO
@@ -59,20 +64,23 @@ tools:
   - 14e648d05cce
   - 36ad790eda96
   - 98b0b4c22e69
+  - df0797c61790
   tool_panel_section_id: presto
   tool_panel_section_label: pRESTO
 - name: presto_filterseq
   owner: iuc
   revisions:
   - 196b83ac37f2
   - 33a09d40751f
+  - 4a4e086f6e38
   - 7b102129b1e8
   tool_panel_section_id: presto
   tool_panel_section_label: pRESTO
 - name: presto_collapseseq
   owner: iuc
   revisions:
   - 3364fd7073ca
+  - 852e7ca7f7de
   - c60bd515e46d
   - d1a1b738c119
   tool_panel_section_id: presto
@@ -83,6 +91,7 @@ tools:
   - 1844a3d2c887
   - 5b059629cce0
   - 7c7df98db5a9
+  - ef31bdd0c9ed
   tool_panel_section_id: presto
   tool_panel_section_label: pRESTO
 - name: presto_assemblepairs
@@ -91,13 +100,15 @@ tools:
   - 0af48f0b7eb8
   - 44c980933450
   - 540fcbdac82e
+  - af855eb44091
   tool_panel_section_id: presto
   tool_panel_section_label: pRESTO
 - name: presto_alignsets
   owner: iuc
   revisions:
   - 0b4bd722367d
   - 40102188d44e
+  - b401018e0614
   - fa4cf8d895f4
   tool_panel_section_id: presto
   tool_panel_section_label: pRESTO
diff --git a/usegalaxy.org/rna_seq.yml.lock b/usegalaxy.org/rna_seq.yml.lock
@@ -180,6 +180,7 @@ tools:
   owner: iuc
   revisions:
   - 0f710191a66d
+  - 3c5e024a18cf
   - 3c97c841a443
   - f99dd58de04f
   tool_panel_section_id: rna_seq
@@ -534,5 +535,6 @@ tools:
   - 05f8e9d1e8b8
   - 3198f52bffaa
   - 928a52b5c938
+  - d3b0390f325f
   tool_panel_section_id: rna_seq
   tool_panel_section_label: RNA-seq
diff --git a/usegalaxy.org/single_cell.yml.lock b/usegalaxy.org/single_cell.yml.lock
@@ -8,6 +8,7 @@ tools:
   revisions:
   - 0185bd174ea0
   - 1072ce66b426
+  - 40812a65a78b
   - 6adf98e782f3
   - 6f5349dd5c49
   - 70fa84e99463
@@ -23,6 +24,7 @@ tools:
   owner: iuc
   revisions:
   - 3081ff5c84a3
+  - 4338bf96809e
   - 5c3ebe2adc77
   - 6bd82ed14acd
   - 6c145a6868cc
@@ -49,11 +51,13 @@ tools:
   - b409c2486353
   - d636ce5cde16
   - f87ed6503715
+  - fc0321c000a3
   tool_panel_section_id: single_cell
   tool_panel_section_label: Single-cell
 - name: scanpy_normalize
   owner: iuc
   revisions:
+  - 146ae5d70b47
   - 51d945eab1e1
   - 5342ce58cd1e
   - 56c0d4acef02
@@ -79,6 +83,7 @@ tools:
   - 6f83f8fd381f
   - aaa5da8e73a9
   - b2df381a6004
+  - cb43c5d3acd3
   - edec35114f72
   - f9353ee6a0d4
   tool_panel_section_id: single_cell
@@ -97,6 +102,7 @@ tools:
   - c65fce500915
   - d18e7a6e5cd4
   - e66884b1c1a5
+  - fe8f16c594ec
   tool_panel_section_id: single_cell
   tool_panel_section_label: Single-cell
 - name: anndata_export

diff --git a/usegalaxy.org/variant_calling.yml.lock b/usegalaxy.org/variant_calling.yml.lock
@@ -121,6 +121,7 @@ tools:
   - 3b4b2121842f
   - 4805fe3d8fda
   - 65432c3abf6c
+  - b11e8e9c23bf
   - dfadc322b065
   - e1461b5c52a0
   tool_panel_section_id: variant_calling