From 1abbc0f0121a01e2ee60af34b90c8f9b380f90de Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Wed, 8 Nov 2023 20:34:02 +0100 Subject: [PATCH] Revert "Revert "Update tools"" --- usegalaxy.org/annotation.yml.lock | 4 +++ usegalaxy.org/assembly.yml.lock | 3 +++ usegalaxy.org/chip_seq.yml.lock | 1 + usegalaxy.org/fasta_fastq.yml.lock | 1 + usegalaxy.org/get_data.yml.lock | 2 ++ usegalaxy.org/graph_display_data.yml.lock | 1 + usegalaxy.org/machine_learning.yml.lock | 30 +++++++++++++++++++++ usegalaxy.org/metagenomic_analysis.yml.lock | 4 +++ usegalaxy.org/multiple_alignments.yml.lock | 3 +++ usegalaxy.org/ncbi_blast_.yml.lock | 1 + usegalaxy.org/rna_seq.yml.lock | 3 +++ usegalaxy.org/single_cell.yml.lock | 10 +++++++ usegalaxy.org/statistics.yml.lock | 1 + 13 files changed, 64 insertions(+) diff --git a/usegalaxy.org/annotation.yml.lock b/usegalaxy.org/annotation.yml.lock index 2a5d49e9..393193ef 100644 --- a/usegalaxy.org/annotation.yml.lock +++ b/usegalaxy.org/annotation.yml.lock @@ -303,6 +303,7 @@ tools: - name: sortmerna owner: rnateam revisions: + - 10b84b577117 - 1eafcc450052 - 65c38d020fea - eb35257d2e29 @@ -372,18 +373,21 @@ tools: revisions: - 30f08d74024f - a7ce2601500c + - e94187d661df tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: funannotate_annotate owner: iuc revisions: - 582fd74dc2a1 + - 756376aeb1ae - 9feee7fc49a1 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: funannotate_predict owner: iuc revisions: + - 1bc5a03faf2e - 51b6ee65ef7f - f31125bb85ea tool_panel_section_id: annotation diff --git a/usegalaxy.org/assembly.yml.lock b/usegalaxy.org/assembly.yml.lock index 947002e8..3f08ac6c 100644 --- a/usegalaxy.org/assembly.yml.lock +++ b/usegalaxy.org/assembly.yml.lock @@ -168,6 +168,7 @@ tools: - 8d1af5db538d - ad80238462c1 - d9f6a00b6db7 + - ee17a294d3a3 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: spades @@ -192,6 +193,7 @@ tools: owner: bgruening revisions: - 39bed8de8017 + - 78c533842eeb - 7c847ec300b8 - 936f0b5e7fcc - a199cd7ac344 @@ -203,6 +205,7 @@ tools: owner: bgruening revisions: - 045c7c3d8e59 + - 0ee0c3089254 - 366a11d316a7 - 3f7be05a1597 - 5bec28269d95 diff --git a/usegalaxy.org/chip_seq.yml.lock b/usegalaxy.org/chip_seq.yml.lock index 7f43dc8b..432b8545 100644 --- a/usegalaxy.org/chip_seq.yml.lock +++ b/usegalaxy.org/chip_seq.yml.lock @@ -27,6 +27,7 @@ tools: revisions: - 424aefbd7777 - 640d3af5d833 + - 86e2413cf3f8 tool_panel_section_id: chip_seq tool_panel_section_label: ChIP-seq - name: sicer diff --git a/usegalaxy.org/fasta_fastq.yml.lock b/usegalaxy.org/fasta_fastq.yml.lock index 7e58bc80..54266733 100644 --- a/usegalaxy.org/fasta_fastq.yml.lock +++ b/usegalaxy.org/fasta_fastq.yml.lock @@ -283,6 +283,7 @@ tools: - name: filtlong owner: iuc revisions: + - 1f296803dfa3 - 41b2ad601cf0 - 8880fb74ef56 - a72af9de6bf5 diff --git a/usegalaxy.org/get_data.yml.lock b/usegalaxy.org/get_data.yml.lock index 69893077..aac74e55 100644 --- a/usegalaxy.org/get_data.yml.lock +++ b/usegalaxy.org/get_data.yml.lock @@ -10,6 +10,7 @@ tools: - 4317d3cb6cba - 4df8de2d0e48 - 653e89d73fc4 + - 6591f049cf7e - 69ebb7f46e45 - 6ea73833cf67 - 7068f48d0ef9 @@ -74,6 +75,7 @@ tools: owner: iuc revisions: - 6cb20e130473 + - 7d87a9d58aa1 - f9db47f68e5e tool_panel_section_id: get_data tool_panel_section_label: Get Data diff --git a/usegalaxy.org/graph_display_data.yml.lock b/usegalaxy.org/graph_display_data.yml.lock index faf63f68..daf05f6e 100644 --- a/usegalaxy.org/graph_display_data.yml.lock +++ b/usegalaxy.org/graph_display_data.yml.lock @@ -11,6 +11,7 @@ tools: - 222c02df5d55 - 4a229a7ad638 - 6fabdcde0214 + - 8334dc98c48e - a536d2736c2d - c7655b5a94af - c80db5d6fd8c diff --git a/usegalaxy.org/machine_learning.yml.lock b/usegalaxy.org/machine_learning.yml.lock index 760999ce..cfa5bc85 100644 --- a/usegalaxy.org/machine_learning.yml.lock +++ b/usegalaxy.org/machine_learning.yml.lock @@ -7,6 +7,7 @@ tools: owner: bgruening revisions: - 1e088aa741eb + - 25b46af53232 - 29e4122c90de - 60c726f5cc5e - 65820fb7257b @@ -25,6 +26,7 @@ tools: - 2a853a2d2e72 - 2b8d85927742 - 2d8478144bb2 + - 4d81e3e2fb63 - 61a6132df9e0 - 8a794e6d3388 - 94d91334c787 @@ -39,6 +41,7 @@ tools: - 053570bac5ea - 1f0c955fabc7 - 20cd4269deb2 + - 522137aaa9c4 - 5b35833076f0 - 66d7efc06000 - 772e0e89fc68 @@ -56,6 +59,7 @@ tools: - 3814a92c1416 - 4a5266c96889 - 508ce0649bec + - 61b2d8f8811e - 77c04469e8b8 - 7f6079deac6f - 9d77b259ef27 @@ -86,12 +90,14 @@ tools: - ddc4fe317a92 - e03a58b31c12 - e23cfe4be9d4 + - f6ea9fc38223 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_estimator_attributes owner: bgruening revisions: - 07843f917990 + - 30d21a6041f6 - 5a125d1ac9b9 - 5ae00d2908f2 - 867caa39eaa4 @@ -116,6 +122,7 @@ tools: - 887e0aaa482e - 9dc28a4b6ca8 - bfc7bdfcb423 + - e06ab1e112cc tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_svm_classifier @@ -126,6 +133,7 @@ tools: - 14fa42b095c4 - 6d23883e0b94 - 73d2ef652879 + - 80852884053f - b7c3e9a3b954 - d2afc87db26b - f458724cc317 @@ -144,6 +152,7 @@ tools: - ab9977548806 - b4ba9602a36e - db7eb7302fc9 + - e99cccc3ca13 - eb41d87cb1de - fed1850f01c3 tool_panel_section_id: machine_learning @@ -157,6 +166,7 @@ tools: - 25ab6b4e376e - 301e07345c93 - 36e8d6d5d01b + - 7626ea9c2e1b - a36a45cb96fa - d37a7f17e35d - e5a5ad882f1f @@ -169,6 +179,7 @@ tools: - 0c74d3164ac8 - 118e230e85ce - 3f25f37ee3db + - 4c4ec859c31a - 7388ffedf12c - 7442b94d6a1e - 840f29aad145 @@ -187,6 +198,7 @@ tools: - 226524df8c6c - 2a1afd3481ce - 7366e5108e9f + - 7614281473da - b07416ec8d16 - c84ab9ca4e5c - e79200975daf @@ -202,6 +214,7 @@ tools: - 4db563e8d453 - 7ae443e6217d - 823ecc0bce45 + - 8b1b2b91f8d0 - 9871a634540f - aa83e7e3c398 - cd02bf168d23 @@ -219,12 +232,14 @@ tools: - ad7e0b4291ee - aeca97d9a214 - bb9fc9d46ea4 + - e10e776f2109 - e13a7c05b3a4 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_ensemble owner: bgruening revisions: + - 060ca94ac049 - 1682df52c084 - 1a53edc4b438 - 315f01a9d2c2 @@ -246,6 +261,7 @@ tools: - 5773e98921fc - 6d21b03e00a1 - 74adae8d7b0f + - 96bb4c49e30e - a7c667ff83fe - ae0fafb53c1d - c2cd3219543a @@ -260,6 +276,7 @@ tools: - 1bef885255e0 - 50b3e080cef0 - 6c030fe29722 + - 761269451e98 - 80074b842ebd - 826c3e68e7a9 - a5c2ce4ea328 @@ -273,6 +290,7 @@ tools: - 0ee984c1cbd6 - 15bcf1a7543b - 55703205546f + - 6ffedbe712c0 - 80ca74b1cb36 - adc6137e7c73 - ae69f6918abe @@ -289,6 +307,7 @@ tools: - 1e98dbb8d5bc - 5c9fb40ae174 - 6000c1589f33 + - 627be0156505 - 6db5c1dfb076 - 70c5a9127f99 - 7d98dfb04d27 @@ -304,6 +323,7 @@ tools: - 237ae72d58a3 - 2d032cff49eb - 4335cec181ba + - 6adef419e041 - 7696d389675c - 87cb9cb44d1f - 893285b150f8 @@ -324,6 +344,7 @@ tools: - 927586a18553 - c648d0716fb0 - c9969328b42f + - d4808d5b83da - dc4b5fd604a6 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning @@ -335,6 +356,7 @@ tools: - 734c66aa945a - 8e447b95e6a8 - adb084b901cc + - f0ede473a7e8 - fb17e19b62a4 - fc2e64a27e90 - fc70bf5c3b58 @@ -350,6 +372,7 @@ tools: - 3312fb686ffb - 33c564caa3c4 - 6e25381dad5c + - a2e3cf2f9f40 - b6f5443c4f58 - ce2fd1edbc6e - e10ffa9e0b90 @@ -361,6 +384,7 @@ tools: revisions: - 044729657181 - 0926c2b1315f + - 22e73afd5206 - 4a1cd790e323 - 61fb99c55558 - bfc44324a773 @@ -379,6 +403,7 @@ tools: - 612ca26c197d - 61634a87efc7 - a4f18bbb4eca + - caeb57858702 - f93f0cdbaf18 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning @@ -390,6 +415,7 @@ tools: - 222c02df5d55 - 4a229a7ad638 - 6fabdcde0214 + - 8334dc98c48e - a536d2736c2d - c7655b5a94af - c80db5d6fd8c @@ -403,6 +429,7 @@ tools: - 3045d322d4ac - 74f96ebc5554 - 8e95b68b178b + - b7d104ede67e - c48ffc96fe79 - d562708bb095 tool_panel_section_id: machine_learning @@ -414,6 +441,7 @@ tools: - 24c1cc2dd4a4 - 3af626081467 - 945a53c248de + - c17f3eacdb14 - caf164dd0e18 - f06ad033c114 tool_panel_section_id: machine_learning @@ -422,6 +450,7 @@ tools: owner: bgruening revisions: - 0af678661e20 + - 2af1346e68c9 - 470aed90aa41 - 818f9b69d8a0 - e1317b5502fa @@ -438,6 +467,7 @@ tools: - 6d1a9fae57eb - 92e09b827300 - 9f9cf31e3111 + - b7e93c1deb3f - e6893a4bcb7b tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning diff --git a/usegalaxy.org/metagenomic_analysis.yml.lock b/usegalaxy.org/metagenomic_analysis.yml.lock index 880324a2..511b9d3a 100644 --- a/usegalaxy.org/metagenomic_analysis.yml.lock +++ b/usegalaxy.org/metagenomic_analysis.yml.lock @@ -18,6 +18,7 @@ tools: - 54f751e413f4 - 62c9df8382c2 - 64be1ac21109 + - e8ac2b53f262 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: vsearch @@ -92,6 +93,7 @@ tools: - 4a6ee918c13a - 6ef0b5664c69 - a3b86937ead6 + - dad9da48a09a - e3cbd2287f63 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis @@ -103,6 +105,7 @@ tools: - 54ccb7e1f49a - 584008e574b2 - 72ed72122deb + - a4db66553a61 - bd46669113b9 - e177a8ea0bf1 tool_panel_section_id: metagenomic_analysis @@ -356,6 +359,7 @@ tools: - name: maxbin2 owner: mbernt revisions: + - 2bc40bfbcfb4 - 8a0473eb465e - cfd50144a871 tool_panel_section_id: metagenomic_analysis diff --git a/usegalaxy.org/multiple_alignments.yml.lock b/usegalaxy.org/multiple_alignments.yml.lock index f12f2dd1..5fc2d2bf 100644 --- a/usegalaxy.org/multiple_alignments.yml.lock +++ b/usegalaxy.org/multiple_alignments.yml.lock @@ -16,6 +16,7 @@ tools: revisions: - 0c84cce7b030 - 5a92f4c476b5 + - 87c1c223c704 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: interval2maf @@ -30,6 +31,7 @@ tools: - name: mafft owner: rnateam revisions: + - 6f28e90db932 - a65296ffb4a0 - aaefa93c2dd2 - c5908940967d @@ -40,6 +42,7 @@ tools: owner: devteam revisions: - 4daabc25df00 + - 5b097fde95dd - d6694932c5e0 - d9c2b2fde6a3 tool_panel_section_id: multiple_alignments diff --git a/usegalaxy.org/ncbi_blast_.yml.lock b/usegalaxy.org/ncbi_blast_.yml.lock index fb129f14..6063c0cf 100644 --- a/usegalaxy.org/ncbi_blast_.yml.lock +++ b/usegalaxy.org/ncbi_blast_.yml.lock @@ -9,6 +9,7 @@ tools: - 0e3cf9594bb7 - 2889433c7ae1 - 5edc472ec434 + - a52d2d93e595 - e25d3acf6e68 tool_panel_section_id: ncbi_blast_ tool_panel_section_label: NCBI BLAST+ diff --git a/usegalaxy.org/rna_seq.yml.lock b/usegalaxy.org/rna_seq.yml.lock index 8b486a6c..0efc094e 100644 --- a/usegalaxy.org/rna_seq.yml.lock +++ b/usegalaxy.org/rna_seq.yml.lock @@ -16,6 +16,7 @@ tools: - name: edger owner: iuc revisions: + - 070900306913 - 0cb907a2a810 - 334ce9b1bac5 - 3d89af8a44f0 @@ -87,6 +88,7 @@ tools: - 54f751e413f4 - 62c9df8382c2 - 64be1ac21109 + - e8ac2b53f262 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: kallisto_quant @@ -496,6 +498,7 @@ tools: owner: rnateam revisions: - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: isoformswitchanalyzer diff --git a/usegalaxy.org/single_cell.yml.lock b/usegalaxy.org/single_cell.yml.lock index ccf53a74..b6fdd597 100644 --- a/usegalaxy.org/single_cell.yml.lock +++ b/usegalaxy.org/single_cell.yml.lock @@ -8,6 +8,7 @@ tools: revisions: - 6adf98e782f3 - 7647e5cd1b8b + - 95777145cb92 - 9a169729c9f9 - aa0c474463c2 tool_panel_section_id: single_cell @@ -15,6 +16,7 @@ tools: - name: scanpy_inspect owner: iuc revisions: + - 6bd82ed14acd - 6c145a6868cc - 9d33775ec67d - c5d3684f7c4c @@ -24,6 +26,7 @@ tools: - name: scanpy_filter owner: iuc revisions: + - 2d02d9702d3a - 3c86f71498bc - 5511647110ff - b409c2486353 @@ -37,6 +40,7 @@ tools: - 5342ce58cd1e - a407e7f8bdc1 - ab55fe8030b6 + - c9cb76cf8d6c tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_cluster_reduce_dimension @@ -46,12 +50,14 @@ tools: - 3e4e1cf73d98 - aaa5da8e73a9 - b2df381a6004 + - edec35114f72 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_remove_confounders owner: iuc revisions: - 215733a383f2 + - 73ab2ac53d06 - 80d4e2cac903 - bf2017df9837 - c2ef03559dc6 @@ -414,17 +420,20 @@ tools: owner: iuc revisions: - 02b1fe7aed76 + - 4fff5a293013 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: baredsc_2d owner: iuc revisions: + - aa4a6f0916b4 - c29e7bb492bf tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: baredsc_combine_1d owner: iuc revisions: + - 050cf43887d3 - c32347702e12 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -432,5 +441,6 @@ tools: owner: iuc revisions: - 239193b96d72 + - ae969fdb8442 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell diff --git a/usegalaxy.org/statistics.yml.lock b/usegalaxy.org/statistics.yml.lock index 00c0ce00..3fc3b20b 100644 --- a/usegalaxy.org/statistics.yml.lock +++ b/usegalaxy.org/statistics.yml.lock @@ -198,6 +198,7 @@ tools: - 6d1a9fae57eb - 92e09b827300 - 9f9cf31e3111 + - b7e93c1deb3f - e6893a4bcb7b tool_panel_section_id: statistics tool_panel_section_label: Statistics