From 715803dd186614fd8c7607df744976cfe0d69332 Mon Sep 17 00:00:00 2001 From: martenson <1814954+martenson@users.noreply.github.com> Date: Wed, 23 Sep 2026 13:52:40 +0000 Subject: [PATCH] Update all tools of usegalaxy.cz --- usegalaxy.cz/assembly.yml.lock | 9 ++++++ usegalaxy.cz/deeptools.yml.lock | 18 ++++++++++++ usegalaxy.cz/extract_features.yml.lock | 1 + usegalaxy.cz/fasta_fastq.yml.lock | 1 + usegalaxy.cz/machine_learning.yml.lock | 32 ++++++++++++++++++++++ usegalaxy.cz/metagenomic_analysis.yml.lock | 22 +++++++++++++++ usegalaxy.cz/ncbi_blast.yml.lock | 1 + usegalaxy.cz/proteomics.yml.lock | 9 ++++++ usegalaxy.cz/statistics.yml.lock | 1 + usegalaxy.cz/variant_calling.yml.lock | 1 + 10 files changed, 95 insertions(+) diff --git a/usegalaxy.cz/assembly.yml.lock b/usegalaxy.cz/assembly.yml.lock index 2283b88..0223ccb 100644 --- a/usegalaxy.cz/assembly.yml.lock +++ b/usegalaxy.cz/assembly.yml.lock @@ -322,6 +322,7 @@ tools: owner: nml revisions: - 1f04936b96f3 + - 263af8401aed - 33368fec3b70 - 822954de3f59 - b512435320e3 @@ -352,6 +353,7 @@ tools: revisions: - 04d81e5f25e9 - 2ecf5a570907 + - 434f2a6c3ade - 697c9156dafe - f192c2fbe13f - fd128c111ab0 @@ -370,6 +372,7 @@ tools: - 1d06c8b38e77 - 5bd3f053c303 - aa1ac2f7a688 + - c6ba8470ed01 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: meryl @@ -488,6 +491,7 @@ tools: - name: spades_rnaviralspades owner: iuc revisions: + - 7170a53ee406 - a9aa4115cb68 - d5645713603a - d5fb354f745d @@ -501,6 +505,7 @@ tools: - 388dbecbf03b - 6fb81bb0fe3e - b40b77418372 + - c4e781659379 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: spades_metaviralspades @@ -509,12 +514,14 @@ tools: - 328aa71f0f3c - 6766a94ef559 - c4ba6aa27088 + - dcaf2403747d - ed32d95f436a tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: spades_metaplasmidspades owner: iuc revisions: + - 9911ca348668 - ae96f644b722 - c5c4fa59be65 - e5a3b75a271f @@ -526,6 +533,7 @@ tools: revisions: - 045c8498d2dd - 152ff7d1817a + - 2c650dcc6190 - 2cf8a2028ddc - 34305b013402 tool_panel_section_id: assembly @@ -534,6 +542,7 @@ tools: owner: iuc revisions: - 051fd2db8a27 + - 162a7ff870e9 - 5e7a2a927b56 - 60b8f1668552 - afac6d6bd02b diff --git a/usegalaxy.cz/deeptools.yml.lock b/usegalaxy.cz/deeptools.yml.lock index 07bfb0f..f47081f 100644 --- a/usegalaxy.cz/deeptools.yml.lock +++ b/usegalaxy.cz/deeptools.yml.lock @@ -5,6 +5,7 @@ tools: - name: deeptools_plot_profile owner: bgruening revisions: + - 43b85f471fe2 - 6662b1a8d326 - 75756ed34963 - e9429e484e25 @@ -15,6 +16,7 @@ tools: revisions: - 037a701703b2 - 42cb23d80271 + - 7fdfac4711b2 - e4c7985d4585 tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -23,6 +25,7 @@ tools: revisions: - 1ad8b24eca7c - 231994413f89 + - 3208df1c919e - 7fda5607e777 tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -37,6 +40,7 @@ tools: - name: deeptools_compute_matrix_operations owner: bgruening revisions: + - 3decd0bfc388 - be95d48dd27f - c424cde8a352 - e6d0bff01239 @@ -48,12 +52,14 @@ tools: - 07418a30ed01 - '216825708741' - 7989c6ddf634 + - dc53544cb243 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - 3f9dc453c0e8 + - 5d44209e86ad - 915b324e649f - c06951d10364 tool_panel_section_id: deeptools @@ -61,6 +67,7 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - 09d1214b45d1 - 10ebedbfee31 - c89b665b45e4 - c929a006727f @@ -69,6 +76,7 @@ tools: - name: deeptools_alignmentsieve owner: bgruening revisions: + - 3d254090aba8 - 6b3c9fa6bc2c - 97b384b7bfb0 - e5a296ce8fbb @@ -79,6 +87,7 @@ tools: revisions: - 0e49b109abc2 - 4df95152a39e + - 7dcc58a57476 - d13c066a4751 tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -87,6 +96,7 @@ tools: revisions: - 01fb6a7654e6 - 1fcb7adc39b8 + - 3d5024351691 - b4e53394fced - db9bba3f6180 tool_panel_section_id: deeptools @@ -97,11 +107,13 @@ tools: - 443d9a9d6d11 - 7784523d9743 - 851020617ea1 + - c59e0acb4e0b tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_compute_matrix owner: bgruening revisions: + - 1030f37ff2f0 - 19bb3e6d9e31 - a60c359ec43c - d9ccce056684 @@ -121,6 +133,7 @@ tools: - 137c4beed34b - 459cfa861f0b - a3f625719b3f + - ec28c2928823 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_correlation @@ -129,6 +142,7 @@ tools: - 2c66e43f1c86 - 45a7f5f0fed0 - bad3ca889618 + - c3dfef526d03 - e44978659400 tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -137,6 +151,7 @@ tools: revisions: - 4ed32329e0ed - bed4b253dc69 + - c0893efd5a8f - ca8a7f0ea872 tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -145,12 +160,14 @@ tools: revisions: - 309af65f003c - 4431f39ede55 + - 88b89b29d871 - 88ce7fed1488 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_estimatereadfiltering owner: bgruening revisions: + - 3fac11f2adb3 - 4da54a84303b - 71082dac170c - c72a755904a9 @@ -160,6 +177,7 @@ tools: owner: bgruening revisions: - 35b2d3ebd6d7 + - 3c478e39df6a - 4a53856a5b85 tool_panel_section_id: deeptools tool_panel_section_label: deepTools diff --git a/usegalaxy.cz/extract_features.yml.lock b/usegalaxy.cz/extract_features.yml.lock index 98da114..e8c2c29 100644 --- a/usegalaxy.cz/extract_features.yml.lock +++ b/usegalaxy.cz/extract_features.yml.lock @@ -25,6 +25,7 @@ tools: - name: b2btools_single_sequence owner: iuc revisions: + - b4c7df5324fb - b694a77ca1e8 tool_panel_section_id: extract_features tool_panel_section_label: Extract Features diff --git a/usegalaxy.cz/fasta_fastq.yml.lock b/usegalaxy.cz/fasta_fastq.yml.lock index f57cdc6..e3505c4 100644 --- a/usegalaxy.cz/fasta_fastq.yml.lock +++ b/usegalaxy.cz/fasta_fastq.yml.lock @@ -262,6 +262,7 @@ tools: - 241decaaff3e - 25c59c0ceb55 - 281054a26e41 + - 36be11c58dac - 4557b2da9e7f - 480ddbd12a03 - 65b93b623c77 diff --git a/usegalaxy.cz/machine_learning.yml.lock b/usegalaxy.cz/machine_learning.yml.lock index 1264bef..f71aa0a 100644 --- a/usegalaxy.cz/machine_learning.yml.lock +++ b/usegalaxy.cz/machine_learning.yml.lock @@ -16,6 +16,7 @@ tools: - 2d7016b3ae92 - 3af626081467 - 435592ba3087 + - 8a82f0a52e73 - c17f3eacdb14 - c716b8c86c5d - f06ad033c114 @@ -29,6 +30,7 @@ tools: - 1b7ab45c7858 - 27f8bd20a936 - a459c68692ca + - a46f6d5ea764 - b7d104ede67e - c12485d058aa - d562708bb095 @@ -40,6 +42,7 @@ tools: revisions: - 1bdac8249aa1 - 1dd433d2c92c + - 2468c4e3baed - 27903ce9b4be - 37e193b3fdd7 - 4bbaf77573ef @@ -60,6 +63,7 @@ tools: - 253b3aaf0d91 - 59f53bbe6ba9 - 6717e5cc4d05 + - 9ec25da5ece0 - ae4b593c99f8 - b78007bf1cb8 - b94babda32e4 @@ -72,6 +76,7 @@ tools: - 2af1346e68c9 - 31f6bf2382dc - 6ecb3d77d46e + - 7def2a4df843 - 818f9b69d8a0 - 8ddb3557710d - aeee74692508 @@ -87,6 +92,7 @@ tools: - 1588f9076e32 - 1d2a478bb514 - 21730620a849 + - 5eca6ce3ce7b - 5f9c0e99016f - 72c0d2747dc9 - 8334dc98c48e @@ -110,6 +116,7 @@ tools: - b7c3e9a3b954 - da0a22cdcce7 - de94341feadb + - df690bb42687 - e1b37bdc5fbd - f9639b488779 tool_panel_section_id: machine_learning @@ -125,6 +132,7 @@ tools: - b3a4682eabb6 - bde62c243b7e - bf2bcf7bd617 + - c003af3882f6 - ddc4fe317a92 - e03a58b31c12 - f6ea9fc38223 @@ -136,6 +144,7 @@ tools: - 1552b8cb4a94 - 25b46af53232 - 29e4122c90de + - 3dd539570a60 - 475b5171945f - 83228baae3c5 - 919198d656dd @@ -151,6 +160,7 @@ tools: revisions: - 04b160a26690 - 3bdb5b6c8ee8 + - 3c063985a4d0 - 4ba68dd788b3 - 6cf2a66c46f1 - 7068b5fcd623 @@ -180,6 +190,7 @@ tools: - c411ff569a26 - d0352e8b4c10 - e19359b23e54 + - fd51b7456c2a tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_searchcv @@ -196,6 +207,7 @@ tools: - 7509d7059040 - 7626ea9c2e1b - 82b6104d4682 + - 9a01835cdead - c6ae57f774c6 - e5a5ad882f1f - f484f41ea0dd @@ -211,6 +223,7 @@ tools: - 52c4e0ef580a - 7442b94d6a1e - 775b004b7920 + - 78eb20e5bdd3 - 840f29aad145 - 99038af8deda - 9c3e1d3235c8 @@ -224,6 +237,7 @@ tools: owner: bgruening revisions: - 226524df8c6c + - 23a37a52a899 - 3ff43fbb7ccf - 5bd0866dbc7a - 7614281473da @@ -242,6 +256,7 @@ tools: - name: sklearn_nn_classifier owner: bgruening revisions: + - 0c612f257a48 - 187226dceb22 - 2c58b83c9bad - 4cc980df6265 @@ -265,6 +280,7 @@ tools: - 060ca94ac049 - 0b98933cf0f7 - 1a53edc4b438 + - 26844ef7ab2b - 2e69c6ca6e91 - 360330a867f0 - 39ae276e75d9 @@ -292,6 +308,7 @@ tools: - 74adae8d7b0f - 96bb4c49e30e - 9e0e31bd8392 + - dd786bc16fdb - e918f33f7d4f - fcadeadd51ae tool_panel_section_id: machine_learning @@ -300,6 +317,7 @@ tools: owner: bgruening revisions: - 0ff864fabfe9 + - 191eac3065de - 1b5cd2d16fb1 - 484a98c44f00 - 685046e0381a @@ -326,6 +344,7 @@ tools: - 68afcd163b3d - 6ffedbe712c0 - 80ca74b1cb36 + - 85f43dfa9ad3 - 9728636c1e41 - a0061a087409 - a7067bbf1e58 @@ -339,6 +358,7 @@ tools: revisions: - 268ecaf96b68 - 28d51b976c29 + - 31fca3ff2a46 - 3badea963c3b - 4e6ada84d334 - 5c9fb40ae174 @@ -362,6 +382,7 @@ tools: - 3e2921875c58 - 4335cec181ba - 4ee087eeda62 + - 5408544bc348 - 686d0c3e3b62 - 6adef419e041 - 75bcb7c19fcf @@ -379,6 +400,7 @@ tools: - 40f4447733b2 - 57938c2f6ef5 - 67881a837f46 + - 84dad16ed802 - 91c4e3331208 - 927586a18553 - 9d3a024cf2da @@ -394,6 +416,7 @@ tools: - name: sklearn_model_validation owner: bgruening revisions: + - 0bd433f34317 - 33d2606fdb3f - 492d34a75de6 - 56f6ebf69ddc @@ -415,6 +438,7 @@ tools: revisions: - 22e73afd5206 - 2e69c6de354e + - 3c7df2c09956 - 4a1cd790e323 - 9a3cb21a3661 - bfc44324a773 @@ -435,6 +459,7 @@ tools: - 8e447b95e6a8 - 9084156b2bb5 - a293d7937700 + - cde5fc214cc8 - f0ede473a7e8 - fc70bf5c3b58 - fe4e36598917 @@ -444,6 +469,7 @@ tools: owner: bgruening revisions: - 376dd641af44 + - 5314ae25fbe1 - 6e25381dad5c - 910ebff96ddc - a2e3cf2f9f40 @@ -466,11 +492,13 @@ tools: - 61b2d8f8811e - 679e4ede1191 - 9afec58b2bf9 + - ab2372b0d73d tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: keras_model_builder owner: bgruening revisions: + - 0319fbb09b30 - 522137aaa9c4 - 65571555c486 - 66d7efc06000 @@ -487,6 +515,7 @@ tools: - 00b2ee48b412 - 00d1889e9ecc - 01131463df86 + - 08b52ffcd2b4 - 1046cf73236b - 1f1fc37cfb42 - 4d81e3e2fb63 @@ -498,6 +527,7 @@ tools: owner: bgruening revisions: - 233aab4c1be8 + - 25254e963e6e - 29200ecec39d - 602b5fb7ef09 - a84e6ffd3735 @@ -517,6 +547,7 @@ tools: - 14180f9c831e - 61634a87efc7 - 6b59e9b96071 + - 791fa244e44d - 89f11e2b0673 - caeb57858702 - ec69cbe34b73 @@ -546,6 +577,7 @@ tools: owner: bgruening revisions: - 1e006ebbcaf5 + - 549937c7349c - 6c1c7a89d333 - 9b067af194b7 - ac52a5916963 diff --git a/usegalaxy.cz/metagenomic_analysis.yml.lock b/usegalaxy.cz/metagenomic_analysis.yml.lock index fe75a75..c70da9a 100644 --- a/usegalaxy.cz/metagenomic_analysis.yml.lock +++ b/usegalaxy.cz/metagenomic_analysis.yml.lock @@ -807,6 +807,7 @@ tools: - 46a99bd1f10e - 6000b8a8dd9d - 6a067bbd4e16 + - f09a7ce2f629 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: phyloseq_plot_ordination @@ -815,6 +816,7 @@ tools: - 11d43fa12aab - 2715e89adff4 - 32f892954ef6 + - 47fffb4462d8 - cee4982a717b tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis @@ -823,6 +825,7 @@ tools: revisions: - 10a7732528b2 - 7ed99cb39c9d + - 83c8e8560d8f - 92b82deaaed1 - fd170b83f148 tool_panel_section_id: metagenomic_analysis @@ -1162,6 +1165,7 @@ tools: - 2e921a1efd45 - 6b8580e02e99 - b0b7bba11507 + - bd120bdc6b91 - bd518ee51da5 - e50ac6ad263b - e9168eec404c @@ -1173,6 +1177,7 @@ tools: - 0c069fc2471c - 22767c01e0cf - 3ea43408e5db + - 5bca1feefea5 - 5e4e2b612a4f - 69cce076e0cf - f339ecec9e21 @@ -1182,6 +1187,7 @@ tools: owner: iuc revisions: - 09604c87987c + - 43d85021770e - 49c0d34d583f - 96bc42baaa74 - 9cc284833af9 @@ -1197,6 +1203,7 @@ tools: - 54ea08f9fd97 - 61aa0f3b4d74 - e10b5eebd415 + - e5309c637e9d - fc70cfa151cd tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis @@ -1206,6 +1213,7 @@ tools: - 09bcc3d5e672 - 0feab98f9577 - 301a6ffaf2a2 + - 8dd9cc5291e0 - ac3774320d28 - dfb9413825cc - e0b095891b28 @@ -1218,6 +1226,7 @@ tools: - 1979fdd0914f - 241140d6680a - 3e5c1fdd0e45 + - 4a7449938377 - 7c3248a397fd - c980e4bd48f2 tool_panel_section_id: metagenomic_analysis @@ -1225,6 +1234,7 @@ tools: - name: ampvis2_load owner: iuc revisions: + - 05d7672c6bed - 27ac516ba719 - 5029fd9d572e - 738474880da8 @@ -1242,6 +1252,7 @@ tools: - 35d71afa93f4 - 378ce300fb3d - c7d03a7b52d6 + - fcb11c718c5e tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: ampvis2_mergereplicates @@ -1249,6 +1260,7 @@ tools: revisions: - 0e10df6f37c6 - 414355492c32 + - 73a9f35d4ba2 - 77f9ed2bb200 - c9143bcb2072 - f34ea612eecf @@ -1261,6 +1273,7 @@ tools: - 33087ecbd8f4 - 7b81221e7925 - 9fa62bb69dc4 + - c6ad82bee17b - cb617c2139fa - d5edda7f75eb - d939a8b3defe @@ -1272,6 +1285,7 @@ tools: - 7825694588d6 - 7a168b554d65 - 9742e8636a10 + - ad46c4548d8f - be1918c80d9f - c465a1ea3da2 - dc31a6f9fb2f @@ -1284,6 +1298,7 @@ tools: - 37a617dca128 - 5ca81dc9b5d9 - 7822d7a5a496 + - 9b75e02c05e7 - a9fd4ada4d2a - bb054c50a96c tool_panel_section_id: metagenomic_analysis @@ -1291,6 +1306,7 @@ tools: - name: ampvis2_rankabundance owner: iuc revisions: + - 0da1af3c1ffc - 2c21c267391c - 4140e26cafbc - 838946d86683 @@ -1306,6 +1322,7 @@ tools: - 2828d52a8910 - 3063daee0d8b - 7723ef4c9163 + - 93bfcfcee5e6 - 9f4d491ebad2 - aeca454c398e tool_panel_section_id: metagenomic_analysis @@ -1317,6 +1334,7 @@ tools: - 1615e0550c98 - 638503db7271 - 7f5dd19dc792 + - 8447d4027c28 - a9dacd650ad5 - e7afc79b841e tool_panel_section_id: metagenomic_analysis @@ -1326,6 +1344,7 @@ tools: revisions: - 14b38ec15fe9 - 492eb6dcfe5c + - 75a2a80e5ad0 - b268ffb0e321 - bd4aaf683c79 - ef800b2766c4 @@ -1337,6 +1356,7 @@ tools: revisions: - 227d169951d9 - 35010c1c2d1b + - 4bd2b0a9e529 - 70a98af91147 - 76cb398e9110 - ac98ca3ff0d2 @@ -1346,6 +1366,7 @@ tools: - name: ampvis2_timeseries owner: iuc revisions: + - 4568a232b84e - 4dac39937879 - 77d2f88d8716 - ad262a9581bf @@ -1363,6 +1384,7 @@ tools: - dcbe3affb349 - ed963e5316b7 - f28f2faad83b + - f56762079f69 - f5987fb716a2 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis diff --git a/usegalaxy.cz/ncbi_blast.yml.lock b/usegalaxy.cz/ncbi_blast.yml.lock index 92e1dad..f1f1493 100644 --- a/usegalaxy.cz/ncbi_blast.yml.lock +++ b/usegalaxy.cz/ncbi_blast.yml.lock @@ -38,6 +38,7 @@ tools: - 9553180705b7 - 98037ef3d2a9 - a02aa0dfb850 + - ad7226fac56d tool_panel_section_id: ncbi_blast tool_panel_section_label: NCBI Blast - name: taxonomy_krona_chart diff --git a/usegalaxy.cz/proteomics.yml.lock b/usegalaxy.cz/proteomics.yml.lock index e8678b0..7f9f446 100644 --- a/usegalaxy.cz/proteomics.yml.lock +++ b/usegalaxy.cz/proteomics.yml.lock @@ -1937,29 +1937,34 @@ tools: revisions: - aa442a308682 - acb8aba959ed + - c2cb1ff0962e tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: proteomiqon_peptidedb owner: galaxyp revisions: - 1e5400393797 + - 66f710aad78d tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: proteomiqon_peptidespectrummatching owner: galaxyp revisions: + - 8e21018caeaa - a79a24eb9e76 tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: proteomiqon_psmstatistics owner: galaxyp revisions: + - 069d68c36c6c - 9ac2e8232c5c tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: proteomiqon_proteininference owner: galaxyp revisions: + - 449e3432c8cc - 7729b9043b80 tool_panel_section_id: proteomics tool_panel_section_label: Proteomics @@ -1973,11 +1978,13 @@ tools: owner: galaxyp revisions: - 4abcc674fc0b + - 4b94e02a71cd tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: proteomiqon_joinquantpepionswithproteins owner: galaxyp revisions: + - e68a11ae0c63 - f7e1c904ac2c tool_panel_section_id: proteomics tool_panel_section_label: Proteomics @@ -1985,12 +1992,14 @@ tools: owner: galaxyp revisions: - 764e011f1b0e + - 9b3f055fafc5 tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: proteomiqon_labelfreeproteinquantification owner: galaxyp revisions: - 39fa1ddd587d + - ba8c254ac79f tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: feature_alignment diff --git a/usegalaxy.cz/statistics.yml.lock b/usegalaxy.cz/statistics.yml.lock index 5d95101..47c7286 100644 --- a/usegalaxy.cz/statistics.yml.lock +++ b/usegalaxy.cz/statistics.yml.lock @@ -106,6 +106,7 @@ tools: revisions: - 201b4f13b374 - 233aab4c1be8 + - 25254e963e6e - 27c0b1a050df - 29200ecec39d - 42b513bed40b diff --git a/usegalaxy.cz/variant_calling.yml.lock b/usegalaxy.cz/variant_calling.yml.lock index ec5e6fb..8aa0a1b 100644 --- a/usegalaxy.cz/variant_calling.yml.lock +++ b/usegalaxy.cz/variant_calling.yml.lock @@ -932,6 +932,7 @@ tools: - c8ecdd5bdb32 - c91e09b60325 - cf3f306bce1b + - e0e39f5335de - fdbd97ff825e - ffb42698e28f tool_panel_section_id: variant_calling