From 3bb4f1b78671e163a4f1ab6db0606be1ca432ae1 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Wed, 8 Nov 2023 14:22:17 +0000 Subject: [PATCH] Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.1.3 to 0.1.4 --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 198 ++++++++---------- .../CHANGELOG.md | 11 + 2 files changed, 101 insertions(+), 108 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 3d6fad6b1..c49b850fe 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -19,7 +19,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.3", + "release": "0.1.4", "name": "Assembly-Hifi-HiC-phasing-VGP4", "steps": { "0": { @@ -165,7 +165,7 @@ "input_connections": {}, "inputs": [ { - "description": "Provide lineage for BUSCO (e.g., Vertebrata)", + "description": "", "name": "Lineage" } ], @@ -321,7 +321,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", "errors": null, "id": 11, "input_connections": { @@ -368,15 +368,15 @@ "output_name": "out1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "135b80fb1ac2", + "changeset_revision": "8c0175e03cee", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": \" \", \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": null, \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}], \"cut\": \"0\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0+galaxy1", + "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": \" \", \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": null, \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}], \"cut\": \"0\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "4.4+galaxy0", "type": "tool", "uuid": "64ce3a66-9497-4937-a1b6-7f72814f1fe1", "when": null, @@ -466,7 +466,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -593,7 +593,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -687,7 +687,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy4", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0", "errors": null, "id": 19, "input_connections": { @@ -717,7 +717,7 @@ "name": "Hifiasm", "outputs": [ { - "name": "noseq files", + "name": "noseq_files", "type": "input" }, { @@ -796,15 +796,15 @@ "output_name": "noseq files" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "5f625c63b8bc", + "changeset_revision": "0ee0c3089254", "name": "hifiasm", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"set\", \"__current_case__\": 1, \"h1\": {\"__class__\": \"ConnectedValue\"}, \"h2\": {\"__class__\": \"ConnectedValue\"}, \"seed\": null, \"n_weight\": null, \"n_perturb\": null, \"f_perturb\": null, \"l_msjoin\": \"500000\"}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.16.1+galaxy4", + "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"set\", \"__current_case__\": 1, \"h1\": {\"__class__\": \"ConnectedValue\"}, \"h2\": {\"__class__\": \"ConnectedValue\"}, \"seed\": null, \"n_weight\": null, \"n_perturb\": null, \"f_perturb\": null, \"l_msjoin\": \"500000\"}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.19.8+galaxy0", "type": "tool", "uuid": "0178b5a1-d244-43bc-85e4-e83d1360a94e", "when": null, @@ -1328,7 +1328,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1388,7 +1388,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1529,7 +1529,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1543,7 +1543,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "errors": null, "id": 3, "input_connections": { @@ -1572,15 +1572,15 @@ "output_name": "out_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "746e8e4bf929", + "changeset_revision": "4c07ddedc198", "name": "datamash_ops", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"grouping\": \"\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"absmax\", \"op_column\": \"3\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0+galaxy2", + "tool_version": "1.8+galaxy0", "type": "tool", "uuid": "1cdafa6b-ccdb-4b90-8dc6-ea1f92425715", "when": null, @@ -1588,7 +1588,7 @@ }, "4": { "annotation": "", - "content_id": "addValue", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", "errors": null, "id": 4, "input_connections": { @@ -1617,9 +1617,15 @@ "output_name": "out_file1" } }, - "tool_id": "addValue", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", + "tool_shed_repository": { + "changeset_revision": "023f0a3760b3", + "name": "add_value", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0", + "tool_version": "1.0.1", "type": "tool", "uuid": "9a266291-d20c-42ff-b55f-bb334bd520d8", "when": null, @@ -1724,12 +1730,7 @@ "output_name": "out1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -1758,7 +1759,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0", "type": "tool", "uuid": "c93568ca-103f-4d8e-af88-d6de721e30cd", @@ -1773,7 +1774,7 @@ } }, "tags": "", - "uuid": "7bd25948-5c58-440c-af93-0d71235a782a" + "uuid": "62d1d989-4abe-4f18-a548-ffddb7c0c8bd" }, "tool_id": null, "type": "subworkflow", @@ -1904,7 +1905,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1918,7 +1919,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "errors": null, "id": 3, "input_connections": { @@ -1947,15 +1948,15 @@ "output_name": "out_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "746e8e4bf929", + "changeset_revision": "4c07ddedc198", "name": "datamash_ops", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"grouping\": \"\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"absmax\", \"op_column\": \"3\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0+galaxy2", + "tool_version": "1.8+galaxy0", "type": "tool", "uuid": "1cdafa6b-ccdb-4b90-8dc6-ea1f92425715", "when": null, @@ -1963,7 +1964,7 @@ }, "4": { "annotation": "", - "content_id": "addValue", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", "errors": null, "id": 4, "input_connections": { @@ -1992,9 +1993,15 @@ "output_name": "out_file1" } }, - "tool_id": "addValue", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", + "tool_shed_repository": { + "changeset_revision": "023f0a3760b3", + "name": "add_value", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0", + "tool_version": "1.0.1", "type": "tool", "uuid": "9a266291-d20c-42ff-b55f-bb334bd520d8", "when": null, @@ -2099,12 +2106,7 @@ "output_name": "out1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -2133,7 +2135,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0", "type": "tool", "uuid": "c93568ca-103f-4d8e-af88-d6de721e30cd", @@ -2148,7 +2150,7 @@ } }, "tags": "", - "uuid": "7bd25948-5c58-440c-af93-0d71235a782a" + "uuid": "8797cb2f-b06d-44d1-bcd1-41baf03e95b4" }, "tool_id": null, "type": "subworkflow", @@ -2274,7 +2276,7 @@ }, "35": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0", "errors": null, "id": 35, "input_connections": { @@ -2287,12 +2289,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -2347,15 +2344,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0", "tool_shed_repository": { - "changeset_revision": "41030a6c03b7", + "changeset_revision": "94170eee0ad8", "name": "busco", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.3.2+galaxy0", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.4.6+galaxy0", "type": "tool", "uuid": "a4957dee-45cc-4f34-ae2e-e07f93b9fcc4", "when": null, @@ -2374,7 +2371,7 @@ }, "36": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3", "errors": null, "id": 36, "input_connections": { @@ -2465,15 +2462,15 @@ "output_name": "wig_files" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3", "tool_shed_repository": { - "changeset_revision": "f8113c25bc6b", + "changeset_revision": "09c589057ee8", "name": "merqury", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}, \"assembly_02\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": true, \"output_selector\": [\"qv\", \"plots\", \"stats\", \"log\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy2", + "tool_version": "1.3+galaxy3", "type": "tool", "uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291", "when": null, @@ -2487,7 +2484,7 @@ }, "37": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0", "errors": null, "id": 37, "input_connections": { @@ -2500,12 +2497,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Busco", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Busco", "outputs": [ @@ -2560,15 +2552,15 @@ "output_name": "summary_image" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0", "tool_shed_repository": { - "changeset_revision": "41030a6c03b7", + "changeset_revision": "94170eee0ad8", "name": "busco", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.3.2+galaxy0", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.4.6+galaxy0", "type": "tool", "uuid": "08066bc3-0992-4606-844d-16be3c56691a", "when": null, @@ -2758,7 +2750,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", "errors": null, "id": 4, "input_connections": { @@ -2791,15 +2783,15 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", "tool_shed_repository": { - "changeset_revision": "745871c0b055", + "changeset_revision": "023f0a3760b3", "name": "add_value", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"exp\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0", + "tool_version": "1.0.1", "type": "tool", "uuid": "8bc6adbb-1346-4521-bd69-ffa2738bad07", "when": null, @@ -2807,7 +2799,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", "errors": null, "id": 5, "input_connections": { @@ -2840,15 +2832,15 @@ "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", "tool_shed_repository": { - "changeset_revision": "745871c0b055", + "changeset_revision": "023f0a3760b3", "name": "add_value", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"exp\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0", + "tool_version": "1.0.1", "type": "tool", "uuid": "63c7b63c-5179-4ab3-9682-7d150029446e", "when": null, @@ -2983,7 +2975,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -2992,12 +2984,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Scatterplot with ggplot2", - "name": "input1" - } - ], + "inputs": [], "label": "Nx Plot", "name": "Scatterplot with ggplot2", "outputs": [ @@ -3026,15 +3013,15 @@ "output_name": "output1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "5fe1dc76176e", + "changeset_revision": "3b12bf9b4b87", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"x\", \"xplot\": \"2\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.4.0+galaxy0", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"x\", \"xplot\": \"2\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.4.0+galaxy1", "type": "tool", "uuid": "18c6ac70-f4d3-4d68-93f8-c08afafbc6c5", "when": null, @@ -3048,7 +3035,7 @@ }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, "id": 10, "input_connections": { @@ -3057,12 +3044,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Scatterplot with ggplot2", - "name": "input1" - } - ], + "inputs": [], "label": "Size Plot", "name": "Scatterplot with ggplot2", "outputs": [ @@ -3091,15 +3073,15 @@ "output_name": "output1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "5fe1dc76176e", + "changeset_revision": "3b12bf9b4b87", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"Scaffold number\", \"xplot\": \"2\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.4.0+galaxy0", + "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"Scaffold number\", \"xplot\": \"2\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.4.0+galaxy1", "type": "tool", "uuid": "cce1fe43-55c6-4c1a-a957-ac7af9271c46", "when": null, @@ -3113,7 +3095,7 @@ } }, "tags": "", - "uuid": "34d71948-bc67-4261-ad4c-6de491826e89" + "uuid": "2c345153-8e28-420e-b110-6cb43e156e95" }, "tool_id": null, "type": "subworkflow", @@ -3165,7 +3147,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -3210,7 +3192,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index 5dea9baf5..49b32029d 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [0.1.4] 2023-11-08 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1` +- `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1` + All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),