31734e42148b0358ee38a154aa343e2d1c0b258f hiram Thu Jun 11 17:20:55 2026 -0700 kegAlign updated to accept scoring matrix refs #31811 diff --git src/hg/utils/automation/kegAlign.json.ga src/hg/utils/automation/kegAlign.json.ga index fcd892feb26..0b8f5708e6c 100644 --- src/hg/utils/automation/kegAlign.json.ga +++ src/hg/utils/automation/kegAlign.json.ga @@ -1,96 +1,96 @@ { "a_galaxy_workflow": "true", - "annotation": "Should now have axtChainScoreScheme and axtChainLinearGap input options", + "annotation": "kegAlign updated to accept scoringMatrix", "comments": [ - { - "color": "none", - "data": { - "text": "Assemblies in fasta format, masked. " - }, - "id": 1, - "position": [ - 42.09072708051447, - 778.882939520563 - ], - "size": [ - 310, - 55 - ], - "type": "markdown" - }, { "child_comments": [ 1 ], "child_steps": [ 11, 9 ], "color": "blue", "data": { "title": "" }, "id": 0, "position": [ 17.29072708051447, 738.882939520563 ], "size": [ 414, 276 ], "type": "frame" + }, + { + "color": "none", + "data": { + "text": "Assemblies in fasta format, masked. " + }, + "id": 1, + "position": [ + 42.09072708051447, + 778.882939520563 + ], + "size": [ + 310, + 55 + ], + "type": "markdown" } ], "creator": [ { "class": "Organization", "name": "Penn State University", "url": "https://www.ccbb.psu.edu/" }, { "class": "Person", "identifier": "https://orcid.org/0000-0002-9318-1781", "name": "Martin \u010cech" } ], "format-version": "0.1", "license": "MIT", - "name": "align, chain, and 2x liftOver with input options", + "name": "kegAlign_2026-06-11", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, "steps": { "0": { "annotation": "default: both - can be: minus or plus BLASTZ_B=2", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "default: both - can be: minus or plus BLASTZ_B=2", "name": "strand_selectorB" } ], "label": "strand_selectorB", "name": "Input parameter", "outputs": [], "position": { "left": 16.792180016306407, - "top": 0.0 + "top": 0 }, "tool_id": null, "tool_state": "{\"default\": \"both\", \"multiple\": false, \"validators\": [], \"restrictions\": [\"both\", \"minus\", \"plus\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "4bd8509b-bd3c-458e-bec7-8eb33693918a", "when": null, "workflow_outputs": [] }, "1": { "annotation": "to supply a score matrix to the lastz operation", "content_id": null, "errors": null, "id": 1, "input_connections": {}, @@ -509,31 +509,31 @@ "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"code\": \"BEGIN{FS=\\\" \\\"} /^>/ {print $1; next} {print}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"variables\": [], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "5b8d95b6-7fd1-4447-ba6f-35fabc159ffb", "when": null, "workflow_outputs": [] }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/kegalign/kegalign/0.1.2.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/kegalign/kegalign/0.1.2.9+galaxy3", "errors": null, "id": 16, "input_connections": { "gapped_extension_options|gappedthresh": { "id": 7, "output_name": "output" }, "gapped_extension_options|ydrop": { "id": 6, "output_name": "output" }, "interpolation_options|inner": { "id": 8, "output_name": "output" }, @@ -571,132 +571,145 @@ } }, "inputs": [ { "description": "runtime parameter for tool KegAlign", "name": "gapped_extension_options" }, { "description": "runtime parameter for tool KegAlign", "name": "gapped_extension_options" }, { "description": "runtime parameter for tool KegAlign", "name": "interpolation_options" }, + { + "description": "runtime parameter for tool KegAlign", + "name": "query" + }, { "description": "runtime parameter for tool KegAlign", "name": "scoring_options" }, { "description": "runtime parameter for tool KegAlign", "name": "seeding_options" }, { "description": "runtime parameter for tool KegAlign", "name": "seeding_options" }, { "description": "runtime parameter for tool KegAlign", "name": "sequence_options" }, + { + "description": "runtime parameter for tool KegAlign", + "name": "target" + }, { "description": "runtime parameter for tool KegAlign", "name": "ungapped_extension_options" }, { "description": "runtime parameter for tool KegAlign", "name": "ungapped_extension_options" } ], "label": "kegalign_step", "name": "KegAlign", "outputs": [ { "name": "kegalign_output", "type": "tgz" } ], "position": { "left": 494.57770192925574, "top": 43.847290417174904 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/kegalign/kegalign/0.1.2.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/kegalign/kegalign/0.1.2.9+galaxy3", "tool_shed_repository": { - "changeset_revision": "f885abcfe3a0", + "changeset_revision": "c05177db395f", "name": "kegalign", "owner": "richard-burhans", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"gapped_extension_options\": {\"ydrop\": {\"__class__\": \"ConnectedValue\"}, \"gappedthresh\": {\"__class__\": \"ConnectedValue\"}, \"notrivial\": false}, \"interpolation_options\": {\"inner\": {\"__class__\": \"ConnectedValue\"}}, \"output_options\": {\"format\": {\"format_selector\": \"axt\", \"__current_case__\": 4, \"axt_type\": \"axt\"}}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"scoring_options\": {\"scoring\": {\"__class__\": \"RuntimeValue\"}, \"ambiguous_selector\": \"x\", \"ambiguous_params\": {\"set_ambiguous_params_selector\": \"false\", \"__current_case__\": 0}}, \"seeding_options\": {\"seed\": {\"seed_selector\": \"12of19\", \"__current_case__\": 0}, \"step\": {\"__class__\": \"ConnectedValue\"}, \"notransition\": {\"__class__\": \"ConnectedValue\"}}, \"sequence_options\": {\"strand_selector\": {\"__class__\": \"ConnectedValue\"}}, \"system_options\": {\"wga_chunk_size\": \"250000\", \"lastz_interval_size\": \"10000000\", \"seq_block_size\": \"400000000\", \"num_gpu\": \"-1\", \"debug\": false}, \"target\": {\"__class__\": \"ConnectedValue\"}, \"ungapped_extension_options\": {\"xdrop\": {\"__class__\": \"ConnectedValue\"}, \"hspthresh\": {\"__class__\": \"ConnectedValue\"}, \"noentropy\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"developer\": {\"alignment_type\": \"vertebrates_default\"}, \"gapped_extension_options\": {\"ydrop\": {\"__class__\": \"ConnectedValue\"}, \"gappedthresh\": {\"__class__\": \"ConnectedValue\"}, \"notrivial\": false}, \"interpolation_options\": {\"inner\": {\"__class__\": \"ConnectedValue\"}}, \"output_options\": {\"format\": {\"format_selector\": \"axt\", \"__current_case__\": 4, \"axt_type\": \"axt\"}}, \"query\": {\"__class__\": \"RuntimeValue\"}, \"scoring_options\": {\"scoring\": {\"__class__\": \"RuntimeValue\"}, \"ambiguous_selector\": \"x\", \"ambiguous_params\": {\"set_ambiguous_params_selector\": \"false\", \"__current_case__\": 0}}, \"seeding_options\": {\"seed\": {\"seed_selector\": \"12of19\", \"__current_case__\": 0}, \"step\": {\"__class__\": \"ConnectedValue\"}, \"notransition\": {\"__class__\": \"ConnectedValue\"}}, \"sequence_options\": {\"strand_selector\": {\"__class__\": \"ConnectedValue\"}}, \"system_options\": {\"wga_chunk_size\": \"250000\", \"lastz_interval_size\": \"10000000\", \"seq_block_size\": \"400000000\", \"num_gpu\": \"-1\", \"debug\": false}, \"target\": {\"__class__\": \"RuntimeValue\"}, \"ungapped_extension_options\": {\"xdrop\": {\"__class__\": \"ConnectedValue\"}, \"hspthresh\": {\"__class__\": \"ConnectedValue\"}, \"noentropy\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.1.2.9+galaxy1", + "tool_version": "0.1.2.9+galaxy3", "type": "tool", "uuid": "7bd758b4-e2cc-4d43-8612-3cd939405586", "when": null, "workflow_outputs": [ { "label": "kegalign_out", "output_name": "kegalign_output", "uuid": "24f83c68-0256-4320-a26f-89c323a9fb00" } ] }, "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/batched_lastz/batched_lastz/1.04.22+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/batched_lastz/batched_lastz/1.04.22+galaxy7", "errors": null, "id": 17, "input_connections": { "input": { "id": 16, "output_name": "kegalign_output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Batched LASTZ", + "name": "input" + } + ], "label": "batched_lastz_step", "name": "Batched LASTZ", "outputs": [ { "name": "output", "type": "auto" } ], "position": { - "left": 925.677131659099, - "top": 174.02599347763862 + "left": 925.699951171875, + "top": 175.0333251953125 }, "post_job_actions": { "ChangeDatatypeActionoutput": { "action_arguments": { "newtype": "axt" }, "action_type": "ChangeDatatypeAction", "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/batched_lastz/batched_lastz/1.04.22+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/batched_lastz/batched_lastz/1.04.22+galaxy7", "tool_shed_repository": { - "changeset_revision": "79182c2a8c80", + "changeset_revision": "8cf5c6162cae", "name": "batched_lastz", "owner": "richard-burhans", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"developer\": {\"debug_enabled\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"developer\": {\"debug_enabled\": false, \"alignment_type\": \"vertebrates_default\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.04.22+galaxy6", + "tool_version": "1.04.22+galaxy7", "type": "tool", "uuid": "cd784f91-7a6a-4f48-847d-2761981ca7fe", "when": null, "workflow_outputs": [ { "label": "batched_lastz_out", "output_name": "output", "uuid": "8acf1b56-2262-4e1d-ad4e-23b4810d3011" } ] }, "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_axtchain/ucsc_axtchain/482+galaxy1", "errors": null, @@ -1413,31 +1426,31 @@ "target_reference_index_source|in_tar_ref_index": { "id": 6, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool chainNet", "name": "query_reference_index_source" }, { "description": "runtime parameter for tool chainNet", "name": "target_reference_index_source" } ], - "label": "chainne_step", + "label": "chainnet_step", "name": "chainNet", "outputs": [ { "name": "targetNet", "type": "ucsc.net" }, { "name": "queryNet", "type": "ucsc.net" } ], "position": { "left": 2228.970370728072, "top": 457.7125181265065 }, @@ -2188,31 +2201,31 @@ "target_reference_index_source|in_tar_ref_index": { "id": 6, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool chainNet", "name": "query_reference_index_source" }, { "description": "runtime parameter for tool chainNet", "name": "target_reference_index_source" } ], - "label": "chainne_step", + "label": "chainnet_step", "name": "chainNet", "outputs": [ { "name": "targetNet", "type": "ucsc.net" }, { "name": "queryNet", "type": "ucsc.net" } ], "position": { "left": 2228.970370728072, "top": 457.7125181265065 }, @@ -2383,18 +2396,18 @@ "label": "swap.lift.over", "output_name": "liftover_chain_file", "uuid": "852e2cb0-b4dd-476f-9c8b-e86fa30b347e" } ] } }, "tags": [ "ucsc", "alignment", "lastz", "kegalign", "chain", "net" ], - "uuid": "125f8508-9453-48c8-8e0f-93da0be031c7", + "uuid": "45670dee-8499-4871-bc3a-c8e9391c8220", "version": 1 }