2cbbc4621cd9e83ffd450178330665df5ae36fe0 hiram Wed Apr 15 16:56:37 2026 -0700 closing in on a galaxy lastz workflow that may be useful refs #31811 diff --git src/hg/utils/automation/kegAlign.json.ga src/hg/utils/automation/kegAlign.json.ga new file mode 100644 index 00000000000..7a1b807faa4 --- /dev/null +++ src/hg/utils/automation/kegAlign.json.ga @@ -0,0 +1,2353 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Should now have axtChainScoreScheme and axtChainLinearGap input options", + "comments": [ + { + "child_comments": [ + 1 + ], + "child_steps": [ + 9, + 8 + ], + "color": "blue", + "data": { + "title": "" + }, + "id": 0, + "position": [ + 17.29072708051447, + 695.0356491033881 + ], + "size": [ + 414, + 276 + ], + "type": "frame" + }, + { + "color": "none", + "data": { + "text": "Assemblies in fasta format, masked. " + }, + "id": 1, + "position": [ + 42.09072708051447, + 735.0356491033881 + ], + "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", + "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": 6.969707608149614, + "top": 22.086266148506436 + }, + "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": "--step or Z=1 default", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "--step or Z=1 default", + "name": "stepZ" + } + ], + "label": "stepZ", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 3.529330207209202, + "top": 130.1734203457517 + }, + "tool_id": null, + "tool_state": "{\"default\": 1, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "a9327d57-01f6-4e5d-908c-3d88a99fd0b2", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "true == --notransition false == -transition this is BLASTZ_T default 1 or 3", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "true == --notransition false == -transition this is BLASTZ_T default 1 or 3", + "name": "noTransitionT" + } + ], + "label": "noTransitionT", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 4.413474126983308, + "top": 209.84303396423985 + }, + "tool_id": null, + "tool_state": "{\"default\": true, \"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "c871c94d-d1e8-4cc0-ab18-0d1b6413dcb8", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "xdrop option to lastz, default 910", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "xdrop option to lastz, default 910", + "name": "xdropX" + } + ], + "label": "xdropX", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 0.17426400315015156, + "top": 291.022144528618 + }, + "tool_id": null, + "tool_state": "{\"default\": 910, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "abf41b9c-e453-463f-986c-34b893384c21", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "BLASTZ_K == --hspthresh default 3000", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "BLASTZ_K == --hspthresh default 3000", + "name": "hspthreshK" + } + ], + "label": "hspthreshK", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 3.111621798696479, + "top": 373.6699645506831 + }, + "tool_id": null, + "tool_state": "{\"default\": 3000, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "b9c13a54-08e7-4007-bfde-52e20fcc6a9a", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "default 9400", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "default 9400", + "name": "ydropY" + } + ], + "label": "ydropY", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 2.9781360951763647, + "top": 455.0827362160491 + }, + "tool_id": null, + "tool_state": "{\"default\": 9400, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "93652cc4-7c1a-4ec3-8928-d30e6f8a59dc", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "integer for the --gappedthresh BLASTZ_L argument", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "integer for the --gappedthresh BLASTZ_L argument", + "name": "gappedthreshL" + } + ], + "label": "gappedthreshL", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 4.3597736220213745, + "top": 528.4530394194131 + }, + "tool_id": null, + "tool_state": "{\"default\": 3000, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "e97d87e0-2df4-494d-af78-c7b49664f027", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "innerH" + } + ], + "label": "innerH", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 0, + "top": 602.6281670301672 + }, + "tool_id": null, + "tool_state": "{\"default\": 3000, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "d67c9c1e-024f-4ec1-8f9b-3e0fb53f2122", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "Assemblies in fasta format, masked. ", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, + "inputs": [ + { + "description": "Assemblies in fasta format, masked. ", + "name": "TARGET_Sequence" + } + ], + "label": "TARGET_Sequence", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 61.54140818169743, + "top": 795.7024074792059 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "85fb7a10-67cf-42df-b1d8-ba4a90c07e2e", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "Assemblies in fasta format, masked. ", + "content_id": null, + "errors": null, + "id": 9, + "input_connections": {}, + "inputs": [ + { + "description": "Assemblies in fasta format, masked. ", + "name": "QUERY_Sequence" + } + ], + "label": "QUERY_Sequence", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 65.41210375986545, + "top": 883.5319639758811 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "6e8cdde2-a9f4-4ee5-936d-5eee44c1e257", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "the -minScore argument to axtChain", + "content_id": null, + "errors": null, + "id": 10, + "input_connections": {}, + "inputs": [ + { + "description": "the -minScore argument to axtChain", + "name": "axtChainMinScore" + } + ], + "label": "axtChainMinScore", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 847.1784982523703, + "top": 327.8676532349488 + }, + "tool_id": null, + "tool_state": "{\"default\": 1000, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "a5c62d0c-7ed5-4dfe-84b9-8afaabc3f8ef", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "To supply the -linearGap option", + "content_id": null, + "errors": null, + "id": 11, + "input_connections": {}, + "inputs": [ + { + "description": "To supply the -linearGap option", + "name": "axtChainLinearGap" + } + ], + "label": "axtChainLinearGap", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 842.0531692565773, + "top": 434.8711130026786 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "166abb8b-dd9b-448b-9925-2ecd116b0ed9", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "input a scoring matrix to axtChain. Going to be the 4 by 4 matrix of A C G T and with O=400 and E = 30", + "content_id": null, + "errors": null, + "id": 12, + "input_connections": {}, + "inputs": [ + { + "description": "input a scoring matrix to axtChain. Going to be the 4 by 4 matrix of A C G T and with O=400 and E = 30", + "name": "axtChainScoreScheme" + } + ], + "label": "axtChainScoreScheme", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 837.4832247419432, + "top": 536.3238812275557 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "f86d7c3c-b66c-42eb-863d-f027cc717dde", + "when": null, + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", + "errors": null, + "id": 13, + "input_connections": { + "infile": { + "id": 8, + "output_name": "output" + } + }, + "inputs": [], + "label": "TARGET trim sequence names", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 532.3114150162568, + "top": 731.8327655968853 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", + "tool_shed_repository": { + "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": "1d736295-f9d4-40b7-9140-d6e4ab905ba8", + "when": null, + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", + "errors": null, + "id": 14, + "input_connections": { + "infile": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [], + "label": "QUERY trim sequence names 2", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 533.2460594202081, + "top": 879.2369818615593 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", + "tool_shed_repository": { + "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": [] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/kegalign/kegalign/0.1.2.9+galaxy1", + "errors": null, + "id": 15, + "input_connections": { + "gapped_extension_options|gappedthresh": { + "id": 6, + "output_name": "output" + }, + "gapped_extension_options|ydrop": { + "id": 5, + "output_name": "output" + }, + "interpolation_options|inner": { + "id": 7, + "output_name": "output" + }, + "query": { + "id": 14, + "output_name": "outfile" + }, + "seeding_options|notransition": { + "id": 2, + "output_name": "output" + }, + "seeding_options|step": { + "id": 1, + "output_name": "output" + }, + "sequence_options|strand_selector": { + "id": 0, + "output_name": "output" + }, + "target": { + "id": 13, + "output_name": "outfile" + }, + "ungapped_extension_options|hspthresh": { + "id": 4, + "output_name": "output" + }, + "ungapped_extension_options|xdrop": { + "id": 3, + "output_name": "output" + } + }, + "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": "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": "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": 0 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/kegalign/kegalign/0.1.2.9+galaxy1", + "tool_shed_repository": { + "changeset_revision": "f885abcfe3a0", + "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_uuid": null, + "tool_version": "0.1.2.9+galaxy1", + "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" + } + ] + }, + "16": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/batched_lastz/batched_lastz/1.04.22+galaxy6", + "errors": null, + "id": 16, + "input_connections": { + "input": { + "id": 15, + "output_name": "kegalign_output" + } + }, + "inputs": [], + "label": "batched_lastz_step", + "name": "Batched LASTZ", + "outputs": [ + { + "name": "output", + "type": "auto" + } + ], + "position": { + "left": 925.677131659099, + "top": 130.1787030604637 + }, + "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_shed_repository": { + "changeset_revision": "79182c2a8c80", + "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_uuid": null, + "tool_version": "1.04.22+galaxy6", + "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" + } + ] + }, + "17": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_axtchain/ucsc_axtchain/482+galaxy1", + "errors": null, + "id": 17, + "input_connections": { + "in_axt": { + "id": 16, + "output_name": "output" + }, + "in_query": { + "id": 14, + "output_name": "outfile" + }, + "in_target": { + "id": 13, + "output_name": "outfile" + }, + "linear_gap_options|lineargap_input": { + "id": 11, + "output_name": "output" + }, + "minScore": { + "id": 10, + "output_name": "output" + }, + "scoreScheme": { + "id": 12, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool axtChain", + "name": "linear_gap_options" + } + ], + "label": "axtchain_step", + "name": "axtChain", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 1237.5970406420554, + "top": 307.1868521067106 + }, + "post_job_actions": { + "RenameDatasetActionout": { + "action_arguments": { + "newname": "allChain" + }, + "action_type": "RenameDatasetAction", + "output_name": "out" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_axtchain/ucsc_axtchain/482+galaxy1", + "tool_shed_repository": { + "changeset_revision": "64d732725a73", + "name": "ucsc_axtchain", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_axt\": {\"__class__\": \"ConnectedValue\"}, \"in_query\": {\"__class__\": \"ConnectedValue\"}, \"in_target\": {\"__class__\": \"ConnectedValue\"}, \"linear_gap_options\": {\"linear_gap\": \"linear_gap_file\", \"__current_case__\": 2, \"lineargap_input\": {\"__class__\": \"ConnectedValue\"}}, \"minScore\": {\"__class__\": \"ConnectedValue\"}, \"scoreScheme\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy1", + "type": "tool", + "uuid": "c248d115-b952-4b3a-ab3b-ed91a94ea6af", + "when": null, + "workflow_outputs": [ + { + "label": "all_chain", + "output_name": "out", + "uuid": "d3eff1f8-a6e8-4af6-83bd-9a5f108d5bff" + } + ] + }, + "18": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainswap/ucsc_chainswap/482+galaxy0", + "errors": null, + "id": 18, + "input_connections": { + "in_chain": { + "id": 17, + "output_name": "out" + } + }, + "inputs": [], + "label": "chainswap_step", + "name": "chainSwap", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 1476.4911560768403, + "top": 628.8001019939747 + }, + "post_job_actions": { + "RenameDatasetActionout": { + "action_arguments": { + "newname": "allChainSwap" + }, + "action_type": "RenameDatasetAction", + "output_name": "out" + }, + "TagDatasetActionout": { + "action_arguments": { + "tags": "#reverse_chain" + }, + "action_type": "TagDatasetAction", + "output_name": "out" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainswap/ucsc_chainswap/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "6a7085c7777e", + "name": "ucsc_chainswap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "3bbdbbe9-c326-49f3-ad76-72c46e90242f", + "when": null, + "workflow_outputs": [ + { + "label": "chainSwap", + "output_name": "out", + "uuid": "da08bdb1-37c4-40a8-b077-49558df48985" + } + ] + }, + "19": { + "annotation": "", + "id": 19, + "input_connections": { + "QUERY_Sequence": { + "id": 14, + "input_subworkflow_step_id": 2, + "output_name": "outfile" + }, + "TARGET_Sequence": { + "id": 13, + "input_subworkflow_step_id": 1, + "output_name": "outfile" + }, + "chain": { + "id": 17, + "input_subworkflow_step_id": 0, + "output_name": "out" + } + }, + "inputs": [ + { + "description": "", + "name": "liftOver" + } + ], + "label": "liftOver", + "name": "chain to liftover (subworkflow)", + "outputs": [], + "position": { + "left": 1853.3578552955903, + "top": 302.7667767986622 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [ + { + "color": "none", + "data": { + "text": "Assemblies in fasta format, masked. " + }, + "id": 1, + "position": [ + 24.800000000000068, + 234.51597279574764 + ], + "size": [ + 310, + 55 + ], + "type": "markdown" + }, + { + "child_comments": [ + 1 + ], + "child_steps": [ + 2, + 1 + ], + "color": "blue", + "data": { + "title": "" + }, + "id": 0, + "position": [ + 0, + 194.51597279574764 + ], + "size": [ + 414, + 276 + ], + "type": "frame" + } + ], + "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": "chain to liftover (subworkflow)", + "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": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "chain" + } + ], + "label": "chain", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 242.328125, + "top": 9.360592187495683 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "78286bf0-68e8-410e-9624-41689254131c", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "TARGET_Sequence" + } + ], + "label": "TARGET_Sequence", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 44.16273637304573, + "top": 295.1869876848659 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "85fb7a10-67cf-42df-b1d8-ba4a90c07e2e", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "QUERY_Sequence" + } + ], + "label": "QUERY_Sequence", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 48.03343195121374, + "top": 383.0165441815411 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "6e8cdde2-a9f4-4ee5-936d-5eee44c1e257", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "errors": null, + "id": 3, + "input_connections": { + "infile": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": "TARGET trim sequence names", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 553.3383322970775, + "top": 369.9560090641513 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "tool_shed_repository": { + "changeset_revision": "c41d78ae5fee", + "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+galaxy2", + "type": "tool", + "uuid": "1d736295-f9d4-40b7-9140-d6e4ab905ba8", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "errors": null, + "id": 4, + "input_connections": { + "infile": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": "QUERY trim sequence names 2", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 698.499441913828, + "top": 545.2584925326347 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "tool_shed_repository": { + "changeset_revision": "c41d78ae5fee", + "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+galaxy2", + "type": "tool", + "uuid": "5b8d95b6-7fd1-4447-ba6f-35fabc159ffb", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "CONVERTER_fasta_to_2bit", + "errors": null, + "id": 5, + "input_connections": { + "input": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [], + "label": "target_2bit_step", + "name": "Convert FASTA to 2bit", + "outputs": [ + { + "name": "output", + "type": "twobit" + } + ], + "position": { + "left": 1067.7257258120155, + "top": 505.7630205069032 + }, + "post_job_actions": {}, + "tool_id": "CONVERTER_fasta_to_2bit", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.1", + "type": "tool", + "uuid": "38f9fb7f-bfe0-4bd6-bb47-38d37dc9014a", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "errors": null, + "id": 6, + "input_connections": { + "ref|input": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Compute sequence length", + "name": "ref" + } + ], + "label": "target_compute_sequence_length", + "name": "Compute sequence length", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 1539.993755096764, + "top": 422.903841974219 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "tool_shed_repository": { + "changeset_revision": "5cbde03c1103", + "name": "fasta_compute_length", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"ref\": {\"ref_source\": \"history\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"keep_first_word\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.4", + "type": "tool", + "uuid": "f6aa1c46-70e3-4bd6-9804-517d9163ae22", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "CONVERTER_fasta_to_2bit", + "errors": null, + "id": 7, + "input_connections": { + "input": { + "id": 4, + "output_name": "outfile" + } + }, + "inputs": [], + "label": "query_2bit_step", + "name": "Convert FASTA to 2bit", + "outputs": [ + { + "name": "output", + "type": "twobit" + } + ], + "position": { + "left": 1062.68165397853, + "top": 713.1258923119221 + }, + "post_job_actions": {}, + "tool_id": "CONVERTER_fasta_to_2bit", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.1", + "type": "tool", + "uuid": "7bc60e4c-ca3a-4365-98a4-1ed2def66992", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "errors": null, + "id": 8, + "input_connections": { + "ref|input": { + "id": 4, + "output_name": "outfile" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Compute sequence length", + "name": "ref" + } + ], + "label": "query_compute_sequence_length", + "name": "Compute sequence length", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 1557.9660305655827, + "top": 658.4157588998564 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "tool_shed_repository": { + "changeset_revision": "5cbde03c1103", + "name": "fasta_compute_length", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"ref\": {\"ref_source\": \"history\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"keep_first_word\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.4", + "type": "tool", + "uuid": "5765100f-d7f9-4044-acca-232a2ad59a3a", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainantirepeat/ucsc_chainantirepeat/482+galaxy0", + "errors": null, + "id": 9, + "input_connections": { + "in_chain": { + "id": 0, + "output_name": "output" + }, + "in_query": { + "id": 7, + "output_name": "output" + }, + "in_target": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": "chainantirepeat_step", + "name": "chainAntiRepeat", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 1214.7421875, + "top": 0.0 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainantirepeat/ucsc_chainantirepeat/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "9f2d2c96a189", + "name": "ucsc_chainantirepeat", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"in_query\": {\"__class__\": \"ConnectedValue\"}, \"in_target\": {\"__class__\": \"ConnectedValue\"}, \"minScore\": null, \"noCheckScore\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "b0738b52-0d84-4877-8b9b-b8392cd7c2e0", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainprenet/ucsc_chainprenet/482+galaxy0", + "errors": null, + "id": 10, + "input_connections": { + "in_chain": { + "id": 9, + "output_name": "out" + }, + "query_reference_index_source|in_que_ref_index": { + "id": 8, + "output_name": "output" + }, + "target_reference_index_source|in_tar_ref_index": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool chainPreNet", + "name": "query_reference_index_source" + }, + { + "description": "runtime parameter for tool chainPreNet", + "name": "target_reference_index_source" + } + ], + "label": "chainprenet_step", + "name": "chainPreNet", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 1872.234375, + "top": 31.040283203125 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainprenet/ucsc_chainprenet/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "2a417e645e61", + "name": "ucsc_chainprenet", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"inclHap\": false, \"pad\": null, \"query_reference_index_source\": {\"query_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_que_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"target_reference_index_source\": {\"target_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_tar_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "6a3b3723-5073-4a12-862e-badf082e3747", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainsort/ucsc_chainsort/482+galaxy0", + "errors": null, + "id": 11, + "input_connections": { + "in_chain": { + "id": 10, + "output_name": "out" + } + }, + "inputs": [], + "label": "chainsort_step", + "name": "chainSort", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 2294.80306523609, + "top": 159.27204891791922 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainsort/ucsc_chainsort/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "07c87c2ab74b", + "name": "ucsc_chainsort", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"sort_by\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "7f5dbcfd-658a-45f9-b95d-69259eec7b0f", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainnet/ucsc_chainnet/482+galaxy0", + "errors": null, + "id": 12, + "input_connections": { + "in_chain": { + "id": 11, + "output_name": "out" + }, + "query_reference_index_source|in_que_ref_index": { + "id": 8, + "output_name": "output" + }, + "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", + "name": "chainNet", + "outputs": [ + { + "name": "targetNet", + "type": "ucsc.net" + }, + { + "name": "queryNet", + "type": "ucsc.net" + } + ], + "position": { + "left": 2228.970370728072, + "top": 457.7125181265065 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainnet/ucsc_chainnet/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "5b65a92be96c", + "name": "ucsc_chainnet", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"inclHap\": false, \"minFill\": null, \"minScore\": null, \"minSpace\": null, \"query_reference_index_source\": {\"query_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_que_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"target_reference_index_source\": {\"target_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_tar_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"verbose\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "9b11667f-fc6f-4a71-853c-0e3014f95cbc", + "when": null, + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netsyntenic/ucsc_netsyntenic/482+galaxy0", + "errors": null, + "id": 13, + "input_connections": { + "in_net": { + "id": 12, + "output_name": "targetNet" + } + }, + "inputs": [], + "label": "netsyntenic_step", + "name": "netSyntenic", + "outputs": [ + { + "name": "out", + "type": "ucsc.net" + } + ], + "position": { + "left": 2564.153845348722, + "top": 425.45236124501406 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netsyntenic/ucsc_netsyntenic/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "1999f87602f7", + "name": "ucsc_netsyntenic", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_net\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "9828149d-6938-49f4-95e3-ece4b87d38bd", + "when": null, + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netfilter/ucsc_netfilter/482+galaxy0", + "errors": null, + "id": 14, + "input_connections": { + "in_net": { + "id": 13, + "output_name": "out" + } + }, + "inputs": [], + "label": "netfilter_step", + "name": "netFilter", + "outputs": [ + { + "name": "out", + "type": "ucsc.net" + } + ], + "position": { + "left": 2900.086910790546, + "top": 392.10616304438827 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netfilter/ucsc_netfilter/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "5c3fa42d003f", + "name": "ucsc_netfilter", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_net\": {\"__class__\": \"ConnectedValue\"}, \"minGap\": null, \"synteny\": {\"syn_filter\": \"filtersyn\", \"__current_case__\": 1, \"syntype\": \"-syn\", \"minSynScore\": null, \"minSynSize\": null, \"minSynAli\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "24e0d7b4-29bb-4749-a192-a50937a24945", + "when": null, + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netchainsubset/ucsc_netchainsubset/482+galaxy0", + "errors": null, + "id": 15, + "input_connections": { + "in_chain": { + "id": 0, + "output_name": "output" + }, + "in_net": { + "id": 14, + "output_name": "out" + } + }, + "inputs": [], + "label": "netchainsubset_step", + "name": "netChainSubset", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 2068.234375, + "top": 910.8371546874957 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netchainsubset/ucsc_netchainsubset/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "794cf52edccc", + "name": "ucsc_netchainsubset", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"in_net\": {\"__class__\": \"ConnectedValue\"}, \"skipMissing\": false, \"splitOnInsert\": false, \"wholeChains\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "87113072-dc71-4355-87f5-03cb1ad2a9ca", + "when": null, + "workflow_outputs": [ + { + "label": "liftover_chain_file", + "output_name": "out", + "uuid": "8d91d96e-de70-4e8a-a27e-4c78c7e4f901" + } + ] + } + }, + "tags": [], + "uuid": "e0c44203-570a-4ba5-9d9f-ee301d477e52" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "f52733e2-de01-47f1-b632-8fb0922d2b2e", + "when": null, + "workflow_outputs": [ + { + "label": "lift.over.chain", + "output_name": "liftover_chain_file", + "uuid": "e6e778ba-231e-43e8-afca-04999e233b38" + } + ] + }, + "20": { + "annotation": "", + "id": 20, + "input_connections": { + "QUERY_Sequence": { + "id": 13, + "input_subworkflow_step_id": 2, + "output_name": "outfile" + }, + "TARGET_Sequence": { + "id": 14, + "input_subworkflow_step_id": 1, + "output_name": "outfile" + }, + "chain": { + "id": 18, + "input_subworkflow_step_id": 0, + "output_name": "out" + } + }, + "inputs": [ + { + "description": "", + "name": "swapLiftOver" + } + ], + "label": "swapLiftOver", + "name": "chain to liftover (subworkflow)", + "outputs": [], + "position": { + "left": 1836.1911072487153, + "top": 762.766715763506 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [ + { + "color": "none", + "data": { + "text": "Assemblies in fasta format, masked. " + }, + "id": 1, + "position": [ + 24.800000000000068, + 234.51597279574764 + ], + "size": [ + 310, + 55 + ], + "type": "markdown" + }, + { + "child_comments": [ + 1 + ], + "child_steps": [ + 2, + 1 + ], + "color": "blue", + "data": { + "title": "" + }, + "id": 0, + "position": [ + 0, + 194.51597279574764 + ], + "size": [ + 414, + 276 + ], + "type": "frame" + } + ], + "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": "chain to liftover (subworkflow)", + "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": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "chain" + } + ], + "label": "chain", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 242.328125, + "top": 9.360592187495683 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "78286bf0-68e8-410e-9624-41689254131c", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "TARGET_Sequence" + } + ], + "label": "TARGET_Sequence", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 44.16273637304573, + "top": 295.1869876848659 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "85fb7a10-67cf-42df-b1d8-ba4a90c07e2e", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "QUERY_Sequence" + } + ], + "label": "QUERY_Sequence", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 48.03343195121374, + "top": 383.0165441815411 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "6e8cdde2-a9f4-4ee5-936d-5eee44c1e257", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "errors": null, + "id": 3, + "input_connections": { + "infile": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": "TARGET trim sequence names", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 553.3383322970775, + "top": 369.9560090641513 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "tool_shed_repository": { + "changeset_revision": "c41d78ae5fee", + "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+galaxy2", + "type": "tool", + "uuid": "1d736295-f9d4-40b7-9140-d6e4ab905ba8", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "errors": null, + "id": 4, + "input_connections": { + "infile": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": "QUERY trim sequence names 2", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 698.499441913828, + "top": 545.2584925326347 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", + "tool_shed_repository": { + "changeset_revision": "c41d78ae5fee", + "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+galaxy2", + "type": "tool", + "uuid": "5b8d95b6-7fd1-4447-ba6f-35fabc159ffb", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "CONVERTER_fasta_to_2bit", + "errors": null, + "id": 5, + "input_connections": { + "input": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [], + "label": "target_2bit_step", + "name": "Convert FASTA to 2bit", + "outputs": [ + { + "name": "output", + "type": "twobit" + } + ], + "position": { + "left": 1067.7257258120155, + "top": 505.7630205069032 + }, + "post_job_actions": {}, + "tool_id": "CONVERTER_fasta_to_2bit", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.1", + "type": "tool", + "uuid": "38f9fb7f-bfe0-4bd6-bb47-38d37dc9014a", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "errors": null, + "id": 6, + "input_connections": { + "ref|input": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Compute sequence length", + "name": "ref" + } + ], + "label": "target_compute_sequence_length", + "name": "Compute sequence length", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 1539.993755096764, + "top": 422.903841974219 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "tool_shed_repository": { + "changeset_revision": "5cbde03c1103", + "name": "fasta_compute_length", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"ref\": {\"ref_source\": \"history\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"keep_first_word\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.4", + "type": "tool", + "uuid": "f6aa1c46-70e3-4bd6-9804-517d9163ae22", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "CONVERTER_fasta_to_2bit", + "errors": null, + "id": 7, + "input_connections": { + "input": { + "id": 4, + "output_name": "outfile" + } + }, + "inputs": [], + "label": "query_2bit_step", + "name": "Convert FASTA to 2bit", + "outputs": [ + { + "name": "output", + "type": "twobit" + } + ], + "position": { + "left": 1062.68165397853, + "top": 713.1258923119221 + }, + "post_job_actions": {}, + "tool_id": "CONVERTER_fasta_to_2bit", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.1", + "type": "tool", + "uuid": "7bc60e4c-ca3a-4365-98a4-1ed2def66992", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "errors": null, + "id": 8, + "input_connections": { + "ref|input": { + "id": 4, + "output_name": "outfile" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Compute sequence length", + "name": "ref" + } + ], + "label": "query_compute_sequence_length", + "name": "Compute sequence length", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 1557.9660305655827, + "top": 658.4157588998564 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", + "tool_shed_repository": { + "changeset_revision": "5cbde03c1103", + "name": "fasta_compute_length", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"ref\": {\"ref_source\": \"history\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"keep_first_word\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.4", + "type": "tool", + "uuid": "5765100f-d7f9-4044-acca-232a2ad59a3a", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainantirepeat/ucsc_chainantirepeat/482+galaxy0", + "errors": null, + "id": 9, + "input_connections": { + "in_chain": { + "id": 0, + "output_name": "output" + }, + "in_query": { + "id": 7, + "output_name": "output" + }, + "in_target": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": "chainantirepeat_step", + "name": "chainAntiRepeat", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 1214.7421875, + "top": 0.0 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainantirepeat/ucsc_chainantirepeat/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "9f2d2c96a189", + "name": "ucsc_chainantirepeat", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"in_query\": {\"__class__\": \"ConnectedValue\"}, \"in_target\": {\"__class__\": \"ConnectedValue\"}, \"minScore\": null, \"noCheckScore\": null, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "b0738b52-0d84-4877-8b9b-b8392cd7c2e0", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainprenet/ucsc_chainprenet/482+galaxy0", + "errors": null, + "id": 10, + "input_connections": { + "in_chain": { + "id": 9, + "output_name": "out" + }, + "query_reference_index_source|in_que_ref_index": { + "id": 8, + "output_name": "output" + }, + "target_reference_index_source|in_tar_ref_index": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool chainPreNet", + "name": "query_reference_index_source" + }, + { + "description": "runtime parameter for tool chainPreNet", + "name": "target_reference_index_source" + } + ], + "label": "chainprenet_step", + "name": "chainPreNet", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 1872.234375, + "top": 31.040283203125 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainprenet/ucsc_chainprenet/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "2a417e645e61", + "name": "ucsc_chainprenet", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"inclHap\": false, \"pad\": null, \"query_reference_index_source\": {\"query_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_que_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"target_reference_index_source\": {\"target_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_tar_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "6a3b3723-5073-4a12-862e-badf082e3747", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainsort/ucsc_chainsort/482+galaxy0", + "errors": null, + "id": 11, + "input_connections": { + "in_chain": { + "id": 10, + "output_name": "out" + } + }, + "inputs": [], + "label": "chainsort_step", + "name": "chainSort", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 2294.80306523609, + "top": 159.27204891791922 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainsort/ucsc_chainsort/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "07c87c2ab74b", + "name": "ucsc_chainsort", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"sort_by\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "7f5dbcfd-658a-45f9-b95d-69259eec7b0f", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainnet/ucsc_chainnet/482+galaxy0", + "errors": null, + "id": 12, + "input_connections": { + "in_chain": { + "id": 11, + "output_name": "out" + }, + "query_reference_index_source|in_que_ref_index": { + "id": 8, + "output_name": "output" + }, + "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", + "name": "chainNet", + "outputs": [ + { + "name": "targetNet", + "type": "ucsc.net" + }, + { + "name": "queryNet", + "type": "ucsc.net" + } + ], + "position": { + "left": 2228.970370728072, + "top": 457.7125181265065 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_chainnet/ucsc_chainnet/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "5b65a92be96c", + "name": "ucsc_chainnet", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"inclHap\": false, \"minFill\": null, \"minScore\": null, \"minSpace\": null, \"query_reference_index_source\": {\"query_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_que_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"target_reference_index_source\": {\"target_reference_index_source_selector\": \"history\", \"__current_case__\": 1, \"in_tar_ref_index\": {\"__class__\": \"ConnectedValue\"}}, \"verbose\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "9b11667f-fc6f-4a71-853c-0e3014f95cbc", + "when": null, + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netsyntenic/ucsc_netsyntenic/482+galaxy0", + "errors": null, + "id": 13, + "input_connections": { + "in_net": { + "id": 12, + "output_name": "targetNet" + } + }, + "inputs": [], + "label": "netsyntenic_step", + "name": "netSyntenic", + "outputs": [ + { + "name": "out", + "type": "ucsc.net" + } + ], + "position": { + "left": 2564.153845348722, + "top": 425.45236124501406 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netsyntenic/ucsc_netsyntenic/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "1999f87602f7", + "name": "ucsc_netsyntenic", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_net\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "9828149d-6938-49f4-95e3-ece4b87d38bd", + "when": null, + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netfilter/ucsc_netfilter/482+galaxy0", + "errors": null, + "id": 14, + "input_connections": { + "in_net": { + "id": 13, + "output_name": "out" + } + }, + "inputs": [], + "label": "netfilter_step", + "name": "netFilter", + "outputs": [ + { + "name": "out", + "type": "ucsc.net" + } + ], + "position": { + "left": 2900.086910790546, + "top": 392.10616304438827 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netfilter/ucsc_netfilter/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "5c3fa42d003f", + "name": "ucsc_netfilter", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_net\": {\"__class__\": \"ConnectedValue\"}, \"minGap\": null, \"synteny\": {\"syn_filter\": \"filtersyn\", \"__current_case__\": 1, \"syntype\": \"-syn\", \"minSynScore\": null, \"minSynSize\": null, \"minSynAli\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "24e0d7b4-29bb-4749-a192-a50937a24945", + "when": null, + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netchainsubset/ucsc_netchainsubset/482+galaxy0", + "errors": null, + "id": 15, + "input_connections": { + "in_chain": { + "id": 0, + "output_name": "output" + }, + "in_net": { + "id": 14, + "output_name": "out" + } + }, + "inputs": [], + "label": "netchainsubset_step", + "name": "netChainSubset", + "outputs": [ + { + "name": "out", + "type": "chain" + } + ], + "position": { + "left": 2068.234375, + "top": 910.8371546874957 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_netchainsubset/ucsc_netchainsubset/482+galaxy0", + "tool_shed_repository": { + "changeset_revision": "794cf52edccc", + "name": "ucsc_netchainsubset", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"in_chain\": {\"__class__\": \"ConnectedValue\"}, \"in_net\": {\"__class__\": \"ConnectedValue\"}, \"skipMissing\": false, \"splitOnInsert\": false, \"wholeChains\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "482+galaxy0", + "type": "tool", + "uuid": "87113072-dc71-4355-87f5-03cb1ad2a9ca", + "when": null, + "workflow_outputs": [ + { + "label": "liftover_chain_file", + "output_name": "out", + "uuid": "8d91d96e-de70-4e8a-a27e-4c78c7e4f901" + } + ] + } + }, + "tags": [], + "uuid": "e0c44203-570a-4ba5-9d9f-ee301d477e52" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "a12d6b50-066d-4b1d-b9fc-1ddc32e481c2", + "when": null, + "workflow_outputs": [ + { + "label": "swap.lift.over", + "output_name": "liftover_chain_file", + "uuid": "852e2cb0-b4dd-476f-9c8b-e86fa30b347e" + } + ] + } + }, + "tags": [ + "ucsc", + "alignment", + "lastz", + "kegalign", + "chain", + "net" + ], + "uuid": "d04dd299-ec8f-4f4c-adfe-b4121cac9c62", + "version": 1 +} \ No newline at end of file