From c9dd23f686511e07e5f4810d1a26f5a7f1b94ef7 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 31 Jul 2024 17:05:48 -0400 Subject: [PATCH] fix the problem with jbrowse failing when 1 related species was provided --- .../TreeValGal_optionalwindowmasker.ga | 1087 +++++++++++------ 1 file changed, 694 insertions(+), 393 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga index d7046e71e..58df2e5e7 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga @@ -1,24 +1,7 @@ { "a_galaxy_workflow": "true", - "annotation": "Option to skip windowmasker.", + "annotation": "", "comments": [ - { - "color": "blue", - "data": { - "size": 2, - "text": "General:

Uses Delphine's method for optional inputs.

Mashmap reference uses repeatmasker masked sequence to filter noise from low complexity element matches, and \"orthologous\" mapping for both haplotypes and related species. Not sure what's optimal. Advice appeciated

JBrowse tracks can be off in the default view to make things less overwhelming. Need to open the track menu to see them. The independent haplotype paf tracks are hidden by default for example

The output reports on an assembly, optionally mat/pat haplotypes if contig names do not overlap - rubbish will be displayed if they do. With some pacbio reads, the main tracks can be produced. The annotation tracks require human choices for external genes and proteins, and comparison species for pafs.

Mashmap paf tracks are prepared for two comparison species references, and for an independent haplotype or refererence genome.



" - }, - "id": 4, - "position": [ - 20, - 1537.033585622281 - ], - "size": [ - 700, - 870 - ], - "type": "text" - }, { "color": "red", "data": { @@ -36,25 +19,6 @@ ], "type": "text" }, - { - "child_comments": [ - 1 - ], - "color": "black", - "data": { - "title": "" - }, - "id": 0, - "position": [ - 10, - 40 - ], - "size": [ - 1430, - 140 - ], - "type": "frame" - }, { "color": "black", "data": { @@ -74,13 +38,13 @@ }, { "child_steps": [ - 16, 26, 33, 15, + 14, 17, 18, - 14 + 16 ], "color": "red", "data": { @@ -100,14 +64,14 @@ { "child_steps": [ 25, + 7, + 8, + 13, 6, 12, - 8, + 9, 10, - 11, - 7, - 13, - 9 + 11 ], "color": "turquoise", "data": { @@ -124,6 +88,23 @@ ], "type": "frame" }, + { + "color": "blue", + "data": { + "size": 2, + "text": "General:

Uses Delphine's method for optional inputs.

Mashmap reference uses repeatmasker masked sequence to filter noise from low complexity element matches, and \"orthologous\" mapping for both haplotypes and related species. Not sure what's optimal. Advice appeciated

JBrowse tracks can be off in the default view to make things less overwhelming. Need to open the track menu to see them. The independent haplotype paf tracks are hidden by default for example

The output reports on an assembly, optionally mat/pat haplotypes if contig names do not overlap - rubbish will be displayed if they do. With some pacbio reads, the main tracks can be produced. The annotation tracks require human choices for external genes and proteins, and comparison species for pafs.

Mashmap paf tracks are prepared for two comparison species references, and for an independent haplotype or refererence genome.



" + }, + "id": 4, + "position": [ + 20, + 1537.033585622281 + ], + "size": [ + 700, + 870 + ], + "type": "text" + }, { "color": "turquoise", "data": { @@ -140,6 +121,25 @@ 250 ], "type": "text" + }, + { + "child_comments": [ + 1 + ], + "color": "black", + "data": { + "title": "" + }, + "id": 0, + "position": [ + 10, + 40 + ], + "size": [ + 1430, + 140 + ], + "type": "frame" } ], "creator": [ @@ -166,7 +166,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "TreeValGalJuly26_optionalwindowmasker", + "name": "TreeValGalJuly31_optionalwindowmasker", "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" }, @@ -196,7 +196,13 @@ "type": "parameter_input", "uuid": "35d60a1d-85f2-4c8b-af5e-2ac2e8db6ef3", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d8d09aa4-fa86-43dc-88c7-a2a42aa67d9c" + } + ] }, "1": { "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", @@ -277,7 +283,13 @@ "type": "parameter_input", "uuid": "e57810b3-9f4f-477d-97f6-929f5dfca0e9", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "11e983f9-7827-4bc9-bb8d-4d9f48f2e6da" + } + ] }, "4": { "annotation": "dfam is problematic. Aves works for birds! That's why there's also a model free one - windowmasker - for comparison.", @@ -304,7 +316,13 @@ "type": "parameter_input", "uuid": "338f375e-10f9-4461-a938-44eca7c8f966", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ae0eaeff-19d0-4da9-a2f1-a55c9c327848" + } + ] }, "5": { "annotation": "CCCTAA for the treeval test data or for vertebrates seems to work. This uses seqtk-telo and seems to give plausible results with the appropriate repeat element for vertebrates....", @@ -331,7 +349,13 @@ "type": "parameter_input", "uuid": "cb1c7f9f-1bca-43a8-a068-38b00bb37af6", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "a5a2781a-35ee-4b55-9039-d9c40c939653" + } + ] }, "6": { "annotation": "", @@ -358,7 +382,13 @@ "type": "parameter_input", "uuid": "d1f53ba4-a094-44db-b4ce-2e534e0dab16", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "041f7f53-9c55-4468-986b-104cc935e494" + } + ] }, "7": { "annotation": "", @@ -385,7 +415,13 @@ "type": "data_input", "uuid": "00be13df-0a64-4ed0-87c7-3f97e9badf3e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "70ec3f32-42ba-449c-bc38-b2dd1cd6db7a" + } + ] }, "8": { "annotation": "", @@ -412,7 +448,13 @@ "type": "parameter_input", "uuid": "93f00f8e-2226-4ef0-aacf-f9ab84cca0d5", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9fe8a3ef-cf17-49bb-8e60-86bfd1ed9717" + } + ] }, "9": { "annotation": "", @@ -439,7 +481,13 @@ "type": "data_input", "uuid": "05aeefc3-a4b1-4788-9d1b-095621fa1cb3", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c46c8ea8-3179-4336-bfdf-10ce53b103fa" + } + ] }, "10": { "annotation": "", @@ -466,7 +514,13 @@ "type": "parameter_input", "uuid": "0235e72e-1526-4fa4-8601-d4eb5e15d7b4", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "3ab07061-fae3-464a-806c-14f81f660840" + } + ] }, "11": { "annotation": "", @@ -493,7 +547,13 @@ "type": "data_input", "uuid": "b10094d0-c733-4825-bbec-cb56e46239c4", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "84b15f0f-ce00-4aed-90ea-6c20e9b36e61" + } + ] }, "12": { "annotation": "", @@ -520,7 +580,13 @@ "type": "parameter_input", "uuid": "4abbe4ea-96bf-436b-9e8b-24b24700f47e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "0d58a9a6-782f-4bfc-b373-9dddff02ebe4" + } + ] }, "13": { "annotation": "", @@ -547,7 +613,13 @@ "type": "data_input", "uuid": "0efaa539-d992-4816-bb1a-b1d704fef9d8", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "bfd486c3-867e-4e78-a22c-58451db398c9" + } + ] }, "14": { "annotation": "", @@ -574,7 +646,13 @@ "type": "parameter_input", "uuid": "5421a1f3-648c-4994-a4bb-9d9721fdc80b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d452fdb4-8c1f-4c78-bbc9-3e1717a29bbc" + } + ] }, "15": { "annotation": "", @@ -601,7 +679,13 @@ "type": "data_input", "uuid": "3864c5b2-08fd-40ee-9922-363960eeaf5e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5a0153ab-1646-4dbc-9abc-040f17a10771" + } + ] }, "16": { "annotation": "", @@ -628,7 +712,13 @@ "type": "parameter_input", "uuid": "86415a69-308a-4f72-af00-54a93c22680a", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "e72b0f87-a603-422a-a465-d973fe4659bd" + } + ] }, "17": { "annotation": "Sequence mapping syntenic regions will be displayed.", @@ -682,7 +772,13 @@ "type": "data_input", "uuid": "809165da-162b-4354-a5a0-28d82dbe9cb6", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1fe95cfe-de5c-4e06-952d-27788e9f0c1e" + } + ] }, "19": { "annotation": "", @@ -2214,7 +2310,48 @@ "type": "subworkflow", "uuid": "4871e101-dadd-42a4-8523-0286d6c6a045", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "1:output", + "uuid": "037d0cc4-2c6d-46f7-891b-49ba9259a982" + }, + { + "label": null, + "output_name": "2:output", + "uuid": "96361109-d122-4f21-ba12-8bb9b1f1b8c5" + }, + { + "label": null, + "output_name": "3:output", + "uuid": "11ba298c-20eb-430f-b0f3-ecdea8e0e642" + }, + { + "label": null, + "output_name": "4:output", + "uuid": "438c9662-76c6-485c-9dc5-deef0a3c1d9a" + }, + { + "label": null, + "output_name": "5:output", + "uuid": "e15eba00-6e2a-4f90-a7df-3401b8ff0703" + }, + { + "label": null, + "output_name": "6:output", + "uuid": "170bf8d1-8f9b-4c62-817a-840dd8861a55" + }, + { + "label": null, + "output_name": "7:output", + "uuid": "c4229ede-bd89-4e19-8de1-7a2ee58c1ca1" + }, + { + "label": null, + "output_name": "8:output", + "uuid": "96d24b36-230f-44ad-8a00-e0cb539d9ff9" + } + ] }, "26": { "annotation": "", @@ -2265,105 +2402,89 @@ 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"style_cond|type_cond|pick_from_1|value": { - "id": 21, + "id": 19, "output_name": "mashout" }, "when": { @@ -3847,7 +3858,7 @@ } ], "position": { - "left": 1902.8054040950303, + "left": 1893.5085290950303, "top": 1596.5208916866172 }, "post_job_actions": { @@ -3869,7 +3880,7 @@ "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "96557ece-f925-4f98-a191-7501cea79302", + "uuid": "7995f00e-cc30-4795-b63c-7e06311390e1", "when": "$(inputs.when)", "workflow_outputs": [ { @@ -3879,18 +3890,18 @@ } ] }, - "25": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 25, + "id": 23, "input_connections": { "style_cond|type_cond|pick_from_0|value": { - "id": 19, + "id": 17, "output_name": "mashout" }, "style_cond|type_cond|pick_from_1|value": { - "id": 22, + "id": 20, "output_name": "mashout" }, "when": { @@ -3908,7 +3919,7 @@ } ], "position": { - "left": 1370.7637652444037, + "left": 1361.4668902444037, "top": 2333.8559837901257 }, "post_job_actions": { @@ -3930,7 +3941,7 @@ "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "d0c67a75-24d2-403a-961e-800c8343c767", + "uuid": "6a03891e-f490-4682-a45e-8a135fea33b0", "when": "$(inputs.when)", "workflow_outputs": [ { @@ -3942,7 +3953,7 @@ } }, "tags": [], - "uuid": "576b7cf9-d97a-4231-8238-b8b632823027" + "uuid": "61d001dc-e6dc-4d2a-b5ff-9ffaef788cc7" }, "tool_id": null, "type": "subworkflow", @@ -5129,12 +5140,12 @@ }, "assemblies_0|track_groups_1|data_tracks_5|data_format|pafuseuri|annotation": [ { - "id": 27, - "output_name": "data_param" + "id": 17, + "output_name": "output" }, { - "id": 28, - "output_name": "data_param" + "id": 18, + "output_name": "output" } ], "assemblies_0|track_groups_1|data_tracks_5|data_format|useuri|annotation": { @@ -5143,12 +5154,12 @@ }, "assemblies_0|track_groups_1|data_tracks_6|data_format|pafuseuri|annotation": [ { - "id": 27, - "output_name": "data_param" + "id": 17, + "output_name": "output" }, { - "id": 28, - "output_name": "data_param" + "id": 18, + "output_name": "output" } ], "assemblies_0|track_groups_1|data_tracks_6|data_format|useuri|annotation": { @@ -5157,12 +5168,12 @@ }, "assemblies_0|track_groups_1|data_tracks_7|data_format|pafuseuri|annotation": [ { - "id": 27, - "output_name": "data_param" + "id": 17, + "output_name": "output" }, { - "id": 28, - "output_name": "data_param" + "id": 18, + "output_name": "output" } ], "assemblies_0|track_groups_1|data_tracks_7|data_format|useuri|annotation": { @@ -5192,6 +5203,10 @@ "assemblies_0|track_groups_2|data_tracks_2|data_format|useuri|annotation": { "id": 33, "output_name": "independent 5k 98 mashmap" + }, + "when": { + "id": 27, + "output_name": "output_param_boolean" } }, "inputs": [], @@ -5204,8 +5219,8 @@ } ], "position": { - "left": 3309.586394057406, - "top": 925.532902016253 + "left": 3949.0930266411224, + "top": 738.8423384366829 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -5227,7 +5242,7 @@ "tool_version": "2.11.1+galaxy0", "type": "tool", "uuid": "455bd0c0-2cf5-4af7-8aa4-76a114e13f0f", - "when": null, + "when": "$(inputs.when)", "workflow_outputs": [ { "label": " JBrowse2 for viewing", @@ -5284,12 +5299,12 @@ }, "assemblies_0|track_groups_1|data_tracks_5|data_format|pafuseuri|annotation": [ { - "id": 27, - "output_name": "data_param" + "id": 17, + "output_name": "output" }, { - "id": 28, - "output_name": "data_param" + "id": 18, + "output_name": "output" } ], "assemblies_0|track_groups_1|data_tracks_5|data_format|useuri|annotation": { @@ -5298,12 +5313,12 @@ }, "assemblies_0|track_groups_1|data_tracks_6|data_format|pafuseuri|annotation": [ { - "id": 27, - "output_name": "data_param" + "id": 17, + "output_name": "output" }, { - "id": 28, - "output_name": "data_param" + "id": 18, + "output_name": "output" } ], "assemblies_0|track_groups_1|data_tracks_6|data_format|useuri|annotation": { @@ -5312,12 +5327,12 @@ }, "assemblies_0|track_groups_1|data_tracks_7|data_format|pafuseuri|annotation": [ { - "id": 27, - "output_name": "data_param" + "id": 17, + "output_name": "output" }, { - "id": 28, - "output_name": "data_param" + "id": 18, + "output_name": "output" } ], 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