From f8acd11c7693001486197be0d5acc8d73f92394e Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 31 Jul 2024 12:13:22 -0400 Subject: [PATCH 1/8] Creation of branch for TreeValGal Workflow --- .../TreeValGal_optionalwindowmasker.ga | 5398 +++++++++++++++++ 1 file changed, 5398 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga new file mode 100644 index 000000000..d7046e71e --- /dev/null +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga @@ -0,0 +1,5398 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Option to skip windowmasker.", + "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": { + "size": 2, + "text": "Notes on inputs for mashmap pafs:

mashmap settings varied here are % identity and match length - like steps 27-29 to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.

At this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.

Need curator eyeballs and feedback for that.

Two different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available

The 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives.  

There are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?

Need to use the track menu for the main reference vs external reference/haplotype tracks - off by default.

Again there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.
" + }, + "id": 2, + "position": [ + 0, + 257.03358562228095 + ], + "size": [ + 1020, + 1030 + ], + "type": "text" + }, + { + "child_comments": [ + 1 + ], + "color": "black", + "data": { + "title": "" + }, + "id": 0, + "position": [ + 10, + 40 + ], + "size": [ + 1430, + 140 + ], + "type": "frame" + }, + { + "color": "black", + "data": { + "size": 2, + "text": "Technical discussion document under development here:
https://docs.google.com/document/d/1YbQZsFC8oDJIGos5yLFbApumpK4yIz02qfwYEypDfI8" + }, + "id": 1, + "position": [ + 20, + 80 + ], + "size": [ + 1380, + 80 + ], + "type": "text" + }, + { + "child_steps": [ + 16, + 26, + 33, + 15, + 17, + 18, + 14 + ], + "color": "red", + "data": { + "title": "Mashmap paf tracks subworkflow" + }, + "id": 6, + "position": [ + 1300, + 1850 + ], + "size": [ + 950, + 930 + ], + "type": "frame" + }, + { + "child_steps": [ + 25, + 6, + 12, + 8, + 10, + 11, + 7, + 13, + 9 + ], + "color": "turquoise", + "data": { + "title": "Annotation fasta inputs" + }, + "id": 5, + "position": [ + 1300, + 930 + ], + "size": [ + 950, + 900 + ], + "type": "frame" + }, + { + "color": "turquoise", + "data": { + "size": 2, + "text": "Annotation Fasta inputs:

Currently has 4 optional NCBI annotation tracks fasta - genes, cds, rna and one with the proteins - these are mapped with a specialised AA to nucleotide mapper so must be encoded as amino acids.
" + }, + "id": 3, + "position": [ + 0, + 1297.033585622281 + ], + "size": [ + 1000, + 250 + ], + "type": "text" + } + ], + "creator": [ + { + "class": "Person", + "identifier": "", + "name": "Ross Lazarus" + }, + { + "class": "Person", + "identifier": "anna.syme@gmail.com", + "name": "Anna Syme" + }, + { + "class": "Person", + "identifier": "nadibraj@gmail.com", + "name": "Nadolina Brajuka" + }, + { + "class": "Person", + "identifier": "lariviere.delphine@gmail.com", + "name": "Delphine Lariviere" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "TreeValGalJuly26_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" + }, + "steps": { + "0": { + "annotation": "If you have both haplotypes in this assembly, windowmasker may fail.", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "If you have both haplotypes in this assembly, windowmasker may fail.", + "name": "Run windowmasker model-free repeats? 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Not sure if minimap2 mapping preset is right?

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\"LinearBasicDisplay\"}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 3, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Annotation tracks using external data\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"bed\", \"__current_case__\": 4, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"bed\", \"__current_case__\": 4, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"bed\", \"__current_case__\": 4, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 3, \"data_format\": {\"data_format_select\": \"gff\", \"__current_case__\": 2, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"jbstyle\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 4, \"data_format\": {\"data_format_select\": \"bed\", \"__current_case__\": 4, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 5, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 6, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 7, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Sequence similarity with external reference\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}]}]}], \"jbgen\": {\"ucol\": {\"formcoll\": \"form\", \"__current_case__\": 1}, \"zipOut\": true, \"defaultLocation\": \"\", \"session_name\": \"TreeValGal\", \"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.11.1+galaxy0", + "type": "tool", + "uuid": "818e5b20-ecfc-47b2-a99c-042674b803b5", + "when": null, + "workflow_outputs": [ + { + "label": " JBrowse2 for export", + "output_name": "output", + "uuid": "4deefe8c-8c24-41e5-b1fd-f8ba9453f797" + } + ] + } + }, + "tags": [], + "uuid": "3be83288-bf10-4717-8a20-eaabe5fef811", + "version": 15 +} \ No newline at end of file From c9dd23f686511e07e5f4810d1a26f5a7f1b94ef7 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 31 Jul 2024 17:05:48 -0400 Subject: [PATCH 2/8] 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 @@ }, "27": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, "id": 27, "input_connections": { - "style_cond|type_cond|pick_from_0|value": { - "id": 17, + "input_param_type|input_param": { + "id": 16, "output_name": "output" } }, - "inputs": [], - "label": null, - "name": "Pick parameter value", + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": "Run if 0 or 2", + "name": "Map parameter value", "outputs": [ { - "name": "data_param", - "type": "input" + "name": "output_param_boolean", + "type": "expression.json" } ], "position": { - "left": 1755.0721259064787, - "top": 2855.5667487651444 - }, - "post_job_actions": { - "HideDatasetActiondata_param": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "data_param" - }, - 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"uuid": "440f3461-f82a-4614-8810-0692fe02a9d9", "when": "$(inputs.when)", "workflow_outputs": [] }, - "21": { + "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", "errors": null, - "id": 21, + "id": 19, "input_connections": { "query": { "id": 2, "output_name": "output" }, "reflist": { - "id": 8, - "output_name": "data_param" + "id": 4, + "output_name": "output" }, "when": { - "id": 16, + "id": 14, "output_name": "boolean_param" } }, @@ -3666,8 +3677,8 @@ } ], "position": { - "left": 1369.2215246257717, - "top": 1888.4481003884198 + "left": 1378.6863133696631, + "top": 1879.8574982307819 }, "post_job_actions": { "HideDatasetActionmashout": { @@ -3693,26 +3704,26 @@ "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"95.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": 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"style_cond|type_cond|pick_from_1|value": { - "id": 21, + "id": 19, "output_name": "mashout" }, "when": { @@ -3847,7 +3858,7 @@ } ], "position": { - "left": 1902.8054040950303, + "left": 1893.5085290950303, "top": 1596.5208916866172 }, "post_job_actions": { @@ -3869,7 +3880,7 @@ "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "96557ece-f925-4f98-a191-7501cea79302", + "uuid": "7995f00e-cc30-4795-b63c-7e06311390e1", "when": "$(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" } ], "assemblies_0|track_groups_1|data_tracks_7|data_format|useuri|annotation": { @@ -5347,6 +5362,10 @@ "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": [], @@ -5359,13 +5378,13 @@ } ], "position": { - "left": 3844.153647694, - "top": 820.2615397391264 + "left": 4402.412293087849, + "top": 748.4351535500991 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": " JBrowse2 for export" + "newname": " JBrowse2 for viewing" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -5378,21 +5397,303 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"track_groups\": [{\"__index__\": 0, 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"2.11.1+galaxy0", + "type": "tool", + "uuid": "2d196a34-dc52-4993-b48f-1c0eb33f84a3", + "when": "$(inputs.when)", "workflow_outputs": [ { - "label": " JBrowse2 for export", + "label": "JBrowse2 for Export 1 species", "output_name": "output", - "uuid": "4deefe8c-8c24-41e5-b1fd-f8ba9453f797" + "uuid": "2bf1f69b-9908-4220-82e9-3f5d9a893377" } ] } }, "tags": [], - "uuid": "3be83288-bf10-4717-8a20-eaabe5fef811", - "version": 15 + "uuid": "1828e702-9a94-4d58-9c13-1c97f2831252", + "version": 4 } \ No newline at end of file From 5d3d148af30072bc18babb138ea144b9072efd9e Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Thu, 1 Aug 2024 07:19:41 -0400 Subject: [PATCH 3/8] rename outputs' --- .../TreeValGal_optionalwindowmasker.ga | 225 ++++-------------- 1 file changed, 44 insertions(+), 181 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga index 58df2e5e7..1b22b29c1 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga @@ -2,23 +2,6 @@ "a_galaxy_workflow": "true", "annotation": "", "comments": [ - { - "color": "red", - "data": { - "size": 2, - "text": "Notes on inputs for mashmap pafs:

mashmap settings varied here are % identity and match length - like steps 27-29 to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.

At this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.

Need curator eyeballs and feedback for that.

Two different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available

The 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives.  

There are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?

Need to use the track menu for the main reference vs external reference/haplotype tracks - off by default.

Again there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.
" - }, - "id": 2, - "position": [ - 0, - 257.03358562228095 - ], - "size": [ - 1020, - 1030 - ], - "type": "text" - }, { "color": "black", "data": { @@ -64,14 +47,14 @@ { "child_steps": [ 25, + 11, 7, 8, 13, 6, 12, 9, - 10, - 11 + 10 ], "color": "turquoise", "data": { @@ -122,6 +105,23 @@ ], "type": "text" }, + { + "color": "red", + "data": { + "size": 2, + "text": "Notes on inputs for mashmap pafs:

mashmap settings varied here are % identity and match length - like steps 27-29 to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.

At this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.

Need curator eyeballs and feedback for that.

Two different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available

The 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives.  

There are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?

Need to use the track menu for the main reference vs external reference/haplotype tracks - off by default.

Again there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.
" + }, + "id": 2, + "position": [ + 0, + 257.03358562228095 + ], + "size": [ + 1020, + 1030 + ], + "type": "text" + }, { "child_comments": [ 1 @@ -196,13 +196,7 @@ "type": "parameter_input", "uuid": "35d60a1d-85f2-4c8b-af5e-2ac2e8db6ef3", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "d8d09aa4-fa86-43dc-88c7-a2a42aa67d9c" - } - ] + "workflow_outputs": [] }, "1": { "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", @@ -283,13 +277,7 @@ "type": "parameter_input", "uuid": "e57810b3-9f4f-477d-97f6-929f5dfca0e9", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "11e983f9-7827-4bc9-bb8d-4d9f48f2e6da" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "dfam is problematic. Aves works for birds! That's why there's also a model free one - windowmasker - for comparison.", @@ -316,13 +304,7 @@ "type": "parameter_input", "uuid": "338f375e-10f9-4461-a938-44eca7c8f966", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "ae0eaeff-19d0-4da9-a2f1-a55c9c327848" - } - ] + "workflow_outputs": [] }, "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....", @@ -349,13 +331,7 @@ "type": "parameter_input", "uuid": "cb1c7f9f-1bca-43a8-a068-38b00bb37af6", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a5a2781a-35ee-4b55-9039-d9c40c939653" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "", @@ -382,13 +358,7 @@ "type": "parameter_input", "uuid": "d1f53ba4-a094-44db-b4ce-2e534e0dab16", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "041f7f53-9c55-4468-986b-104cc935e494" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -415,13 +385,7 @@ "type": "data_input", "uuid": "00be13df-0a64-4ed0-87c7-3f97e9badf3e", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "70ec3f32-42ba-449c-bc38-b2dd1cd6db7a" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "", @@ -448,13 +412,7 @@ "type": "parameter_input", "uuid": "93f00f8e-2226-4ef0-aacf-f9ab84cca0d5", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "9fe8a3ef-cf17-49bb-8e60-86bfd1ed9717" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -481,13 +439,7 @@ "type": "data_input", "uuid": "05aeefc3-a4b1-4788-9d1b-095621fa1cb3", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "c46c8ea8-3179-4336-bfdf-10ce53b103fa" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "", @@ -514,13 +466,7 @@ "type": "parameter_input", "uuid": "0235e72e-1526-4fa4-8601-d4eb5e15d7b4", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "3ab07061-fae3-464a-806c-14f81f660840" - } - ] + "workflow_outputs": [] }, "11": { "annotation": "", @@ -547,13 +493,7 @@ "type": "data_input", "uuid": "b10094d0-c733-4825-bbec-cb56e46239c4", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "84b15f0f-ce00-4aed-90ea-6c20e9b36e61" - } - ] + "workflow_outputs": [] }, "12": { "annotation": "", @@ -580,13 +520,7 @@ "type": "parameter_input", "uuid": "4abbe4ea-96bf-436b-9e8b-24b24700f47e", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "0d58a9a6-782f-4bfc-b373-9dddff02ebe4" - } - ] + "workflow_outputs": [] }, "13": { "annotation": "", @@ -613,13 +547,7 @@ "type": "data_input", "uuid": "0efaa539-d992-4816-bb1a-b1d704fef9d8", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "bfd486c3-867e-4e78-a22c-58451db398c9" - } - ] + "workflow_outputs": [] }, "14": { "annotation": "", @@ -646,13 +574,7 @@ "type": "parameter_input", "uuid": "5421a1f3-648c-4994-a4bb-9d9721fdc80b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "d452fdb4-8c1f-4c78-bbc9-3e1717a29bbc" - } - ] + "workflow_outputs": [] }, "15": { "annotation": "", @@ -679,13 +601,7 @@ "type": "data_input", "uuid": "3864c5b2-08fd-40ee-9922-363960eeaf5e", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "5a0153ab-1646-4dbc-9abc-040f17a10771" - } - ] + "workflow_outputs": [] }, "16": { "annotation": "", @@ -712,13 +628,7 @@ "type": "parameter_input", "uuid": "86415a69-308a-4f72-af00-54a93c22680a", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e72b0f87-a603-422a-a465-d973fe4659bd" - } - ] + "workflow_outputs": [] }, "17": { "annotation": "Sequence mapping syntenic regions will be displayed.", @@ -772,13 +682,7 @@ "type": "data_input", "uuid": "809165da-162b-4354-a5a0-28d82dbe9cb6", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "1fe95cfe-de5c-4e06-952d-27788e9f0c1e" - } - ] + "workflow_outputs": [] }, "19": { "annotation": "", @@ -2310,48 +2214,7 @@ "type": "subworkflow", "uuid": 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"position": { - "left": 3949.0930266411224, - "top": 738.8423384366829 + "left": 3795.7912942130183, + "top": 791.5810073417651 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -5384,7 +5247,7 @@ "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": " JBrowse2 for viewing" + "newname": " JBrowse2 for Export" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -5397,7 +5260,7 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Assembly properties\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gff\", \"__current_case__\": 2, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, 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"tool_version": "2.11.1+galaxy0", "type": "tool", "uuid": "2e6baf2a-acea-424e-82a1-55461b97a90b", @@ -5666,7 +5529,7 @@ "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": " JBrowse2 for viewing" + "newname": " JBrowse2 for Export" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -5679,7 +5542,7 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Assembly properties\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gff\", \"__current_case__\": 2, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"jbstyle\": 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{\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Sequence similarity with external reference\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_off\"}}]}]}], \"jbgen\": {\"ucol\": {\"formcoll\": \"form\", \"__current_case__\": 1}, \"zipOut\": true, \"defaultLocation\": \"\", \"session_name\": \"TreeValGal\", \"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.11.1+galaxy0", "type": "tool", "uuid": "2d196a34-dc52-4993-b48f-1c0eb33f84a3", @@ -5694,6 +5557,6 @@ } }, "tags": [], - "uuid": "1828e702-9a94-4d58-9c13-1c97f2831252", - "version": 4 + "uuid": "7937d50b-6226-4c7d-adf9-b463f3ffdf1b", + "version": 5 } \ No newline at end of file From ce03938602b04b4eb3c45440c6bb75ef03e59e03 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 14 Aug 2024 09:47:55 -0400 Subject: [PATCH 4/8] simplify the conditionals by using collections instead --- .../TreeValGal_optionalwindowmasker.ga | 3246 ++++++----------- 1 file changed, 1094 insertions(+), 2152 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga index 1b22b29c1..807dc5e66 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga @@ -2,6 +2,59 @@ "a_galaxy_workflow": "true", "annotation": "", "comments": [ + { + "child_comments": [ + 1 + ], + "color": "black", + "data": { + "title": "" + }, + "id": 0, + "position": [ + 10, + 40 + ], + "size": [ + 1430, + 140 + ], + "type": "frame" + }, + { + "color": "red", + "data": { + "size": 2, + "text": "Notes on inputs for mashmap pafs:

mashmap settings varied here are % identity and match length - like steps 27-29 to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.

At this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.

Need curator eyeballs and feedback for that.

Two different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available

The 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives.  

There are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?

Need to use the track menu for the main reference vs external reference/haplotype tracks - off by default.

Again there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.
" + }, + "id": 2, + "position": [ + 0, + 257.03358562228095 + ], + "size": [ + 1020, + 1030 + ], + "type": "text" + }, + { + "color": "turquoise", + "data": { + "size": 2, + "text": "Annotation Fasta inputs:

Currently has 4 optional NCBI annotation tracks fasta - genes, cds, rna and one with the proteins - these are mapped with a specialised AA to nucleotide mapper so must be encoded as amino acids.
" + }, + "id": 3, + "position": [ + 0, + 1297.033585622281 + ], + "size": [ + 1000, + 250 + ], + "type": "text" + }, { "color": "black", "data": { @@ -21,13 +74,12 @@ }, { "child_steps": [ - 26, - 33, + 25, + 30, 15, 14, - 17, - 18, - 16 + 16, + 17 ], "color": "red", "data": { @@ -46,15 +98,15 @@ }, { "child_steps": [ - 25, - 11, + 24, + 6, + 12, 7, + 10, 8, + 11, 13, - 6, - 12, - 9, - 10 + 9 ], "color": "turquoise", "data": { @@ -87,59 +139,6 @@ 870 ], "type": "text" - }, - { - "color": "turquoise", - "data": { - "size": 2, - "text": "Annotation Fasta inputs:

Currently has 4 optional NCBI annotation tracks fasta - genes, cds, rna and one with the proteins - these are mapped with a specialised AA to nucleotide mapper so must be encoded as amino acids.
" - }, - "id": 3, - "position": [ - 0, - 1297.033585622281 - ], - "size": [ - 1000, - 250 - ], - "type": "text" - }, - { - "color": "red", - "data": { - "size": 2, - "text": "Notes on inputs for mashmap pafs:

mashmap settings varied here are % identity and match length - like steps 27-29 to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.

At this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.

Need curator eyeballs and feedback for that.

Two different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available

The 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives.  

There are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?

Need to use the track menu for the main reference vs external reference/haplotype tracks - off by default.

Again there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.
" - }, - "id": 2, - "position": [ - 0, - 257.03358562228095 - ], - "size": [ - 1020, - 1030 - ], - "type": "text" - }, - { - "child_comments": [ - 1 - ], - "color": "black", - "data": { - "title": "" - }, - "id": 0, - "position": [ - 10, - 40 - ], - "size": [ - 1430, - 140 - ], - "type": "frame" } ], "creator": [ @@ -166,7 +165,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "TreeValGalJuly31_optionalwindowmasker", + "name": "TreeValGalAug12_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 +195,13 @@ "type": "parameter_input", "uuid": "35d60a1d-85f2-4c8b-af5e-2ac2e8db6ef3", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "22941942-7c0b-44f2-845d-94089066ff4f" + } + ] }, "1": { "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", @@ -277,7 +282,13 @@ "type": "parameter_input", "uuid": "e57810b3-9f4f-477d-97f6-929f5dfca0e9", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "e49b8515-4e8f-4506-8b9a-5b3b0ff173fa" + } + ] }, "4": { "annotation": "dfam is problematic. Aves works for birds! That's why there's also a model free one - windowmasker - for comparison.", @@ -304,7 +315,13 @@ "type": "parameter_input", "uuid": "338f375e-10f9-4461-a938-44eca7c8f966", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ca457060-575c-4e27-8b60-7b146d5697fd" + } + ] }, "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 +348,13 @@ "type": "parameter_input", "uuid": "cb1c7f9f-1bca-43a8-a068-38b00bb37af6", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "7e0abb41-6311-4e67-8de6-6c0f9c1a4ea2" + } + ] }, "6": { "annotation": "", @@ -358,7 +381,13 @@ "type": "parameter_input", "uuid": "d1f53ba4-a094-44db-b4ce-2e534e0dab16", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "cd12ef9a-4ff5-4c29-ba21-0969f6da461c" + } + ] }, "7": { "annotation": "", @@ -385,7 +414,13 @@ "type": "data_input", "uuid": "00be13df-0a64-4ed0-87c7-3f97e9badf3e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9ed8a017-60e0-4f67-a25c-35a8600c087f" + } + ] }, "8": { "annotation": "", @@ -412,7 +447,13 @@ "type": "parameter_input", "uuid": "93f00f8e-2226-4ef0-aacf-f9ab84cca0d5", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "0a26ce63-af55-4912-a56f-5e04dd7ccd34" + } + ] }, "9": { "annotation": "", @@ -439,7 +480,13 @@ "type": "data_input", "uuid": "05aeefc3-a4b1-4788-9d1b-095621fa1cb3", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "563e0ac9-a7ae-4909-8226-1060c1e58857" + } + ] }, "10": { "annotation": "", @@ -466,7 +513,13 @@ "type": "parameter_input", "uuid": "0235e72e-1526-4fa4-8601-d4eb5e15d7b4", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "be386965-a5f1-4e47-be73-036e06455716" + } + ] }, "11": { "annotation": "", @@ -493,7 +546,13 @@ "type": "data_input", "uuid": "b10094d0-c733-4825-bbec-cb56e46239c4", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "e6fcaede-2d4c-4f25-8296-f269666404de" + } + ] }, "12": { "annotation": "", @@ -520,7 +579,13 @@ "type": "parameter_input", "uuid": "4abbe4ea-96bf-436b-9e8b-24b24700f47e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "2b922eee-d8e9-431a-9246-b9863d7ae121" + } + ] }, "13": { "annotation": "", @@ -547,7 +612,13 @@ "type": "data_input", "uuid": "0efaa539-d992-4816-bb1a-b1d704fef9d8", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f66306c9-eb4a-4fea-97a3-df3e08468965" + } + ] }, "14": { "annotation": "", @@ -574,7 +645,13 @@ "type": "parameter_input", "uuid": "5421a1f3-648c-4994-a4bb-9d9721fdc80b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "196c4974-e55b-4eb2-b9c7-2d1d4296b226" + } + ] }, "15": { "annotation": "", @@ -601,7 +678,13 @@ "type": "data_input", "uuid": "3864c5b2-08fd-40ee-9922-363960eeaf5e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "9b1bba31-20e1-40c6-827f-b67d71246b94" + } + ] }, "16": { "annotation": "", @@ -612,10 +695,10 @@ "inputs": [ { "description": "", - "name": "How many closely related species will you provide for sequence similarity mapping 1?" + "name": "Will you provide a collection of related species for sequence similarity mapping?" } ], - "label": "How many closely related species will you provide for sequence similarity mapping 1?", + "label": "Will you provide a collection of related species for sequence similarity mapping?", "name": "Input parameter", "outputs": [], "position": { @@ -623,72 +706,51 @@ "top": 2276.8321509886423 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"default\": false, \"parameter_type\": \"boolean\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "86415a69-308a-4f72-af00-54a93c22680a", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5633d6e2-a796-4866-9405-7e0e763ce941" + } + ] }, "17": { - "annotation": "Sequence mapping syntenic regions will be displayed.", + "annotation": "", "content_id": null, "errors": null, "id": 17, "input_connections": {}, "inputs": [ { - "description": "Sequence mapping syntenic regions will be displayed.", - "name": "One of two related species reference for mashmap paf for sequence similarity evaluation" + "description": "", + "name": "Collection of related species" } ], - "label": "One of two related species reference for mashmap paf for sequence similarity evaluation", - "name": "Input dataset", + "label": "Collection of related species", + "name": "Input dataset collection", "outputs": [], "position": { - "left": 1354.6945190429688, - "top": 2458.462257385254 + "left": 1347.447300798244, + "top": 2453.615455927678 }, "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": null}", + "tool_state": "{\"optional\": true, \"format\": [\"fasta\"], \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, - "type": "data_input", - "uuid": "f5aa5af1-4451-4f51-9904-ea5085a67863", + "type": "data_collection_input", + "uuid": "e8512a11-a011-4281-b50f-10af1339fd8c", "when": null, "workflow_outputs": [] }, "18": { - "annotation": "Sequence mapping syntenic regions will be displayed.", - "content_id": null, - "errors": null, - "id": 18, - "input_connections": {}, - "inputs": [ - { - "description": "Sequence mapping syntenic regions will be displayed.", - "name": "Two of two related species reference for mashmap paf for sequence similarity evaluation" - } - ], - "label": "Two of two related species reference for mashmap paf for sequence similarity evaluation", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1350, - "top": 2650 - }, - "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "809165da-162b-4354-a5a0-28d82dbe9cb6", - "when": null, - "workflow_outputs": [] - }, - "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 19, + "id": 18, "input_connections": { "input_file": { "id": 1, @@ -723,23 +785,18 @@ "when": null, "workflow_outputs": [] }, - "20": { + "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3", "errors": null, - "id": 20, + "id": 19, "input_connections": { "ref|input": { "id": 1, "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute sequence length", - "name": "ref" - } - ], + "inputs": [], "label": null, "name": "Compute sequence length", "outputs": [ @@ -767,11 +824,11 @@ "when": null, "workflow_outputs": [] }, - "21": { + "20": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/windowmasker/windowmasker_mkcounts/1.0", "errors": null, - "id": 21, + "id": 20, "input_connections": { "fasta_input": { "id": 1, @@ -818,11 +875,11 @@ "when": "$(inputs.when)", "workflow_outputs": [] }, - "22": { + "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0", "errors": null, - "id": 22, + "id": 21, "input_connections": { "fastq_input|fastq_input1": { "id": 2, @@ -833,19 +890,10 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], - "label": null, - "name": "Map with minimap2", - "outputs": [ + "inputs": [], + "label": null, + "name": "Map with minimap2", + "outputs": [ { "name": "alignment_output", "type": "bam" @@ -878,11 +926,11 @@ "when": null, "workflow_outputs": [] }, - "23": { + "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0", "errors": null, - "id": 23, + "id": 22, "input_connections": { "input_fasta": { "id": 1, @@ -957,11 +1005,11 @@ "when": null, "workflow_outputs": [] }, - "24": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0", "errors": null, - "id": 24, + "id": 23, "input_connections": { "in_file": { "id": 1, @@ -1008,9 +1056,9 @@ "when": null, "workflow_outputs": [] }, - "25": { + "24": { "annotation": "", - "id": 25, + "id": 24, "input_connections": { "CDS fasta if available": { "id": 7, @@ -1624,16 +1672,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1686,16 +1725,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1748,16 +1778,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1817,12 +1838,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Miniprot align", - "name": "db" - } - ], + "inputs": [], "label": null, "name": "Miniprot align", "outputs": [ @@ -2214,13 +2230,54 @@ "type": "subworkflow", "uuid": "4871e101-dadd-42a4-8523-0286d6c6a045", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "1:output", + "uuid": "86a66354-3131-44c8-9d32-fe033c534d33" + }, + { + "label": null, + "output_name": "2:output", + "uuid": "8bc050a6-17fc-4deb-929a-859a9f2ab5d9" + }, + { + "label": null, + "output_name": "3:output", + "uuid": "c6250f26-3208-4df9-9e13-abac28c738ab" + }, + { + "label": null, + "output_name": "4:output", + "uuid": "6d4a15eb-5729-4ade-ab31-66e82adf5fd5" + }, + { + "label": null, + "output_name": "5:output", + "uuid": "0fca515d-4d36-4102-a3bd-e810ccca20f4" + }, + { + "label": null, + "output_name": "6:output", + "uuid": "38fdd8d8-9476-4fba-b0b0-1c41a36b6ec4" + }, + { + "label": null, + "output_name": "7:output", + "uuid": "01149453-4bbe-4c21-803c-8cf15035c2ff" + }, + { + "label": null, + "output_name": 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"assemblies_0|track_groups_0|data_tracks_0|data_format|useuri|annotation": { - "id": 23, + "id": 22, "output_name": "output_gff" }, "assemblies_0|track_groups_0|data_tracks_1|data_format|useuri|annotation": { - "id": 40, + "id": 37, "output_name": "count" }, "assemblies_0|track_groups_0|data_tracks_2|data_format|useuri|annotation": { - "id": 36, + "id": 33, "output_name": "count" }, "assemblies_0|track_groups_0|data_tracks_3|data_format|useuri|annotation": { - "id": 32, + "id": 29, "output_name": "outFileName" }, "assemblies_0|track_groups_1|data_tracks_0|data_format|useuri|annotation": { - "id": 25, + "id": 24, "output_name": "cds bed" }, "assemblies_0|track_groups_1|data_tracks_1|data_format|useuri|annotation": { - "id": 25, + "id": 24, "output_name": "genes bed" }, "assemblies_0|track_groups_1|data_tracks_2|data_format|useuri|annotation": { - "id": 25, + "id": 24, "output_name": "rna bed" }, "assemblies_0|track_groups_1|data_tracks_3|data_format|useuri|annotation": { - "id": 25, + "id": 24, "output_name": "protein gff" }, "assemblies_0|track_groups_1|data_tracks_4|data_format|useuri|annotation": { - "id": 24, + "id": 23, "output_name": "default" }, "assemblies_0|track_groups_1|data_tracks_5|data_format|pafuseuri|annotation": { @@ -5465,7 +4411,7 @@ "output_name": "output" }, "assemblies_0|track_groups_1|data_tracks_5|data_format|useuri|annotation": { - "id": 33, + "id": 30, "output_name": "multispecies 1k 93 mashmap" }, "assemblies_0|track_groups_1|data_tracks_6|data_format|pafuseuri|annotation": { @@ -5473,7 +4419,7 @@ "output_name": "output" }, "assemblies_0|track_groups_1|data_tracks_6|data_format|useuri|annotation": { - "id": 33, + "id": 30, "output_name": "multispecies 5k 85 mashmap" }, "assemblies_0|track_groups_1|data_tracks_7|data_format|pafuseuri|annotation": { @@ -5481,40 +4427,36 @@ "output_name": "output" }, "assemblies_0|track_groups_1|data_tracks_7|data_format|useuri|annotation": { - "id": 33, + "id": 30, "output_name": "multispecies 2k 95 mashmap" }, "assemblies_0|track_groups_2|data_tracks_0|data_format|pafuseuri|annotation": { - "id": 26, + "id": 25, "output_name": "data_param" }, "assemblies_0|track_groups_2|data_tracks_0|data_format|useuri|annotation": { - "id": 33, + "id": 30, "output_name": "Independent 1k99 mashmap paf" }, "assemblies_0|track_groups_2|data_tracks_1|data_format|pafuseuri|annotation": { - "id": 26, + "id": 25, "output_name": "data_param" }, "assemblies_0|track_groups_2|data_tracks_1|data_format|useuri|annotation": { - "id": 33, + "id": 30, "output_name": "independent 10k97 mashmap" }, "assemblies_0|track_groups_2|data_tracks_2|data_format|pafuseuri|annotation": { - "id": 26, + "id": 25, "output_name": "data_param" }, "assemblies_0|track_groups_2|data_tracks_2|data_format|useuri|annotation": { - "id": 33, + "id": 30, "output_name": "independent 5k 98 mashmap" - }, - "when": { - "id": 28, - "output_name": "output_param_boolean" } }, "inputs": [], - "label": "JBrowse2 for Export 1 species ", + "label": "JBrowse2 for Export", "name": "JBrowse2", "outputs": [ { @@ -5523,8 +4465,8 @@ } ], "position": { - "left": 5640.202348152071, - "top": 580.9475387343853 + "left": 4347.649607707523, + "top": 817.9076836626685 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -5545,18 +4487,18 @@ "tool_state": "{\"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Assembly properties\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gff\", \"__current_case__\": 2, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"jbstyle\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": 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"7937d50b-6226-4c7d-adf9-b463f3ffdf1b", + "uuid": "7cc58d30-31b2-4fe9-aae0-d73b75ad321c", "version": 5 } \ No newline at end of file From fe3dbb750c1ff817ee3936473dc200ffad325842 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 14 Aug 2024 10:33:05 -0400 Subject: [PATCH 5/8] Create readme for workfow usage --- .../Curation-TreeValGal/README.md | 57 ++++++++++++++++++ .../Curation-TreeValGal/img/JBrowse2.png | Bin 0 -> 307767 bytes 2 files changed, 57 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/README.md create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/img/JBrowse2.png diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md b/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md new file mode 100644 index 000000000..eca70cf2a --- /dev/null +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md @@ -0,0 +1,57 @@ +# TreeValGal workflow + +Workflow to generate pre-curation files and Jbrowse2 instance. + +## Inputs + +### Mandatory + +- `Genome assembly to report on` Single halotypes or concatenated haplotypes (If concatenating the haplotypes, windowmasker could fail. In that case, try re-runing with the option `Run windowmasker model-free repeats?` set as `No`) +- `fastqsanger pacbio sequence reads for coverage bigwig track` Concatenated PacBio reads + +### Optional + +- `Window size for bed to bigwig` Set the window size to generate the histogram tracks (coverage, gaps...) +- `dfam taxon for repeatmasker` Default is vertebrates. A more accurate taxon means more accurate repeat recognition +- `telomere repeat to suit species` Default : CCCTAA. Seems to work for the treeval test data or for vertebrates . + +#### Annotations + +You have the option to provide fasta files for different features. they will be aligned against the assembly and shown in Jbrowse2. + +CDS: +- Set `Will you provide a CDS fasta for annotation?` as `yes` and provide a Fasta in `CDS fasta input` + +Genes +- Set `Will you provide a genes fasta for annotation?` as `yes` and provide a Fasta in `genes fasta input` + +RNA +- Set `Will you provide a rna fasta for annotation?` as `yes` and provide a Fasta in `rna fasta input` + +Proteins +- Set `Will you provide a protein (AA) fasta for annotation?` as `yes` and provide a Fasta in `AA fasta input` + + +#### Sequence similarity Mapping + +You have the option to provide fasta files for a reference or a closely related species (Can also be used to provide the other haplotype of your asembly). These files will be used to produce synteny dotplots and displayed in Jbrowse. + +Independent Reference Genome. The dotplot produced will be filtered with a higher sequence identity: 97%, 98%, and 99%. Suitable for same species genome. +- Set `Will you supply an independent reference genome fasta for sequence similarity "self comparison" mapping? This generates paf tracks viewable as contig dotplots.` to `yes` and provide a fasta of the genome in `Independent haplotype or reference genome if available` + +Closely related species. The dotplot produced will be filtered with a lower sequence identity: 85%, 93%, and 95%. Suitable for same species genome. +- Set `Will you provide a collection of related species for sequence similarity mapping?` to `yes` and provide a **collection** of fasta of one or more related genomes in `Collection of related species` + + +## Outputs + +- A Jbrowse2 instance (on for viewing, in `html` the other for export or download in `zip`) +- Files corresponding to the tracks in Jbrowse2 + + +## Display tracks in Jbrowse2 + +- Add a track: click on the menu icon (`1` in the Jbrowse2 screenshot below) and click on `Open Track Selector`. Select or deselect the desired tracks +- Add dotplote: clid `Add` on the top bar and select `Dotplot View`. Then chose the species to display and click `Launch` (several dotplots can be displayed that way). To display a different identity threshold between the to selected species. Click on the menu icon in the Dotplot Window (`2` in the Jbrowse2 screenshot below) and click on `Open Track Selector`. 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diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga index 807dc5e66..a2fd66043 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_optionalwindowmasker.ga @@ -3,38 +3,36 @@ "annotation": "", "comments": [ { - "child_comments": [ - 1 - ], - "color": "black", + "color": "red", "data": { - "title": "" + "size": 2, + "text": "Notes on inputs for mashmap pafs:

mashmap settings varied here are % identity and match length - like steps 27-29 to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.

At this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.

Need curator eyeballs and feedback for that.

Two different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available

The 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives.  

There are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?

Need to use the track menu for the main reference vs external reference/haplotype tracks - off by default.

Again there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.
" }, - "id": 0, + "id": 2, "position": [ - 10, - 40 + 0, + 257.03358562228095 ], "size": [ - 1430, - 140 + 1020, + 1030 ], - "type": "frame" + "type": "text" }, { - "color": "red", + "color": "blue", "data": { "size": 2, - "text": "Notes on inputs for mashmap pafs:

mashmap settings varied here are % identity and match length - like steps 27-29 to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.

At this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.

Need curator eyeballs and feedback for that.

Two different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available

The 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives.  

There are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?

Need to use the track menu for the main reference vs external reference/haplotype tracks - off by default.

Again there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.
" + "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": 2, + "id": 4, "position": [ - 0, - 257.03358562228095 + 20, + 1537.033585622281 ], "size": [ - 1020, - 1030 + 700, + 870 ], "type": "text" }, @@ -56,28 +54,30 @@ "type": "text" }, { + "child_comments": [ + 1 + ], "color": "black", "data": { - "size": 2, - "text": "Technical discussion document under development here:
https://docs.google.com/document/d/1YbQZsFC8oDJIGos5yLFbApumpK4yIz02qfwYEypDfI8" + "title": "" }, - "id": 1, + "id": 0, "position": [ - 20, - 80 + 10, + 40 ], "size": [ - 1380, - 80 + 1430, + 140 ], - "type": "text" + "type": "frame" }, { "child_steps": [ + 14, 25, 30, 15, - 14, 16, 17 ], @@ -96,17 +96,34 @@ ], "type": "frame" }, + { + "color": "black", + "data": { + "size": 2, + "text": "Technical discussion document under development here:
https://docs.google.com/document/d/1YbQZsFC8oDJIGos5yLFbApumpK4yIz02qfwYEypDfI8" + }, + "id": 1, + "position": [ + 20, + 80 + ], + "size": [ + 1380, + 80 + ], + "type": "text" + }, { "child_steps": [ 24, - 6, 12, 7, 10, 8, 11, 13, - 9 + 9, + 6 ], "color": "turquoise", "data": { @@ -122,23 +139,6 @@ 900 ], "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" } ], "creator": [ @@ -195,13 +195,7 @@ "type": "parameter_input", "uuid": "35d60a1d-85f2-4c8b-af5e-2ac2e8db6ef3", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "22941942-7c0b-44f2-845d-94089066ff4f" - } - ] + "workflow_outputs": [] }, "1": { "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", @@ -282,13 +276,7 @@ "type": "parameter_input", "uuid": "e57810b3-9f4f-477d-97f6-929f5dfca0e9", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e49b8515-4e8f-4506-8b9a-5b3b0ff173fa" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "dfam is problematic. Aves works for birds! That's why there's also a model free one - windowmasker - for comparison.", @@ -315,13 +303,7 @@ "type": "parameter_input", "uuid": "338f375e-10f9-4461-a938-44eca7c8f966", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "ca457060-575c-4e27-8b60-7b146d5697fd" - } - ] + "workflow_outputs": [] }, "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....", @@ -348,13 +330,7 @@ "type": "parameter_input", "uuid": "cb1c7f9f-1bca-43a8-a068-38b00bb37af6", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "7e0abb41-6311-4e67-8de6-6c0f9c1a4ea2" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "", @@ -381,13 +357,7 @@ "type": "parameter_input", "uuid": "d1f53ba4-a094-44db-b4ce-2e534e0dab16", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "cd12ef9a-4ff5-4c29-ba21-0969f6da461c" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -414,13 +384,7 @@ "type": "data_input", "uuid": "00be13df-0a64-4ed0-87c7-3f97e9badf3e", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "9ed8a017-60e0-4f67-a25c-35a8600c087f" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "", @@ -447,13 +411,7 @@ "type": "parameter_input", "uuid": "93f00f8e-2226-4ef0-aacf-f9ab84cca0d5", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "0a26ce63-af55-4912-a56f-5e04dd7ccd34" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -464,10 +422,10 @@ "inputs": [ { "description": "", - "name": "genes fasta in" + "name": "genes fasta input" } ], - "label": "genes fasta in", + "label": "genes fasta input", "name": "Input dataset", "outputs": [], "position": { @@ -480,13 +438,7 @@ "type": "data_input", "uuid": "05aeefc3-a4b1-4788-9d1b-095621fa1cb3", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "563e0ac9-a7ae-4909-8226-1060c1e58857" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "", @@ -513,13 +465,7 @@ "type": "parameter_input", "uuid": "0235e72e-1526-4fa4-8601-d4eb5e15d7b4", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "be386965-a5f1-4e47-be73-036e06455716" - } - ] + "workflow_outputs": [] }, "11": { "annotation": "", @@ -530,10 +476,10 @@ "inputs": [ { "description": "", - "name": "rna fasta in" + "name": "rna fasta input" } ], - "label": "rna fasta in", + "label": "rna fasta input", "name": "Input dataset", "outputs": [], "position": { @@ -546,13 +492,7 @@ "type": "data_input", "uuid": "b10094d0-c733-4825-bbec-cb56e46239c4", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e6fcaede-2d4c-4f25-8296-f269666404de" - } - ] + "workflow_outputs": [] }, "12": { "annotation": "", @@ -579,13 +519,7 @@ "type": "parameter_input", "uuid": "4abbe4ea-96bf-436b-9e8b-24b24700f47e", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2b922eee-d8e9-431a-9246-b9863d7ae121" - } - ] + "workflow_outputs": [] }, "13": { "annotation": "", @@ -596,15 +530,15 @@ "inputs": [ { "description": "", - "name": "AA fasta in" + "name": "AA fasta input" } ], - "label": "AA fasta in", + "label": "AA fasta input", "name": "Input dataset", "outputs": [], "position": { "left": 1350, - "top": 1730 + "top": 1730.40625 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": null}", @@ -612,13 +546,7 @@ "type": "data_input", "uuid": "0efaa539-d992-4816-bb1a-b1d704fef9d8", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "f66306c9-eb4a-4fea-97a3-df3e08468965" - } - ] + "workflow_outputs": [] }, "14": { "annotation": "", @@ -645,13 +573,7 @@ "type": "parameter_input", "uuid": "5421a1f3-648c-4994-a4bb-9d9721fdc80b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "196c4974-e55b-4eb2-b9c7-2d1d4296b226" - } - ] + "workflow_outputs": [] }, "15": { "annotation": "", @@ -678,13 +600,7 @@ "type": "data_input", "uuid": "3864c5b2-08fd-40ee-9922-363960eeaf5e", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": 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workflows/VGP-assembly-v2/Curation-TreeValGal/TreeValGal_TwoHaps.ga diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/Dimer_density_SV_and_coverage.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/Dimer_density_SV_and_coverage.ga new file mode 100644 index 000000000..eac8da3ff --- /dev/null +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/Dimer_density_SV_and_coverage.ga @@ -0,0 +1,4298 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Annotate dimer density and explore haplotype coverage differences. \nIdeas from Arang Rhie's talk to Galaxy VGP and some code at https://github.com/arangrhie/T2T-Polish/tree/master\n\nTop section generates dimer density bigwig and outlier bed tracks.\n\nSecond section adds any contigs in h2 missing from h1 so there's a synthetic reference that allows each haplotype track to show every contig's contents - even when the other haplotype has nothing there.\n\nThird section force maps all reads to each hap in turn then compares them 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Some cheating to remove all uninformative non-shared contigs that break everything, and to ensure the same header for both hap bams for deeptools.\n\nFourth section maps each hap independently and both together to make coverage bigwigs to compare", + "comments": [ + { + "child_steps": [ + 0, + 1, + 2, + 7, + 10, + 15, + 18, + 28, + 29, + 30, + 31 + ], + "color": "black", + "data": { + "title": "Dimer density and outliers for each haplotype using a subworkflow.." + }, + "id": 0, + "position": [ + 520, + 0 + ], + "size": [ + 1490, + 710 + ], + "type": "frame" + }, + { + "child_steps": [ + 8, + 11, + 19, + 32, + 35, + 40 + ], + "color": "black", + "data": { + "title": "Add h2 unique contigs to hap1 to create a combined reference genome so all unique and shared contig names are in the dropdown. 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One is displayed by default. Comparisons are easy because the other one's tracks are on the menu.\nTakes a collection of closely related species.\nThat part needs the fasta name attached to the contig names for PAF references because JBrowse2 cannot tell which PAF reference a hit in the second of the pair of matches came from :(", + "comments": [ + { + "color": "black", + "data": { + "text": "# Some random notes:\n\nUses Delphine's method for optional inputs.\n\nThe second JBrowse2 is a copy of the first but with the advanced option to write as a zip. \nTo update, only edit the first one. When done, copy it, set the output zip advanced option, then set the label and output name of the copy to include zip\n\nMashmap 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\n\nJBrowse 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\n\nThe 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.\n\nMashmap paf tracks are prepared for two comparison species references, and for an independent haplotype or refererence genome.\n\n\n# Choosing inputs for mashmap pafs:\n\n\nmashmap settings varied here are % identity and match length to cover a range since the evolutionary distances depend on the curator's choice of comparison organisms for some of them.\n\nAt this point, \"tuning\" for dotplots has aimed for a \"reasonable\" number of paf rows. Too many gets slow and dark. Too few and the patterns might be too faint to see clearly or when zoomed.\n\nNeed curator eyeballs and feedback for that.\n\nTwo different mashmap uses - for the selected related species sequence similarity patterns, and for independent haplotype or reference, if available\n\nThe 2 optional related species sequence similarity will depend on evolutionary distance. Discernable diagonal segments of mashmap hits become less likely - although they are seen with close relatives. \n\nThere are two mashmaps to give some spread but more could be added. Nice thing about TreeValGal workflow is that adding tracks is not at all difficult. Adding a wider range of parameters makes sense - particularly once the curators start looking at what they are getting?\n\nNeed to use the track menu for the main reference vs external reference/haplotype tracks - off by default.\n\nAgain there's a spread of 3 mashmap settings to get different numbers of hits - 20-40k seems to be a sweet spot for plots - more gets slower and clumsy but could be important if high resolution needed.\n\n# Annotation Fasta inputs:\n\nCurrently has 4 optional NCBI annotation tracks fasta - genes, cds, rna and one with the proteins - these are mapped with a specialised AA to nucleotide mapper so must be encoded as amino acids. Can be obtained with the appropriate species NCBI taxonId, as the taxon in the Galaxy NCBI gene annotation download tool.\n\n" + }, + "id": 2, + "position": [ + 0, + 1860 + ], + "size": [ + 1200, + 740 + ], + "type": "markdown" + }, + { + "child_steps": [ + 23, + 24, + 27, + 28, + 29, + 21, + 22, + 26 + ], + "color": "black", + "data": { + "title": "Basic reporting - repeats, telomeres, coverage and gaps" + }, + "id": 0, + "position": [ + 290, + 0 + ], + "size": [ + 1920, + 1060 + ], + "type": "frame" + }, + { + "child_steps": [ + 30, + 16, + 14, + 15, + 17, + 13, + 12, + 11, + 18 + ], + "color": "turquoise", + "data": { + "title": "Annotation fasta inputs" + }, + "id": 1, + "position": [ + 1280, + 1100 + ], + "size": [ + 950, + 900 + ], + "type": "frame" + }, + { + "child_steps": [ + 25, + 19, + 20 + ], + "color": "red", + "data": { + "title": "Mashmap paf tracks subworkflow" + }, + "id": 3, + "position": [ + 1280, + 2100 + ], + "size": [ + 960, + 1020 + ], + "type": "frame" + } + ], + "creator": [ + { + "class": "Person", + "identifier": "", + "name": "Ross Lazarus" + }, + { + "class": "Person", + "identifier": "anna.syme@gmail.com", + "name": "Anna Syme" + }, + { + "class": "Person", + "identifier": "nadibraj@gmail.com", + "name": "Nadolina Brajuka" + }, + { + "class": "Person", + "identifier": "lariviere.delphine@gmail.com", + "name": "Delphine Lariviere" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "TreeValGalAugTwoHaps", + "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": "For coverage. 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", + "name": "fastqsanger pacbio sequence reads for coverage bigwig track" + } + ], + "label": "fastqsanger pacbio sequence reads for coverage bigwig track", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 40, + "top": 260 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "0e1b8776-4c7b-46fa-adbd-5cdb50f24e41", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "name": "Haplotype1 same names" + } + ], + "label": "Haplotype1 same names", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 40, + "top": 400 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "42643151-c155-4745-96d5-e39a0eef1937", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "hap1name" + } + ], + "label": "hap1name", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40, + "top": 520 + }, + "tool_id": null, + "tool_state": "{\"default\": \"H1\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "6eb84f2d-8c87-4676-9b78-f58537360f7e", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1c1997b5-044d-48f5-bd97-c36af9a41e09" + } + ] + }, + "3": { + "annotation": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "This will be the sequence, divided into individual fasta contigs, on which tracks are arranged and displayed.", + "name": "Haplotype2 same names" + } + ], + "label": "Haplotype2 same names", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 40, + "top": 620 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "078c7cdf-af94-4aaf-ba96-a380d0237972", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "hap2name" + } + ], + "label": "hap2name", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40, + "top": 740 + }, + "tool_id": null, + "tool_state": "{\"default\": \"H2\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "37d30f59-320f-47ce-a01c-1117278237dc", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1b323fb0-1b55-463a-9939-d27f617d090f" + } + ] + }, + "5": { + "annotation": "TTAGGG or CCCTAA for the treeval test data or for vertebrates seems to work. 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Unsmoothed, the wiggles are more useful over small distances, but zoomed out, they become clumped so are not shown.", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "The wiggles are all smoothed by measuring over a window with default of 50 bases. 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Not sure if minimap2 mapping preset is right?

.


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