From 5d3d148af30072bc18babb138ea144b9072efd9e Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Thu, 1 Aug 2024 07:19:41 -0400 Subject: [PATCH] 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": "4871e101-dadd-42a4-8523-0286d6c6a045", "when": null, - "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" - } - ] + "workflow_outputs": [] }, "26": { "annotation": "", @@ -5219,8 +5082,8 @@ } ], "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\"}}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"jbstyle\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 3, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 6, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 7, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"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_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\": \"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": "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\": {\"show_labels\": false, \"show_descriptions\": false, \"display\": \"LinearBasicDisplay\"}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 3, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 6, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 7, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"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__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"paf\", \"__current_case__\": 8, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"pafuseuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"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_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\": \"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": "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