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Updating workflows/repeatmasking from 0.1 to 0.2
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planemo-autoupdate committed Nov 10, 2023
1 parent 2d39414 commit 00cb1f8
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5 changes: 5 additions & 0 deletions workflows/repeatmasking/CHANGELOG.md
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# Changelog

## [0.2] 2023-11-10

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.5+galaxy0`

## [0.1]

Initial version of the RepeatMasking workflow for genomic sequencing data.
49 changes: 28 additions & 21 deletions workflows/repeatmasking/RepeatMasking-Workflow.ga
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"annotation": "",
"format-version": "0.1",
"license": "MIT",
"release": "0.1",
"release": "0.2",
"name": "Repeat masking with RepeatModeler and RepeatMasker",
"creator": [
{
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"input_connections": {},
"inputs": [
{
"description": "Apply repeat masking to this fasta file",
"description": "",
"name": "input"
}
],
"label": "input",
"name": "Input dataset",
"outputs": [],
"position": {
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"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null}",
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},
"1": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.5+galaxy0",
"errors": null,
"id": 1,
"input_connections": {
Expand All @@ -65,30 +65,32 @@
}
],
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"tool_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.5+galaxy0",
"tool_shed_repository": {
"changeset_revision": "8661b2607b7e",
"changeset_revision": "fbe22cb3c869",
"name": "repeatmodeler",
"owner": "csbl",
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"tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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"label": "RepeatModeler consensus sequences",
"output_name": "sequences",
"label": "RepeatModeler consensus sequences"
"uuid": "b67db590-2881-464a-b176-2b513a3c214f"
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{
"label": "RepeatModeler seeds alignments",
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"label": "RepeatModeler seeds alignments"
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},
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"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
Expand All @@ -140,31 +142,36 @@
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
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"tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"is_only\": false, \"is_clip\": false, \"no_is\": false, \"rodspec\": false, \"primspec\": false, \"nolow\": false, \"noint\": false, \"norna\": false, \"alu\": false, \"div\": false, \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": false, \"nocut\": false, \"xout\": false, \"keep_alignments\": false, \"invert_alignments\": false, \"poly\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"excln\": true, \"gff\": true, \"input_fasta\": null, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"no\", \"__current_case__\": 1, \"species_name\": \"\"}}, \"xsmall\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"is_only\": false, \"is_clip\": false, \"no_is\": false, \"rodspec\": false, \"primspec\": false, \"nolow\": false, \"noint\": false, \"norna\": false, \"alu\": false, \"div\": false, \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": false, \"nocut\": false, \"xout\": false, \"keep_alignments\": false, \"invert_alignments\": false, \"poly\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"excln\": true, \"gff\": true, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"no\", \"__current_case__\": 1, \"species_name\": \"\"}}, \"xsmall\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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"label": "RepeatMasker masked genome",
"output_name": "output_masked_genome",
"label": "RepeatMasker masked genome"
"uuid": "38edc09f-003c-413f-9e64-3c2f63d08033"
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{
"label": "RepeatMasker output log",
"output_name": "output_log",
"label": "RepeatMasker output log"
"uuid": "7bc4dd19-3197-4b9f-ad8c-906fd1f3fbdf"
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{
"label": "RepeatMasker repeat statistics",
"output_name": "output_table",
"label": "RepeatMasker repeat statistics"
"uuid": "a7a5fd7b-00f3-41de-abbd-a73e99b01c8e"
},
{
"label": "RepeatMasker repeat catalog",
"output_name": "output_repeat_catalog",
"label": "RepeatMasker repeat catalog"
"uuid": "3fc59d45-9343-41ba-aaec-9fa866d15f4b"
},
{
"label": "RepeatMasker repeat annotation",
"output_name": "output_gff",
"label": "RepeatMasker repeat annotation"
"uuid": "4b870934-1ccf-4ea7-a40c-54349c4042f0"
}
]
}
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