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Updating workflows/repeatmasking from 0.1 to 0.2 #278

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Updating workflows/repeatmasking from 0.1 to 0.2 #278

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5 changes: 5 additions & 0 deletions workflows/repeatmasking/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.2] 2024-09-24

### 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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Expand Up @@ -3,7 +3,7 @@
"annotation": "",
"format-version": "0.1",
"license": "MIT",
"release": "0.1",
"release": "0.2",
"name": "Repeat masking with RepeatModeler and RepeatMasker",
"creator": [
{
Expand All @@ -21,16 +21,16 @@
"input_connections": {},
"inputs": [
{
"description": "Apply repeat masking to this fasta file",
"description": "",
"name": "input"
}
],
"label": "input",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 10,
"top": 10
"left": 0,
"top": 0
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null}",
Expand All @@ -42,7 +42,7 @@
},
"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 @@
}
],
"position": {
"left": 230,
"top": 10
"left": 220,
"top": 0
},
"post_job_actions": {},
"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": "4a172d211285",
"name": "repeatmodeler",
"owner": "csbl",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0.4+galaxy1",
"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}",
"tool_version": "2.0.5+galaxy0",
"type": "tool",
"uuid": "9312ba36-4275-4d40-8ba6-95eea1b23b11",
"when": null,
"workflow_outputs": [
{
"label": "RepeatModeler consensus sequences",
"output_name": "sequences",
"label": "RepeatModeler consensus sequences"
"uuid": "c99eb0e7-6470-4f85-aaa1-29abc7ec49b7"
},
{
"label": "RepeatModeler seeds alignments",
"output_name": "seeds",
"label": "RepeatModeler seeds alignments"
"uuid": "e2223ce1-9fcd-4a03-abad-9854417143f2"
}
]
},
Expand Down Expand Up @@ -129,8 +131,8 @@
}
],
"position": {
"left": 450,
"top": 10
"left": 440,
"top": 0
},
"post_job_actions": {},
"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"
},
"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}",
"tool_version": "4.1.5+galaxy0",
"type": "tool",
"uuid": "e6c8e6a1-efe8-4291-b12b-5fdb3795b6ca",
"when": null,
"workflow_outputs": [
{
"label": "RepeatMasker masked genome",
"output_name": "output_masked_genome",
"label": "RepeatMasker masked genome"
"uuid": "2e143b9b-038d-45f0-b3bb-232e484b3f42"
},
{
"label": "RepeatMasker output log",
"output_name": "output_log",
"label": "RepeatMasker output log"
"uuid": "0bea14a2-4d6c-4ffc-878d-f9c5a441ea94"
},
{
"label": "RepeatMasker repeat statistics",
"output_name": "output_table",
"label": "RepeatMasker repeat statistics"
"uuid": "81b6ded1-f317-46e2-93b5-69a5a529f4fd"
},
{
"label": "RepeatMasker repeat catalog",
"output_name": "output_repeat_catalog",
"label": "RepeatMasker repeat catalog"
"uuid": "d591f44a-b608-4118-a7f4-cb692d2cce4e"
},
{
"label": "RepeatMasker repeat annotation",
"output_name": "output_gff",
"label": "RepeatMasker repeat annotation"
"uuid": "6c469577-3f6a-4d46-9a3e-8e7459038cb0"
}
]
}
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