Skip to content

Commit

Permalink
Updating workflows/repeatmasking from 0.1 to 0.2
Browse files Browse the repository at this point in the history
  • Loading branch information
planemo-autoupdate committed Sep 23, 2024
1 parent 7907910 commit 38da81e
Show file tree
Hide file tree
Showing 2 changed files with 33 additions and 21 deletions.
5 changes: 5 additions & 0 deletions workflows/repeatmasking/CHANGELOG.md
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.2] 2024-09-23

### 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
View file
Original file line number Diff line number Diff line change
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": "1d2db550-0e41-4b42-9270-ba21eea9566b"
},
{
"label": "RepeatModeler seeds alignments",
"output_name": "seeds",
"label": "RepeatModeler seeds alignments"
"uuid": "7a254309-3ff4-4922-82d0-ffa7fa925387"
}
]
},
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": "bc4428b3-83ed-46b8-96cb-11a230ef945b"
},
{
"label": "RepeatMasker output log",
"output_name": "output_log",
"label": "RepeatMasker output log"
"uuid": "75564367-142c-4fac-8de5-f3c1ca53a65e"
},
{
"label": "RepeatMasker repeat statistics",
"output_name": "output_table",
"label": "RepeatMasker repeat statistics"
"uuid": "c19596d4-f663-4a21-947e-2c26d3be54c7"
},
{
"label": "RepeatMasker repeat catalog",
"output_name": "output_repeat_catalog",
"label": "RepeatMasker repeat catalog"
"uuid": "6911e731-2b63-4fd1-88db-6354bc64bb50"
},
{
"label": "RepeatMasker repeat annotation",
"output_name": "output_gff",
"label": "RepeatMasker repeat annotation"
"uuid": "7839f902-8e16-4dc0-a836-c068222afd2f"
}
]
}
Expand Down

0 comments on commit 38da81e

Please sign in to comment.