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Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 1.3 to 1.4 #1146

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Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 1.3 to 1.4 #1146

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84 changes: 69 additions & 15 deletions workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga
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Expand Up @@ -506,7 +506,12 @@
"output_name": "integer_param"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Map parameter value",
"name": "input_param_type"
}
],
"label": null,
"name": "Map parameter value",
"outputs": [
Expand Down Expand Up @@ -901,7 +906,7 @@
}
},
"tags": [],
"uuid": "33defbd1-e74b-4902-8d84-abe335908dad"
"uuid": "48372b98-5e8e-4a3e-923b-a2bda608cc75"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -930,7 +935,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool NCBI FCS GX",
"name": "mode"
},
{
"description": "runtime parameter for tool NCBI FCS GX",
"name": "mode"
}
],
"label": null,
"name": "NCBI FCS GX",
"outputs": [
Expand Down Expand Up @@ -985,7 +999,12 @@
"output_name": "clean_fasta"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool NCBI BLAST+ dustmasker",
"name": "db_opts"
}
],
"label": "soft-masking ",
"name": "NCBI BLAST+ dustmasker",
"outputs": [
Expand Down Expand Up @@ -1087,7 +1106,20 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool NCBI FCS GX",
"name": "mode"
},
{
"description": "runtime parameter for tool NCBI FCS GX",
"name": "mode"
},
{
"description": "runtime parameter for tool NCBI FCS GX",
"name": "mode"
}
],
"label": null,
"name": "NCBI FCS GX",
"outputs": [
Expand Down Expand Up @@ -1214,7 +1246,16 @@
"output_name": "outfile"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool NCBI FCS GX",
"name": "mode"
},
{
"description": "runtime parameter for tool NCBI FCS GX",
"name": "mode"
}
],
"label": null,
"name": "NCBI FCS GX",
"outputs": [
Expand Down Expand Up @@ -1368,7 +1409,7 @@
},
"18": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2",
"errors": null,
"id": 18,
"input_connections": {
Expand All @@ -1381,7 +1422,20 @@
"output_name": "mito_scaff_names"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
},
{
"description": "runtime parameter for tool gfastats",
"name": "target_condition"
},
{
"description": "runtime parameter for tool gfastats",
"name": "target_condition"
}
],
"label": "removing scaffolds ",
"name": "gfastats",
"outputs": [
Expand All @@ -1403,16 +1457,16 @@
"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2",
"tool_shed_repository": {
"changeset_revision": "0fe699ced54f",
"changeset_revision": "10dc0f5a82e2",
"name": "gfastats",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"sort\": \"\", \"remove_terminal_gaps\": true, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"RuntimeValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"sort\": \"\", \"remove_terminal_gaps\": true, \"homopolymer_compress\": null, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"RuntimeValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "1.3.11+galaxy1",
"tool_version": "1.3.11+galaxy2",
"type": "tool",
"uuid": "5113c945-c811-4cbc-81ac-20d1d80e97ed",
"when": null,
Expand All @@ -1428,7 +1482,7 @@
"tags": [
"VGP_curated"
],
"uuid": "afdeece1-bd77-47b6-be22-c284135bf80c",
"uuid": "2a7adfc0-3bbf-4c61-8226-d8180445331d",
"version": 1,
"release": "1.3"
}
"release": "1.4"
}
5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md
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@@ -1,5 +1,10 @@
# Changelog

## [1.4] - 2026-03-16

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2`

## [1.3] - 2026-01-26

### Automatic update
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