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Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 1.2 to 1.3
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‎workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga‎

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}
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],
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"format-version": "0.1",
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"release": "1.2",
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"license": "BSD-3-Clause",
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"name": "Assembly decontamination VGP9 ",
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"report": {
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"tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"ACTION_TRIM\", \"replace_pattern\": \"FIX\", \"sed_options\": \"\"}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
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"output_name": "clean_fasta"
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"name": "db_opts"
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"label": "soft-masking ",
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"output_name": "output"
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"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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"type": "tool",
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"name": "NCBI FCS GX",
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"output_name": "mito_scaff_names"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool gfastats",
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"name": "mode_condition"
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},
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{
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"description": "runtime parameter for tool gfastats",
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"name": "target_condition"
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{
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"description": "runtime parameter for tool gfastats",
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"name": "target_condition"
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],
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"label": "removing scaffolds ",
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"name": "gfastats",
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"outputs": [
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"tags": [
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"VGP_curated"
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],
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"uuid": "f95bc090-e929-4cec-be3b-d23190f3e784",
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"version": 10
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}
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"uuid": "428204f0-5c30-4144-9f46-06739c1c0c55",
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"version": 1,
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"release": "1.3"
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‎workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md‎

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# Changelog
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## [1.3] - 2026-01-19
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### Automatic update
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- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3`
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- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3`
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- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3`
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## [1.2] - 2025-10-20
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### Changes

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