IWC Bad State Forensics

Forensic analysis of invalid/orphaned parameters found in IWC workflow tool_state dictionaries. Each entry documents what’s wrong, why, and how it got there.

See TRACKING_INVALID_WORKFLOW_PARAMETERS.md for methodology.

1. pe-artic-variation.ga / multiqc / saveLog

Parameter history in tool XML

• Added: Present since at least multiqc 1.8 wrapper. Boolean param controlling whether to save the MultiQC log file as an output.
• Removed: tools-iuc commit 24152e242 (2024-08-25, Bjoern Gruening) — multiqc wrapper updated from 1.23 → 1.24.1. Commit message: “remove the log option, seems to not be supported in the new release”
• Last valid wrapper version: 1.23 (@GALAXY_VERSION@ suffix varies)

Parameter history in workflow

What happened

1. saveLog was a valid boolean parameter in multiqc wrappers through version 1.23.
2. The underlying MultiQC software dropped log-saving support. Wrapper 1.24.1 removed saveLog from the XML.
3. The IWC workflow stayed on multiqc 1.11+galaxy1 (which still had saveLog) through 2024.
4. On 2025-03-17, planemo-autoupdate bot bumped the workflow from 1.11+galaxy1 to 1.27+galaxy3 in commit 8eb0a81e9. The bot carried saveLog forward in tool_state despite it no longer existing in the tool definition. It also changed the value type from boolean false to string "false".

Evidence

# Confirm saveLog absent from current tool XML
git -C /path/to/tools-iuc grep saveLog -- tools/multiqc/
# (no results)

# Find removal commit
git -C /path/to/tools-iuc log --oneline -S 'saveLog' -- tools/multiqc/
# 24152e242 ... remove the log option ...

# Find IWC orphaning commit
git -C /path/to/iwc log --oneline -S '1.27+galaxy3' -- workflows/**/pe-artic-variation.ga
# 8eb0a81e9 ... Automated tool update ...

2. segmentation-and-counting.ga / ip_filter_standard / radius

Note: The root-level filter_type key is also orphaned but is tolerated by allow_root_level_duplicates since it exists as filter.filter_type inside the new conditional.

Parameter history in tool XML

• Before (version 0.0.3-3): radius was a top-level <param name="radius" type="integer" value="3" label="Radius/Sigma" />. Flat structure — filter_type was a plain <select>, radius applied to all filter types. Command: python filter_image.py '$input' '$output' $filter_type $radius
• Refactored: galaxy-image-analysis commit c045f067 (2024-04-04, Leonid Kostrykin) — “Refurbishment (#118)”. Major refactoring of 23 tools. radius replaced by a filter conditional with per-filter-type size params (float for gaussian sigma, integer for median radius, hidden for edge-detection filters). Underlying library changed from scikit-image 0.14.2 to scipy 1.12.0.
• Version after refactoring: 1.12.0+galaxy0, then 1.12.0+galaxy1 (commit c86a1b9, “Suppress non-fatal errors when loading images (#119)“)

Parameter history in workflow

What happened

1. Leonid Kostrykin created the IWC workflow on 2024-02-29 with tool version 0.0.3-3. At that version, radius was a valid top-level integer param.
2. On 2024-04-04, Leonid refactored the tool itself (Refurbishment #118), replacing the flat filter_type+radius structure with a filter conditional containing per-type size params.
3. On 2024-11-07, Leonid upgraded the workflow to 1.12.0+galaxy1. He correctly added the new conditional state ("filter": {"filter_type": "gaussian", "__current_case__": 0, "size": "3.0"}) but did not remove the old flat keys ("radius": "3" and "filter_type": "gaussian").
4. This is not a bot bug — the same person who refactored the tool also upgraded the workflow, but Galaxy’s export preserved the old keys (the params_to_strings serialization bug).

Evidence

# Confirm radius absent from current tool XML
git -C ~/projects/repositories/galaxy-image-analysis grep radius -- tools/2d_simple_filter/
# (no results)

# Find refactoring commit
git -C ~/projects/repositories/galaxy-image-analysis log --oneline -S 'radius' -- tools/2d_simple_filter/
# c045f067 Refurbishment (#118)

# Find IWC upgrade commit
git -C ~/projects/repositories/iwc log --oneline -S '1.12.0+galaxy1' -- workflows/**/segmentation-and-counting.ga
# 0f0c9ade ...

3. segmentation-and-counting.ga / ip_threshold / dark_bg

Note: Root-level block_size is tolerated by allow_root_level_duplicates since it exists inside th_method conditional. dark_bg is the true orphan that causes the validation failure.

Parameter history in tool XML

• Before (version 0.0.5-2): dark_bg was a top-level <param name="dark_bg" type="boolean" checked="true" ...>. block_size was also top-level. th_method was a flat <select>.
• Refactored: galaxy-image-analysis commit 8b9f24c (2024-03-11, Leonid Kostrykin) — PR #109 “Update Threshold image tool”. Commit message includes: “Replace dark_bg by invert_output”. Changes:
  • dark_bg (boolean) → invert_output (boolean) — renamed
  • th_method became a <conditional> with per-method nested params
  • block_size moved from top-level into th_method conditional (only for methods that use it)
  • Tool version jumped from 0.0.5-2 to 0.18.1+galaxy0
• Version trail: 0.18.1+galaxy0 → galaxy1 → galaxy2 → galaxy3 (workflow version)

Parameter history in workflow

What happened

1. Leonid Kostrykin created the IWC workflow on 2024-02-29 with tool version 0.0.5-2. At that version, dark_bg and top-level block_size were valid params.
2. On 2024-03-11, Leonid refactored the tool (PR #109), renaming dark_bg to invert_output and restructuring th_method into a conditional with block_size nested inside.
3. On 2024-11-07, Leonid upgraded the workflow to 0.18.1+galaxy3. Galaxy’s save/export added the new structure (invert_output, nested th_method conditional with inner block_size: "0") but did not strip the old keys (dark_bg: "true", root block_size: "5").
4. The root-level block_size value ("5") actually diverges from the nested value ("0") — the root copy is stale from the old version.

Evidence

# Confirm dark_bg absent from current tool XML
git -C ~/projects/repositories/galaxy-image-analysis grep dark_bg -- tools/2d_auto_threshold/
# (no results)

# Find refactoring commit
git -C ~/projects/repositories/galaxy-image-analysis log --oneline -S 'dark_bg' -- tools/2d_auto_threshold/
# 8b9f24c Update Threshold image tool (#109)

# Same IWC upgrade commit as entry 2 (same workflow, same date)
git -C ~/projects/repositories/iwc log --oneline -S '0.18.1+galaxy3' -- workflows/**/segmentation-and-counting.ga
# 0f0c9ade ...