Conditional: transform or pass through

Tool

Gate the optional transform with Galaxy when:, then merge the transform’s output and the untransformed value with toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 at pick_style: first. Downstream steps connect to the pick_value output and get the transformed value when the transform ran, or the original when it was skipped.

The shape is:

1. Derive or expose a boolean.
2. Connect that boolean to each step of the optional transform as an input with id: when.
3. Set when: $(inputs.when) on each of those steps.
4. Connect the transform’s output to pick_from_0 and the original value to pick_from_1.
5. Connect downstream steps only to the pick_value output.

The fallback works because a skipped step still produces outputs. Galaxy makes each one a hidden expression.json dataset containing null, and pick_value reads that dataset as a null candidate. With first, it passes over the null and returns the original.

When to reach for it

Use this when a workflow should optionally alter a dataset, collection, or report while keeping one downstream input slot. The untransformed value must be a valid downstream input on its own. The transform cleans, relabels, or rewrites it when the user asks for that or the data needs it.

Use conditional-route-between-alternative-outputs instead when the branches are peer routes, such as import mode A or B, one of several annotation modes, or co-assembly versus individual assembly. There each branch produces its own candidate and no original is privileged. Here one candidate is a transform of the other, so both are present whenever the transform runs.

Use conditional-run-optional-step when the optional branch has only side outputs and nothing downstream needs a replacement value.

Use conditional-gate-on-nonempty-result to compute a boolean from whether a result is empty. That boolean can then drive this pattern, as the decontamination exemplar does with a line count.

Do not use this to clean up after a mapped tool leaves empty or failed elements. That is collection-cleanup-after-mapover-failure, with __FILTER_EMPTY_DATASETS__ or __FILTER_FAILED_DATASETS__.

Parameters

On each step of the optional transform:

• An input with id: when, connected from a workflow boolean, map_param_value/output_param_boolean, or another boolean-producing step.
• when: $(inputs.when).

On the pick_value merge step:

• style_cond.pick_style: first.
• style_cond.type_cond.param_type set to the kind being merged, with the matching output read downstream (data_param for datasets).
• The transformed output connected to style_cond|type_cond|pick_from_0|value and the original to style_cond|type_cond|pick_from_1|value.
• One pick_from entry in tool_state for each connection. Without them the tool sees zero candidates and writes the text null, as the route pattern’s verified workflow shows.

The style must be first. The original is always non-null, so whenever the transform runs pick_value sees two non-null candidates, and only fails the job. first_or_error and first_or_default behave like first here, because their fallback cases need every candidate to be null. The expression in the pick_value 0.2.0 wrapper defines all four styles.

The transform tool depends on the operation. The IWC exemplars use compose_text_param, tp_replace_in_line, Filter1, and tp_cat. What this pattern contributes is the gate and the ordered merge.

Galaxy release_26.1 also has a built-in pick_value workflow module with its own modes. The corpus and this page use the Tool Shed tool.

Idiomatic Shape

From the verified workflow, which adds a suffix to FASTA headers on request:

- id: add_suffix_step
  tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3
  in:
    - id: infile
      source: original
    - id: when
      source: add_suffix
  out:
    - id: outfile
  tool_state:
    infile: { __class__: ConnectedValue }
    replacements:
      - find_pattern: ">.+$"
        replace_pattern: "&.H1"
        sed_options: ""
  when: $(inputs.when)

- id: transformed_or_original
  tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
  in:
    - id: style_cond|type_cond|pick_from_0|value
      source: add_suffix_step/outfile
    - id: style_cond|type_cond|pick_from_1|value
      source: original
  out:
    - id: data_param
  tool_state:
    style_cond:
      pick_style: first
      type_cond:
        param_type: data
        pick_from:
          - value: { __class__: ConnectedValue }
          - value: { __class__: ConnectedValue }

With add_suffix: true the output is the suffixed FASTA. With add_suffix: false it is the input file, byte for byte.

In the VGP Hi-C manual-curation workflow, the embedded subworkflow Add suffix to 2 haplotypes has this shape twice, once per haplotype. Gated compose_text_param steps build each suffix expression, gated tp_replace_in_line steps apply it, and two pick_value steps at first list each suffixed haplotype before Hap1 or Hap2. In Assembly decontamination, the Modify action report subworkflow counts the lines of Adaptor Action report with wc_gnu, reads the count with param_value_from_file, and maps it with map_param_value (1 to false, anything else to true). That boolean gates the Filter1 selections, the ACTION_TRIM to FIX replacement, and the tp_cat that rebuilds the report. A final pick_value lists the rebuilt report before the original.

Pitfalls

• Original listed first. first returns the earliest non-null candidate, and the original is never null. With the original in slot 0, the merge returns it even when the transform ran. The verified workflow’s original_first step shows this.
• pick_style: only. It fails the job every time the transform runs, because two candidates are non-null.
• Gating only the first step of a multi-step transform. Each tool step evaluates only its own when:. A skip does not spread to steps that consume the skipped output. Galaxy hands an ungated consumer the null placeholder in place of real data. Gate every step that belongs to the transform. Decontamination leaves one step inside its branch ungated, a single-input pick_value, which accepts a null input.
• Consuming the transform’s output directly. Downstream steps should read the merge, because the transform may have been skipped.
• Duplicating the downstream workflow for each case. Merge once with pick_value and continue on one path.
• Wrapping the pass-through in a no-op transform step. Connect the original value directly as the fallback candidate.
• Reaching for __FILTER_NULL__. The conditionals survey found no uses of it in IWC. That absence does not make it wrong, but it leaves no exemplar to follow.

See Also

• iwc-conditionals-survey — corpus evidence for the transform-then-fallback idiom and its boundary with peer routes.
• galaxy-conditionals-patterns — conditionals map of content.
• conditional-route-between-alternative-outputs — pick_value across peer alternatives, pick_style behavior, and missing pick_from entries.
• conditional-run-optional-step — when: gating with no downstream merge.
• conditional-gate-on-nonempty-result — booleans computed from empty or non-empty results.
• collection-cleanup-after-mapover-failure — collection-state cleanup, not a when plus fallback recipe.