workflow_test_init incorrect run from invocation

[martenson]

outcome of planemo workflow_test_init --from_invocation

The workflow has 4 inputs, 2 fastas and 2 tabular files.

Maybe the fact there are spaces in the input names is causing the duplication here?

❯ ll test-data
total 461808
drwxr-xr-x@ 6 staff   192B Apr 28 10:20 ./
drwxr-xr-x@ 5 staff   160B Apr 28 10:20 ../
-rw-r--r--@ 1 staff    98M Apr 28 10:20 QUERY Seq.fasta
-rw-r--r--@ 1 staff   198B Apr 28 10:20 QUERY fasta index.tabular
-rw-r--r--@ 1 staff    98M Apr 28 10:20 TARGET Seq.fasta
-rw-r--r--@ 1 staff   198B Apr 28 10:20 TARGET fasta index.tabular
❯ cat test-data/QUERY\ fasta\ index.tabular
chrI	15072434	6	50	51
chrII	15279421	15373896	50	51
chrIII	13783801	30958914	50	51
chrIV	17493829	45018399	50	51
chrV	20924180	62862111	50	51
chrX	17718942	84204781	50	51
chrM	13794	102278108	50	51
❯ cat test-data/TARGET\ fasta\ index.tabular
chrI	15072434	6	50	51
chrII	15279421	15373896	50	51
chrIII	13783801	30958914	50	51
chrIV	17493829	45018399	50	51
chrV	20924180	62862111	50	51
chrX	17718942	84204781	50	51
chrM	13794	102278108	50	51

[mvdbeek]

Can you share the invocation ?

[martenson]

I am fairly sure it is this one:

Invocation-of-IWC-Align-chain-and-net-at-2025-04-28T075700195280.tgz

May be unrelated but there is something confusing me. It is an invocation of the workflow in version 2 and it should have label for input 0 TARGET fasta index, but the version of the wf included in the invocation seems to be newer and has a different label for input 0 where I already removed the spaces to prevent problems with the planemo command (TARGET_fasta_index)

content of invocation_export/workflows/*.ga:

"steps": {
        "0": {
            "id": 0,
            "type": "data_input",
            "content_id": null,
            "tool_id": null,
            "tool_version": null,
            "name": "Input dataset",
            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}",
            "errors": null,
            "uuid": "a0e40e9e-6c4b-4e53-8968-f391ba3416e0",
            "label": "TARGET_fasta_index",

[mvdbeek]

Do you have the link to the invocation please ?

[martenson]

@mvdbeek sorry, didn;t realize you wanted a link https://vgp.usegalaxy.org/workflows/invocations/2313cfb3f9e88002