galaxyproject / galaxyproject/planemo

workflow_test_init incorrect run from invocation

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Dominant language
Python
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110
Forks
102
Avg merge
4d 21h
Merged PRs (30d)
13

Description

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
```

Contributor guide

Open the contributing guide

Research direction

Start by reproducing `planemo workflow_test_init --from_invocation` and inspect the generated `test-data` entries, especially the FASTA and tabular files whose names contain spaces. Compare the generated inputs with the four workflow inputs and verify that each file is included once with the correct mapping. The issue does not identify a source file or test to run.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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