Fix glimmer tools error handling #6641
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All the tools that call into python scripts wouldn't fail on non-zero exit codes. They also didn't write to stderr, so in fact they could never fail. Also fixes the remaining lint errors.
tools/glimmer/glimmer_gbk_to_orf.xml
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| @@ -16,8 +16,8 @@ | |||
| <param name="infile" type='data' format="genbank" label="gene bank file"/> | |||
| </inputs> | |||
| <outputs> | |||
| <data name="aa_output" format="fasta" /> | |||
| <data name="nc_output" format="fasta" /> | |||
| <data name="aa_output" format="fasta" label="${tool.name}: Amino acids"/> | |||
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Should we add on_string?
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I absolutely think recording the input datasets in the dataset name is one of the worst ideas that still survives. Feel free to add it.
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I guess we'll eventually figure out a better way to do this. I wish we'd just not fill in ${on_string} and template that on the frontend ...
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mvdbeek
commented
Dec 16, 2024
tools/glimmer/glimmer_gbk_to_orf.xml
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| @@ -16,8 +16,8 @@ | |||
| <param name="infile" type='data' format="genbank" label="gene bank file"/> | |||
| </inputs> | |||
| <outputs> | |||
| <data name="aa_output" format="fasta" /> | |||
| <data name="nc_output" format="fasta" /> | |||
| <data name="aa_output" format="fasta" label="${tool.name}: Amino acids"/> | |||
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Suggested change
| <data name="aa_output" format="fasta" label="${tool.name}: Amino acids"/> | |
| <data name="aa_output" format="fasta" label="${tool.name} on ${on_string}: Amino acids"/> |
mvdbeek
commented
Dec 16, 2024
tools/glimmer/glimmer_gbk_to_orf.xml
Outdated
| <data name="aa_output" format="fasta" /> | ||
| <data name="nc_output" format="fasta" /> | ||
| <data name="aa_output" format="fasta" label="${tool.name}: Amino acids"/> | ||
| <data name="nc_output" format="fasta" label="{tool.name}: Nucleotides"/> |
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Suggested change
| <data name="nc_output" format="fasta" label="{tool.name}: Nucleotides"/> | |
| <data name="nc_output" format="fasta" label="{tool.name} on ${on_string}: Nucleotides"/> |
bernt-matthias
approved these changes
Dec 16, 2024
bernt-matthias
approved these changes
Dec 16, 2024
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All the tools that call into python scripts wouldn't fail on non-zero exit codes. They also didn't write to stderr, so in fact they could never fail. Also fixes the remaining lint errors.
FOR CONTRIBUTOR: