das tool: do not allow empty labels #5955
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just use element identifiers if not given
bgruening
reviewed
Apr 17, 2024
| @@ -46,7 +53,15 @@ DAS_Tool | |||
| <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/> | |||
| <repeat name="binning" title="Bins" min="1"> | |||
| <param argument="--bins" type="data" format="tabular" label="Contigs-to-bin table" help="Tabular with two columns: contig-IDs and bin-IDs. Fasta_to_Contigs2Bin can be used to Converts genome bins in fasta format to Contigs-to-bin table"/> | |||
| <param argument="--labels" type="text" value="" label="Name of binning prediction tool used to generate the table"/> | |||
| <param argument="--labels" type="text" value="" label="Name of binning prediction name" help="If left empty the identifier of the contig-to-bin table is used. Only alphanumeric characters, dash, underscore and dor are allowed. Other characters are replaced by underscore."> | |||
| <sanitizer invalid_char="_"> | |||
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_ is invalid and then you add it again?
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invalid_char specifies the character used as a replacement for invalid characters. _ is a valid char.
Idea is that this does the same as the regexp that is applied to the element_identifiers in the cheetah code (which I took from what we use all the time).
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bump? |
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just use element identifiers if not given. Seems to be what the tool does by default: https://github.com/cmks/DAS_Tool/blob/bb0954f4f45a2340e9cb9b896d412e477c6c49fc/src/DAS_Tool.R#L398
No idea what the
--labelsargument is good for. But with--labels ''the program just fails. So this might be a solution.FOR CONTRIBUTOR: