add: implement tool to add rank names to phyloseq object #6625
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| <output name="output" ftype="phyloseq"> | ||
| <!-- Check if the output contains the first character --> | ||
| <assert_contents> | ||
| <has_text text="B"/> |
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Can you please be a bit more strict in this test?
change version and add profile
| print(tax_table(physeq)) | ||
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| # Zuordnung der Rangnamen | ||
| rank_names <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") # Anpassen je nach Bedarf |
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There could be more ranks, e.g.: super kingdom, subspecies, strain.
Could you make this more generic, e.g.: the use provides a comma separated list of ranks.
You could make "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species" the default.
If the number of ranks does not match the column numbers of the tax_table the tool fails.
| # Zuordnung der Rangnamen | ||
| rank_names <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") # Anpassen je nach Bedarf | ||
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| # Füge eine leere Spalte für Species hinzu, falls sie fehlt |
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I think not needed, if the logic I proposed before is used
| print(tax_table(physeq)) | ||
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| # Extrahiere das erste Zeichen aus dem ersten Eintrag des tax_table (z.B. Kingdom) | ||
| first_char <- substr(tax_table(physeq)[1, 1], 1, 1) |
| <tests> | ||
| <test> | ||
| <param name="input" value="output.phyloseq" ftype="phyloseq"/> | ||
| <output name="output" ftype="phyloseq"> |
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you could compare the new phylosq object to expected output, like:
<output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
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Better just use an has_size assertion and remove value="AalborgWWTPs-subset_samples.rds".
| cat("Current tax_table:\n") | ||
| print(tax_table(physeq)) | ||
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| # Zuordnung der Rangnamen |
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Guess English comments would be better.
| <tests> | ||
| <test> | ||
| <param name="input" value="output.phyloseq" ftype="phyloseq"/> | ||
| <output name="output" ftype="phyloseq"> |
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Better just use an has_size assertion and remove value="AalborgWWTPs-subset_samples.rds".
| cat("Current tax_table:\n") | ||
| print(tax_table(physeq)) | ||
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| # Add a column for Species if missing |
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I don't think this part is needed (the add species part), we cannot really know which rank is missing if it is missing, the user should provide names matching the columns exactly, otherwise the tool should fail, you could change if (ncol(tax_table(physeq)) > length(rank_names)) { to if (ncol(tax_table(physeq)) == length(rank_names)) { instead, and provide a message for further help
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