add: implement tool to add rank names to phyloseq object#6625
add: implement tool to add rank names to phyloseq object#6625bgruening merged 7 commits intogalaxyproject:mainfrom
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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
paulzierep
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paulzierep
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With my more generic approach, it will be good I think.
Please change the code comments to english.
| 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
paulzierep
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@bgruening can we merge this one ?
| @@ -0,0 +1,37 @@ | |||
| <tool id="add_rank_names_to_phyloseq" name="Add Rank Names to Phyloseq Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |||
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| <tool id="add_rank_names_to_phyloseq" name="Add Rank Names to Phyloseq Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| <tool id="phyloseq_add_rank_names" name="Add Rank Names to Phyloseq Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
maybe that ID? All others also start with phyloseq
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