Add phyloseq_tax_glom #6891
Add phyloseq_tax_glom #6891
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| physeq_file <- args[1] | ||
| tax_rank <- args[2] | ||
| use_counts <- "--counts" %in% args |
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I find optparse cleaner:
but this is optional| tax_table_agg <- cbind("OTU ID" = rownames(tax_table_agg), tax_table_agg) | ||
| } | ||
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| if (use_counts) { |
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I do not see a reason to ever exclude it, would not make this optional
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It would make sense to exclude it when using a single column for the specified rank. Because when leaving only the column of the specified rank the NA values will be group together so it will be confusing.
Especially if you include the counts in the same table. The counts of all the NA values will be summed and you and won't represent the values of the OTU ID that is randomly selected. This will be misleading.
| <param argument="--counts" truevalue="--counts" falsevalue="" type="boolean" label="Include OTU counts" optional="true" help="OTU abundances will be included in the output"/> | ||
| <param argument="--exclude_na_values" truevalue="--exclude_na_values" falsevalue="" type="boolean" label="Exclude unknown 'NA' values" optional="true" help="Unknown value 'NA' will be removed"/> | ||
| <conditional name="single_rank_cond"> | ||
| <param name="exclude_otu_ids" type="select" label="Exclude OTU IDs from output" help="OTU IDs will be excluded from the output table"> |
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why not like: argument="--exclude_na_values" truevalue="--exclude_na_values" falsevalue="" type="boolean" ?
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To not get this linting warning: WARNING (ConditionalParamTypeBool): Conditional [single_rank_cond] first param of type="boolean" is discouraged, use a select
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| - *Taxonomic rank for agglomeration:* Specify the rank to merge OTUs at. | ||
| - *Include OTU counts:* If enabled, OTU abundances will be included in the output. | ||
| - *Exclude OTU IDs:* If enabled, OTU IDs will be excluded from the output table. |
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we should add that a random OTU id form the ranks used for agg is taken
| - *Include OTU counts:* If enabled, OTU abundances will be included in the output. | ||
| - *Exclude OTU IDs:* If enabled, OTU IDs will be excluded from the output table. | ||
| - *Keep only specified rank column:* If enabled, only the selected taxonomic rank will be kept. | ||
| - *Exclude NA values:* If enabled, unknown will be removed. |
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can you add all symbols removed ?
FOR CONTRIBUTOR:
@paulzierep