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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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Metadata example command #149

Closed docxology closed 9 months ago

docxology commented 9 months ago

At: https://github.com/kfuku52/amalgkit/wiki/Amalgkit-metadata

I see the following example usage of "amalgkit metadata":

amalgkit metadata --out_dir "./" --entrez_email "example@email.com" --search_string 'metadata --redo no --search_string '("platform illumina"[Properties]) AND ("type rnaseq"[Filter]) AND ("Nepenthaceae"[Organism]) NOT ("DNA"[Source])' This is a bit confusing because --search_string is given twice, once with 'metadata (?) and once with a longer string that seems more relevant for that required argument.

I am getting successful operation with the use of: amalgkit metadata --search_string '("platform illumina"[Properties]) AND ("type rnaseq"[Filter]) AND ("Apis mellifera"[Organism]) NOT ("DNA"[Source])'

kfuku52 commented 9 months ago

Thank you for bringing this to our attention! This has now been corrected.

docxology commented 9 months ago

Thank you Kenji. I am making sure that my pipeline continues to work with the recent updates to amalgkit & will let you know if I have any other questions.

kfuku52 commented 9 months ago

Thank you for your continued support!