How can I do the equivalent of this bash command in Galaxy with a collection of datasets (dataset1, 2, 3, etc)?
paste <(cut -f1,2,3 dataset1) <(cut -f3 dataset2) <(cut -f3 dataset3) ...
Hi @tshtatland,
you can use the Cut columns from a table tool to extract specific columns from a dataset, and the Concatenate datasets tail-to-head tool to join those. However, it requires the same number of columns. If you pretend to join datasets side-by-side you can use the Paste two files side by side tool.
Regards
I am using tools as part of a workflow. Cut columns from a table tool (and its parameters, such as which columns to keep) applies to the entire collection. How can I apply different parameters to dataset1 in a collection vs dataset2, dataset3, etc? I need to cut columns 1, 2, and 3 in dataset1, but only column 3 in the rest of the datasets.
Also, what is the analog of Paste two files side by side tool for collections? That is, I want to collapse the results of the above operation (= a collection) into a single dataset, using an analog of Paste. It should be under Collection tools section, but I cannot find it there.
Hi @tshtatland,
you need to unzip your colleciton by using the Unzip collection tool in order to apply the Cut columns from a table tool in each dataset. How many datasets do you have?
Regards
I have a variable number of datasets per collection (typical range: 2-100), depending on the user’s input. The goal is to make a single workflow that handles any number of datasets per collection, as is typical in Galaxy.