Thank you very much for your answers,
- As far as my previous topic has been closed (Galaxy Plink doesn’t accept pbed composite dataset when uploaded from local disk), I will reply here. I addressed that issue to the developer of the galaxy plink tool on GitHub. He advised to look at files in working directory. So we found the reason of the problem:
We found that the error occures because Galaxy assigns files’ names the in composite dataset not the way Plink tool expects. When upload composite pbed dataset to Galaxy we get the following files: “Composite Dataset.bim”, “Composite Dataset.bed”, “Composite Dataset.fam”. And the Plink tool expects theese names: “RgeneticsData.bim”, “RgeneticsData.bed”, “RgeneticsData.fam”.
When we manually changed files’ names to the expected ones on our server, Plink accepted the dataset and worked correctly. But there is no option to change files’ names in the composite dataset using Galaxy’s GUI, so ordinary users with no admin rights are not able work with pbed composite dataset when it is uploaded from local disc. - This is my reply about this topic. My aim is to make a workflow using plink. However I have a couple of steps in my workflow where I must process .bim files directly as text files (.bim is a part of the pbed dataset). The Galaxy version of plink is somewhat restricted in functionality so it cannot produce just .bim file - only the whole dataset (no analogue of the command-line-plink option --make-just-bim). So I wonder if there are any options to break pbed dataset into separate files. It seems to me that I will have to make a custom tool to extract .bim file from pbed.