I would appreciate any help with my problem.
I work with current version of Galaxy plink (Galaxy | Tool Shed)
When I upload pbed composite file (as RgeneticsData.bed, *.bim and *.fam) and try to use it with plink, I get the following report: “Error: Failed to open plink_input/plink_input.bed”.
When I upload a vcf file, plink works with it correctly and makes pbed dataset which further can successfully be used as input for new plink operations. But when I download the 3 files from the obtained pbed dataset and upload them as pbed composite file - plink doesn’t accept it again.
What Galaxy server are you working at? URL please or describe if otherwise.
Was the datatype set correctly for the Uploaded data?
Was that auto-detected during Upload, or assigned by you after Upload? Maybe try the other if one method didn’t work or guess correctly.
Does that datatype match what is expected on the tool form? This is how to check for any tool, for any user supplied input(s) from the history. fastq unavailable -- Tool does not recognize inputs? How to check why
Next, you could check if the test data in that tool repository works or not. That would isolate the problem to your data (or, more complex data in general).
Please give those a check first, then post more details about where you are working and consider creating and posting a shared history link. Make that history as small and as representative as possible please. Galaxy Training!