I’m working on adding a couple custom tools to our Galaxy install, and one problem I’m running across is with the names of datasets.
More specifically, one tool we use requires all input files to be in a certain “input” directory. So, first thing my custom tool XML does is copy (using
cp) the datasets from the list a user chooses as input (see below) to this folder. However, the datasets all have names such as dataset_9964.dat, dataset_9967.dat, etc. and not their names in the history/original names such as bin1.fasta, bin2.fasta, etc.
As such, when running this tool, the output (see second image below) in tabular TSV format things that all my user_genomes which I submitted to the tool are in fact called dataset_9964, dataset_9963, etc. as it uses the input file names to determine row names in output.
I’m wondering if there’s any way I can retrieve the original files’ names upon job submission.
Our input section for the tool XML is as follows:
<inputs> <param name="input_files" type="data" multiple="true" format="fasta" label="Input FASTA files" /> </inputs>
Input list/collection of FASTA files:
First column of output TSV, column name is “user_genome”, and each row should represent a different input file (dataset_9963 = bin1.fasta, etc.):
Thanks in advance!