The best GTF choice for this specific pipeline is hosted by iGenomes. It contains all of the attributes utilized by these tools. Download the tar.gz archive locally, navigate to the genes.gft file, then upload that to Galaxy for use with tools. http://support.illumina.com/sequencing/sequencing_software/igenome.html
If you choose a genome build that is a match for a native Galaxy indexed genome, genome mismatch problems will be avoided.
The alternative is to use a GTF based on genome build not included in Galaxy (public server or local/cloud). In this case, load the matching reference genome and use it as a Custom Genome/Build. The iGenomes tar bundle includes more than the gtf file, including the genome itself and other annotation files. These can be individually loaded and used as needed.
More about reference genomes, including mismatch problems: https://wiki.galaxyproject.org/Support#Reference_genomes
More about how to use a Custom Genome/Build: https://wiki.galaxyproject.org/Support#Custom_reference_genome
Best, Jen, Galaxy team
Ps: If a dataset is not recognized, it may be that the "datatype" metadata attribute needs to be assigned to the input datasets. This is how: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset
Hi Jen, Thank you for your kind response. My reference genome is Chicken (Gallus gallus), currently the chicken indexed genome available in GALAXY build genome option for HISAT and Tophat tools.The genome version is galGAL3 and galGAL4. Shall i download UCSC version of galGAL4 file instead of other two source (ENSEMBL and NCBI) file available in iGENOME and subsequently i can use this gtf file for annotation?