I run a command on command line like :

cuffdiff -o diff_out4 -b ../genome/ce10.fa -p 2 -L larval,early -u merged_asm/merged.gtf ../tophat/em/SRR493359_60_61_thout/accepted_hits.bam ../tophat/em/SRR493363_64_65_thout/accepted_hits.bam

Both bam files are separated with "space".

Now the same command I gave a call in python script:

do.call([cfg.tool_cmd("cuffdiff"),

                        "-b",  str(cfg.project["genome"]["fasta"]),
                        "-u", cfg.project["experiment"]["merged"],
                        "-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"]
                                                cfg.project["samples"][1]["files"]["bam"]],
                                                 cfg.project["analysis"]["log_file"])

It gave me a syntax error because of the space. Can anyone help me how to use this.