make.file and make.contigs " (2)" in fastq file names

I have some projects where I’m resequencing samples. I’d like to use sequences from both runs for the samples. make.file can’t deal with the space, so I make the file.file by hand. Now make.contigs doesn’t like that file because it looks like there are 5 columns. I’d rather not rename the files since these are exactly the names that are on BaseSpace. Can I quote the file names? what flavor of quotes '`"?

RID306Blank     RID306Blank.RID306Blank_S54_L001_R1_001.fastq.gz        RID306Blank.RID306Blank_S54_L001_R2_001.fastq.gz
RID323Blank     RID323Blank (2).RID323Blank_S131_L001_R1_001.fastq.gz RID323Blank (2).RID323Blank_S131_L001_R2_001.fastq.gz

Can you replace the spaces with an undescore “_”?