group.add_argument('-i','--illumina-dir',metavar='DIR',help='Directory containing the fastq input files generated by Illumina. The fastq files should be in paired-end mode. If your fastq files are not coming from an Illumina sequencer, please use option -f to specify a file listing the fastq input files. (REQUIRED if no "-f")',dest='illuminadir')
group.add_argument('-f','--fastq-file',metavar='FILE',help='File describing the fastq input file. This file should be tab delimited. First column: full path of Forward file; second column: full path of Reverse file. The fastq files should be in paired-end mode. If your fastq files were generated by an Illumina sequencer, you can use option "-i" to specify the directory containing the fastq input files. (REQUIRED if no "-i")',type=argparse.FileType('rt'),dest='fastqfile')
group.add_argument('-a','--reanalyze',action='store_true',help='Flag to indicate that this run will be a re-analysis which needs the already demultiplexed fastq files (one per sample)',dest='reanalyze')
parser.add_argument('-r','--reference-dir',metavar='DIR',help='Directory containing the reference files. It is recommended that you use this option if you have already used this pipeline and downloaded genome files.',dest='referencedir')
parser.add_argument('-c','--conditions',metavar='FILE',help='Tab delimited file with no headers indicating which conditions to compare during differential expression analysis. Columns must be "project condition1 condition2". If not specified, only primary analysis will be performed',type=argparse.FileType('rt'),required=False,dest='conditions')
parser.add_argument('--minGenes',metavar='N',type=int,help='Minimum genes detected necessary for a sample to pass the filtering step in secondary analysis. (Default 5000)',default=5000,required=False,dest='minGenes')
...
...
@@ -231,13 +232,7 @@ for project in d["comparisons"]:
eprint("ERROR make_srp_config.py: ","You must specify EITHER an illumina directory containing fastq input files with option \"-i\" or a file describing your fastq input files with option \"-f\"")
eprint("ERROR make_srp_config.py: ","You must specify EITHER an illumina directory containing fastq input files with option \"-i\" OR a file describing your fastq input files with option \"-f\", not both")