- sampleCSVFilename := flags.String("labels-csv", "", "use first two columns of `labels.csv` as id->color mapping")
- sampleFastaDirname := flags.String("sample-fasta-dir", "", "`directory` containing fasta input files")
+ outputFilename := flags.String("o", "", "output `filename` (e.g., './plot.png')")
+ sampleListFilename := flags.String("samples", "", "use second column of `samples.csv` as complete list of sample IDs")
+ phenotypeFilename := flags.String("phenotype", "", "use `phenotype.csv` as id->phenotype mapping (column 0 is sample id)")
+ cat1Column := flags.Int("phenotype-cat1-column", 1, "0-based column `index` of 1st category in phenotype.csv file")
+ cat2Column := flags.Int("phenotype-cat2-column", -1, "0-based column `index` of 2nd category in phenotype.csv file")
+ xComponent := flags.Int("x", 1, "1-based PCA component to plot on x axis")
+ yComponent := flags.Int("y", 2, "1-based PCA component to plot on y axis")
+ priority := flags.Int("priority", 500, "container request priority")
+ runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")