Fix validation flag in slice-numpy -pca sample list output.

[lightning.git] / manhattan.go

diff --git a/manhattan.go b/manhattan.go
index 4ae44796be3ffba00626889e15951dc48b84dcfa..a6a58fb5cf06dbf8e7964c4366e8e68329726728 100644 (file)
--- a/manhattan.go
+++ b/manhattan.go
@@ -32,6 +32,8 @@ func (cmd *manhattanPlot) RunCommand(prog string, args []string, stdin io.Reader
        projectUUID := flags.String("project", "", "project `UUID` for output data")
        inputDirectory := flags.String("i", "-", "input `directory` (output of slice-numpy -single-onehot)")
        outputFilename := flags.String("o", "", "output `filename` (e.g., './plot.png')")
+       csvOutputFilename := flags.String("csv-output", "", "csv output `filename` (e.g., './tile-locations-pvalues.csv')")
+       csvOutputThreshold := flags.Float64("csv-output-threshold", 0, "logpvalue threshold for csv output (0 for none)")
        priority := flags.Int("priority", 500, "container request priority")
        runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
        err = flags.Parse(args)
@@ -65,10 +67,13 @@ func (cmd *manhattanPlot) RunCommand(prog string, args []string, stdin io.Reader
                        return 1
                }
                *outputFilename = "/mnt/output/plot.png"
+               *csvOutputFilename = "/mnt/output/tile-locations-pvalues.csv"
        }
        args = []string{
                *inputDirectory,
                *outputFilename,
+               fmt.Sprintf("%g", *csvOutputThreshold),
+               *csvOutputFilename,
        }
        if *runlocal {
                if *outputFilename == "" {