--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alevinQC_galaxy/run_alevinQC.R	Thu Apr 01 00:55:48 2021 +0000
@@ -0,0 +1,30 @@
+## Run alevinQC inside of Galaxy
+
+## Check that input files are formatted correctly
+library(alevinQC)
+
+## Check that all input files required are present in working directory
+checkAlevinInputFiles(baseDir = ".")
+
+## Read in alevin output files as alevin object
+alevin <- readAlevinQC(baseDir = ".")
+
+# ## Write table with statistics of run
+summaryTable <- alevin$summaryTables$fullDataset
+
+write.table(summaryTable,
+            file ="./summaryTable.tab",
+            sep = "\t",
+            col.names = FALSE,
+            row.names = TRUE,
+            quote = FALSE)
+
+## Plot knee plot
+pdf(file = "./alevin_kneeplot.pdf")
+plotAlevinKneeRaw(alevin$cbTable)
+dev.off()
+
+## Barcode collapse plot
+pdf(file = "./alevin_barodeFrequency_quant.pdf", width = 12, height = 9)
+plotAlevinQuant(alevin$cbTable)
+dev.off()
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