# HG changeset patch
# User lecorguille
# Date 1523027564 14400
# Node ID 954499828c1d0600eb5416b98a56b367aad6ccce
# Parent  60b156e5852954ed2eb3d0342aeff80701287ea6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d6c70bb63fd89932c9f95010d6f2c9297df96155

diff -r 60b156e58529 -r 954499828c1d xcms_plot_chromatogram.r
--- a/xcms_plot_chromatogram.r	Thu Apr 05 18:06:32 2018 -0400
+++ b/xcms_plot_chromatogram.r	Fri Apr 06 11:12:44 2018 -0400
@@ -54,6 +54,9 @@
 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") }
 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
 
+if (exists("chromTIC_adjusted")) chromTIC <- chromTIC_adjusted
+if (exists("chromBPI_adjusted")) chromBPI <- chromBPI_adjusted
+
 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")