# HG changeset patch
# User workflow4metabolomics
# Date 1721059406 0
# Node ID 520448a32548c6c9f1a2729bc4d5db13eeec1f77
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
diff -r 000000000000 -r 520448a32548 macros_xcms_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_xcms_plot.xml Mon Jul 15 16:03:26 2024 +0000
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+ 4.0.0
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+ XCMS
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+ 10.1021/ac051437y
+ 10.3390/metabo12020173
+ 10.5281/zenodo.11185520
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\ No newline at end of file
diff -r 000000000000 -r 520448a32548 test-data/raw_plot.png
Binary file test-data/raw_plot.png has changed
diff -r 000000000000 -r 520448a32548 test-data/xcms_plot_raw_testdata.mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xcms_plot_raw_testdata.mzML Mon Jul 15 16:03:26 2024 +0000
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\ No newline at end of file
diff -r 000000000000 -r 520448a32548 xcms_plot_raw.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_plot_raw.xml Mon Jul 15 16:03:26 2024 +0000
@@ -0,0 +1,55 @@
+
+ Plot raw data filtered by m/z range and retention time (RT) range
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+ macros_xcms_plot.xml
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+
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+ bioconductor-xcms
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+library(xcms)
+library(MsExperiment)
+library(Spectra)
+mse = readMsExperiment(file.path('${input}'))
+mz_offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
+rt_offset = ${rt_range} / 2
+raw = mse |>
+ filterRt(rt = ${rt} + c(-rt_offset, rt_offset)) |>
+ filterMzRange(mz = ${mz_value} + c(-mz_offset, mz_offset))
+png(filename = '${output_filename}')
+par(oma = c(0.5, 2, 0.5, 1))
+plot(raw)
+dev.off()
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\ No newline at end of file