# HG changeset patch
# User galaxyp
# Date 1630221607 0
# Node ID aa479a0cfb434324bca7ee731407dbb49846f295
# Parent e0bbaf9f7da0f705e3bb019eb8c38e4a3584089f
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
diff -r e0bbaf9f7da0 -r aa479a0cfb43 macros.xml
--- a/macros.xml Tue Nov 03 22:41:21 2020 +0000
+++ b/macros.xml Sun Aug 29 07:20:07 2021 +0000
@@ -1,5 +1,5 @@
- 2.6.0
+ 2.10.0
diff -r e0bbaf9f7da0 -r aa479a0cfb43 preprocessing.xml
--- a/preprocessing.xml Tue Nov 03 22:41:21 2020 +0000
+++ b/preprocessing.xml Sun Aug 29 07:20:07 2021 +0000
@@ -1,4 +1,4 @@
-
+
mass spectrometry imaging preprocessing
@@ -7,7 +7,7 @@
r-gridextra
- r-ggplot2
+ r-ggplot2
= $method.methods_conditional.mz_range.min_mz & mz(msidata) <= $method.methods_conditional.mz_range.max_mz,]
- msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
- #end if
- #elif str( $method.methods_conditional.mz_range.features_filtering) == 'none':
+ #elif str($method.methods_conditional.mz_range.features_filtering) == 'none':
msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+ #elif str($method.methods_conditional.mz_range.features_filtering) == 'bin_to_reference':
+
+ bin_reference_mz = read.delim("$method.methods_conditional.mz_range.mz_tabular", header = $method.methods_conditional.mz_range.feature_header, stringsAsFactors = FALSE)
+ bin_reference_mz = bin_reference_mz[,$method.methods_conditional.mz_range.feature_column]
+
+ msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun,
+ ref=bin_reference_mz)
+
#end if
msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
@@ -385,7 +418,7 @@
print('log2 transformation')
## replace 0 with NA to prevent Inf
- spectra_df = spectra(msidata) ## convert into R matrix
+ spectra_df = as.matrix(spectra(msidata)) ## convert into R matrix
spectra_df[spectra_df ==0] = NA
print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra_df))))
spectra(msidata) = spectra_df
@@ -422,25 +455,14 @@
################################################################################
## save msidata as imzML file, will only work if there is at least 1 m/z left
-
- #if str($imzml_output) == "cont_format":
- #set $continuous_format = True
- #end if
if (nrow(msidata) > 0){
## make sure that coordinates are integers
coord(msidata)\$y = as.integer(coord(msidata)\$y)
coord(msidata)\$x = as.integer(coord(msidata)\$x)
- #if $used_peak_picking:
- #if $continuous_format:
- msidata = as(msidata, "MSContinuousImagingExperiment")
- #end if
- #elif $used_peak_alignment
- #if $continuous_format:
- msidata = as(msidata, "MSContinuousImagingExperiment")
- #end if
- #end if
- writeImzML(msidata, "out")
+ ## only continuous files can currently be exported
+ msidata = as(msidata, "MSContinuousImagingExperiment")
+ writeImzML(msidata, "out")
}
plot(0,type='n',axes=FALSE,ann=FALSE)
@@ -463,6 +485,7 @@
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@@ -541,6 +564,26 @@
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@@ -645,7 +692,6 @@
-
@@ -666,10 +712,8 @@
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@@ -702,7 +746,6 @@
-