# HG changeset patch
# User galaxyp
# Date 1677957271 0
# Node ID 60ee8c592b13359948bdb98c3dfcfe728aff2c32
# Parent 71411ac28268c7e3f4a555e4ac89ebbb24407493
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
diff -r 71411ac28268 -r 60ee8c592b13 maldi_macros.xml
--- a/maldi_macros.xml Fri Feb 15 10:26:00 2019 -0500
+++ b/maldi_macros.xml Sat Mar 04 19:14:31 2023 +0000
@@ -1,6 +1,5 @@
- 1.18.0
+ 1.22.0
- r-base
- bioconductor-cardinal
- r-maldiquantforeign
- r-maldiquant
- r-ggplot2
+ r-base
+ r-maldiquantforeign
+ r-maldiquant
+ r-ggplot2
r-gridextra
@@ -31,6 +29,7 @@
10.1093/bioinformatics/bts447
10.1007/978-3-319-45809-0_6
+ 10.1093/gigascience/giz143
diff -r 71411ac28268 -r 60ee8c592b13 maldi_quant_preprocessing.xml
--- a/maldi_quant_preprocessing.xml Fri Feb 15 10:26:00 2019 -0500
+++ b/maldi_quant_preprocessing.xml Sat Mar 04 19:14:31 2023 +0000
@@ -1,4 +1,4 @@
-
+
Preprocessing of mass-spectrometry imaging data
@@ -19,8 +19,6 @@
du infile.hdr &&
du infile.img &&
du -s -B1 infile.hdr &&
- #else
- ln -s $infile infile.RData &&
#end if
Rscript "${maldi_quant_preprocessing}" &&
@@ -59,22 +57,6 @@
## Import analyze7.5 file
maldi_data = importAnalyze( 'infile.hdr' )
coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
- #else
- loadRData <- function(fileName){
- ##loads an RData file, and returns it
- load(fileName)
- get(ls()[ls() != "fileName"])
- }
- msidata = loadRData('infile.RData')
- ## save coordinates
- cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
- ## save mz values
- cardinal_mzs = Cardinal::mz(msidata)
- ## create MALDIquant MassSpectrum object, order of pixels in iData is same as in coord(msidata):
- maldi_data = list()
- for(number_spectra in 1:ncol(msidata)){
- maldi_data[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
- }
#end if
#end if
@@ -344,10 +326,6 @@
if (length(findEmptyMassObjects(maldi_data))>0)
{
- #if $infile.ext == 'rdata'
- cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
- #end if
-
maldi_data = removeEmptyMassObjects(maldi_data)
}
#end if
@@ -386,11 +364,7 @@
## export imzML file
if (length(maldi_data)>0){
- #if $infile.ext == 'rdata'
- MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
- #else
MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
- #end if
}else{"All spectra are empty, outputfiles will be empty,too."}
@@ -398,7 +372,7 @@
-
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@@ -529,7 +503,7 @@
-
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@@ -579,33 +553,12 @@
-
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@@ -615,7 +568,7 @@
@@ -631,8 +584,7 @@
- MSI data: 2 types of input data can be used:
- - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format `_
- - Cardinal "MSImageSet" data saved as .RData
+ - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format `_
- Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported.
diff -r 71411ac28268 -r 60ee8c592b13 test-data/Example_Processed.ibd
Binary file test-data/Example_Processed.ibd has changed
diff -r 71411ac28268 -r 60ee8c592b13 test-data/Example_Processed.imzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_Processed.imzML Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,380 @@
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/annotations.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations.tabular Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,4 @@
+x y pixel_index annotation
+3 1 3 col3
+2 2 5 col2
+1 3 7 col1
diff -r 71411ac28268 -r 60ee8c592b13 test-data/annotations_output3.tabular
--- a/test-data/annotations_output3.tabular Fri Feb 15 10:26:00 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-x y pixel_index annotation
-3 1 3 col3
-2 2 5 col2
-1 3 7 col1
diff -r 71411ac28268 -r 60ee8c592b13 test-data/int3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int3.tabular Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,102 @@
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/int4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int4.tabular Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,408 @@
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/masspeaks3.tabular
--- a/test-data/masspeaks3.tabular Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/masspeaks3.tabular Sat Mar 04 19:14:31 2023 +0000
@@ -1,298 +1,123 @@
snr mass intensity spectrum
-Inf 304.595254080636 1.76512676262064e-05 xy_1_1
-Inf 305.119057791574 1.62699820283052e-09 xy_1_1
-Inf 305.66667175293 1.02237303638199e-13 xy_1_1
-Inf 306.32292175293 7.71168242810122e-18 xy_1_1
-Inf 307.031265258789 5.54882387838857e-22 xy_1_1
-Inf 307.614593505859 3.61475171997316e-26 xy_1_1
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/masspeaks4.tabular
--- a/test-data/masspeaks4.tabular Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/masspeaks4.tabular Sat Mar 04 19:14:31 2023 +0000
@@ -1,1862 +1,1083 @@
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peak_detection4.ibd
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peak_detection4.imzml
--- a/test-data/peak_detection4.imzml Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection4.imzml Sat Mar 04 19:14:31 2023 +0000
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peak_detection4.imzml.txt
--- a/test-data/peak_detection4.imzml.txt Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection4.imzml.txt Sat Mar 04 19:14:31 2023 +0000
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imzML file:
-total 80
--rw-r--r-- 1 meli meli 29792 Feb 14 18:45 ibd
--rw-r--r-- 1 meli meli 45290 Feb 14 18:45 imzml
+total 40
+-rw-rw-r-- 1 meli meli 17328 Mar 3 23:28 ibd
+-rw-rw-r-- 1 meli meli 19635 Mar 3 23:28 imzml
diff -r 71411ac28268 -r 60ee8c592b13 test-data/peak_detection5.ibd
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peak_detection5.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peak_detection5.imzml Sat Mar 04 19:14:31 2023 +0000
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peak_detection5.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peak_detection5.imzml.txt Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,4 @@
+imzML file:
+total 16
+-rw-rw-r-- 1 meli meli 1744 Mar 4 18:10 ibd
+-rw-rw-r-- 1 meli meli 9244 Mar 4 18:10 imzml
diff -r 71411ac28268 -r 60ee8c592b13 test-data/peakdetection1_QC.pdf
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peakdetection2_QC.pdf
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peakdetection3_QC.pdf
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peakdetection4_QC.pdf
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/peakdetection5_QC.pdf
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/preprocessing_results3.ibd
Binary file test-data/preprocessing_results3.ibd has changed
diff -r 71411ac28268 -r 60ee8c592b13 test-data/preprocessing_results3.imzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results3.imzML Sat Mar 04 19:14:31 2023 +0000
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diff -r 71411ac28268 -r 60ee8c592b13 test-data/testfile_squares.rdata
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