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Update Cardinal Version 3.4.3 #763

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merged 18 commits into from
Jul 4, 2024
Merged

Update Cardinal Version 3.4.3 #763

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aa7f3c5
change description
MarenStillger Oct 10, 2023
b44dfc6
change description
MarenStillger Oct 10, 2023
f841786
Initial commit
MarenStillger Jun 27, 2024
4c10440
Change description
MarenStillger Jun 27, 2024
4fb6609
Fix tests
MarenStillger Jun 27, 2024
efeb016
Fix test
MarenStillger Jun 27, 2024
db40ec0
Fix version token in requirements
MarenStillger Jun 28, 2024
308bd65
Fix tests and requirements
MarenStillger Jun 28, 2024
e3e7d8d
Fix tests
MarenStillger Jul 1, 2024
a1f3bd7
Fix tests
MarenStillger Jul 1, 2024
16c814a
Merge branch 'master' into Update_test
bgruening Jul 1, 2024
6732b02
Fix input linking
MarenStillger Jul 2, 2024
4f54d86
Merge remote-tracking branch 'origin/Update_test' into Update_test
MarenStillger Jul 2, 2024
a402082
Fix tests
MarenStillger Jul 2, 2024
6e1eb51
Fix tests
MarenStillger Jul 2, 2024
8bef62c
Fix tests
MarenStillger Jul 2, 2024
371f840
Fix profile and requirements
MarenStillger Jul 3, 2024
523c7c8
Merge branch 'master' into Update_test
bgruening Jul 4, 2024
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1,006 changes: 632 additions & 374 deletions tools/cardinal/classification.xml
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6 changes: 2 additions & 4 deletions tools/cardinal/colocalization.xml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,9 @@
<tool id="cardinal_colocalization" name="MSI colocalization" version="@VERSION@.0">
<tool id="cardinal_colocalization" name="MSI colocalization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<description>mass spectrometry imaging colocalization</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements">
<requirement type="package" version="2.3">r-gridextra</requirement>
</expand>
<expand macro="requirements"/>
<command detect_errors="exit_code">
<![CDATA[

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31 changes: 10 additions & 21 deletions tools/cardinal/combine.xml
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Original file line number Diff line number Diff line change
@@ -1,25 +1,21 @@
<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0">
<tool id="cardinal_combine" name="MSI combine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<description>
combine several mass spectrometry imaging datasets into one
</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements">
<requirement type="package" version="3.3.5">r-ggplot2</requirement>
<requirement type="package" version="0.12">r-maldiquantforeign</requirement>
<requirement type="package" version="1.20">r-maldiquant</requirement>
</expand>
<expand macro="requirements"/>
<command detect_errors="exit_code">
<![CDATA[
#for $i, $infile in enumerate($infiles):
#if $infile.ext == 'imzml'
ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
cp '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
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Is copying really necessary?

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unfortunately yes, otherwise neither imzml nor analyze75 files will be loaded

cp '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
#elif $infile.ext == 'analyze75'
ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr &&
ln -s '${infile.extra_files_path}/img' infile_${i}.img &&
ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
cp '${infile.extra_files_path}/hdr' infile_${i}.hdr &&
cp '${infile.extra_files_path}/img' infile_${i}.img &&
cp '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
#else
ln -s '$infile' infile_${i}.RData &&
#end if
Expand Down Expand Up @@ -103,14 +99,8 @@ all_files = $num_infiles
get(ls()[ls() != "fileName"])
}
msidata_$i = loadRData('infile_${i}.RData')
## keep compatibility with old .RData files:
msidata_$i\$column1 = NULL
msidata_$i\$column2 = NULL
msidata_$i\$column3 = NULL
msidata_$i\$column4 = NULL
msidata_$i\$column5 = NULL
msidata_$i\$combined_sample = NULL
msidata_$i <- as(msidata_$i, "MSImagingExperiment")

#end if

## remove duplicated coordinates, otherwise combine will fail
Expand All @@ -128,7 +118,6 @@ all_files = $num_infiles
############ 3) Read and process annotation tabular files ######################

#if str($annotation_cond.annotation_tabular) == 'annotation'
print("annotations")

## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE)
Expand All @@ -138,7 +127,7 @@ all_files = $num_infiles
colnames(msidata_coordinates)[3] = "pixel_index"

annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]## orders pixel according to msidata
annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]
annotation_df_sorted\$pixel_index = NULL

## extract columnnames from (last) annotation tabular (for QC plot names)
Expand Down Expand Up @@ -171,7 +160,7 @@ all_files = $num_infiles

#elif str( $combine_conditional.combine_method ) == 'automatic_combine':

## use name of Galaxy inputfile as sample annotation
## use name of Galaxy input file as sample annotation
sample_name = character()
#set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))

Expand Down
20 changes: 12 additions & 8 deletions tools/cardinal/data_exporter.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.0">
<tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<description>
exports imzML and Analyze7.5 to tabular files
</description>
Expand Down Expand Up @@ -102,7 +102,7 @@ if (class(msidata) == "MSImageSet"){
count = 1
for (subsample in levels(msidata\$annotation)){
subsample_pixels = msidata[,msidata\$annotation == subsample]
subsample_calc = rowMeans(spectra(subsample_pixels), na.rm=TRUE)
subsample_calc = rowMeans(as.matrix(spectra(subsample_pixels)), na.rm=TRUE)
sample_matrix = cbind(sample_matrix, subsample_calc)
count = count+1}
sample_matrix_mean = cbind(mz_names,sample_matrix)
Expand All @@ -117,7 +117,7 @@ if (class(msidata) == "MSImageSet"){
count = 1
for (subsample in levels(msidata\$annotation)){
subsample_pixels = msidata[,msidata\$annotation == subsample]
subsample_calc = apply(spectra(subsample_pixels),1,median, na.rm=TRUE)
subsample_calc = apply(as.matrix(spectra(subsample_pixels)),1,median, na.rm=TRUE)
sample_matrix = cbind(sample_matrix, subsample_calc)
count = count+1}
sample_matrix_median = cbind(mz_names,sample_matrix)
Expand Down Expand Up @@ -190,13 +190,13 @@ if (class(msidata) == "MSImageSet"){

for (mass in 1:length(inputcalibrantmasses)){
filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
if (nrow(filtered_data) > 1 & sum(spectra(filtered_data),na.rm=TRUE) > 0){
if (nrow(filtered_data) > 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){
## intensity of all m/z > 0
intensity_sum = colSums(spectra(filtered_data), na.rm=TRUE) > 0
intensity_sum = colSums(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0

}else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data), na.rm=TRUE) > 0){
}else if(nrow(filtered_data) == 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){
## intensity of only m/z > 0
intensity_sum = spectra(filtered_data) > 0
intensity_sum = as.matrix(spectra(filtered_data)) > 0
}else{
intensity_sum = rep(FALSE, ncol(filtered_data))}
## for each pixel add sum of intensities > 0 in the given m/z range
Expand Down Expand Up @@ -343,7 +343,11 @@ if (class(msidata) == "MSImageSet"){
<param name="feature_header" value="False"/>
<param name="plusminus_ppm" value="200"/>
</conditional>
<output name="feature_output" file="features_out4.tabular"/>
<output name="feature_output">
<assert_contents>
<has_text text="100.120072029209"/>
</assert_contents>
</output>
<output name="pixel_output" file="pixel_out4.tabular"/>
</test>
</tests>
Expand Down
7 changes: 2 additions & 5 deletions tools/cardinal/filtering.xml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,9 @@
<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.0">
<tool id="cardinal_filtering" name="MSI filtering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<description>tool for filtering mass spectrometry imaging data</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements">
<requirement type="package" version="2.3">r-gridextra</requirement>
<requirement type="package" version="3.3.5">r-ggplot2</requirement>
</expand>
<expand macro="requirements"/>
<expand macro="print_version"/>
<command detect_errors="exit_code">
<![CDATA[
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36 changes: 23 additions & 13 deletions tools/cardinal/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,20 @@
<macros>
<token name="@VERSION@">2.10.0</token>
<token name="@TOOL_VERSION@">3.4.3</token>
<token name="@VERSION_SUFFIX@">0</token>

<xml name="requirements">
<requirements>
<requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
<!--requirement type="package" version="3.6.1">r-base</requirement-->
<requirement type="package" version="@TOOL_VERSION@">bioconductor-cardinal</requirement>
<requirement type="package" version="2.3">r-gridextra</requirement>
<requirement type="package" version="3.5.1">r-ggplot2</requirement>
<requirement type="package" version="0.14.1">r-maldiquantforeign</requirement>
<requirement type="package" version="1.22.2">r-maldiquant</requirement>
<requirement type="package" version="3.50.0">bioconductor-sva</requirement>
<requirement type="package" version="1.1.0.1">r-randomcolor</requirement>
<requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>
<requirement type="package" version="2.23_24">r-kernsmooth</requirement>
<requirement type="package" version="1.3.0">r-scales</requirement>
<requirement type="package" version="1.0.12">r-pheatmap</requirement>
<yield/>
</requirements>
</xml>
Expand All @@ -17,12 +27,12 @@ echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanil

<token name="@INPUT_LINKING@"><![CDATA[
#if $infile.ext == 'imzml'
ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
cp '${infile.extra_files_path}/imzml' infile.imzML &&
cp '${infile.extra_files_path}/ibd' infile.ibd &&
#elif $infile.ext == 'analyze75'
ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
ln -s '${infile.extra_files_path}/img' infile.img &&
ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
cp '${infile.extra_files_path}/hdr' infile.hdr &&
cp '${infile.extra_files_path}/img' infile.img &&
cp '${infile.extra_files_path}/t2m' infile.t2m &&
#else
ln -s $infile infile.RData &&
#end if
Expand All @@ -38,13 +48,13 @@ echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanil
get(ls()[ls() != "fileName"])
}


#if $infile.ext == 'imzml'
#if str($processed_cond.processed_file) == "processed":
msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units")
msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous
centroided(msidata) = $centroids
#else
msidata <- readImzML('infile', attach.only=TRUE)
msidata <- readImzML('infile')
centroided(msidata) = $centroids
#end if
#elif $infile.ext == 'analyze75'
Expand Down Expand Up @@ -95,7 +105,7 @@ echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanil
msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
centroided(msidata) = $centroids
#else
msidata <- readImzML('infile', attach.only=TRUE)
msidata <- readImzML('infile')
centroided(msidata) = $centroids
#end if
#elif $infile.ext == 'analyze75'
Expand All @@ -117,13 +127,13 @@ echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanil
<token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
########################### QC numbers ########################
## including intensity calculations which need data in RAM

int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use
## Number of NA in spectra matrix
NAcount = sum(is.na(int_matrix))
## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata
int_matrix[is.na(int_matrix)] <- 0



## Number of features (mz)
maxfeatures = length(features(msidata))
## Range mz
Expand Down
22 changes: 10 additions & 12 deletions tools/cardinal/mz_images.xml
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Original file line number Diff line number Diff line change
@@ -1,13 +1,11 @@
<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0">
<tool id="cardinal_mz_images" name="MSI mz images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<description>
mass spectrometry imaging m/z heatmaps
</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements">
<requirement type="package" version="2.3">r-gridextra</requirement>
</expand>
<expand macro="requirements"/>
<command detect_errors="aggressive">
<![CDATA[
@INPUT_LINKING@
Expand Down Expand Up @@ -83,8 +81,8 @@ if (ncol(msidata)>0 & nrow(msidata) >0){
print("svg pixel image")
## reverse y axis for svg output = correct order and nice svg image
coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1
## works only with MSImageSet as expected
msidata = as(msidata, "MSImageSet")

msidata = as(msidata,"MSImagingExperiment")

svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
Expand Down Expand Up @@ -132,7 +130,7 @@ dev.off()
<expand macro="pdf_filename"/>
<expand macro="reading_2_column_mz_tabular"/>

<param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/>
<param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/z" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/>
<param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
<option value="none" selected="True">none</option>
<option value="suppression">suppression</option>
Expand Down Expand Up @@ -193,7 +191,7 @@ dev.off()
</data>
</outputs>
<tests>
<test>
<test expect_num_outputs="1">
<expand macro="infile_imzml"/>
<param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
<param name="mz_column" value="1"/>
Expand All @@ -204,7 +202,7 @@ dev.off()
<param name="colorkey" value="True"/>
<output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>
</test>
<test>
<test expect_num_outputs="2">
<expand macro="infile_analyze75"/>
<param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
<param name="mz_column" value="1"/>
Expand All @@ -218,7 +216,7 @@ dev.off()
<output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
<output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
</test>
<test>
<test expect_num_outputs="1">
<param name="infile" value="preprocessed.RData" ftype="rdata"/>
<param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
<param name="mz_column" value="1"/>
Expand All @@ -228,7 +226,7 @@ dev.off()
<param name="filename" value="Testfile_rdata"/>
<output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>
</test>
<test>
<test expect_num_outputs="1">
<param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
<param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
<param name="mz_column" value="1"/>
Expand All @@ -239,7 +237,7 @@ dev.off()
<param name="filename" value="Testfile_rdata"/>
<output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>
</test>
<test>
<test expect_num_outputs="1">
<expand macro="processed_infile_imzml"/>
<conditional name="processed_cond">
<param name="processed_file" value="processed"/>
Expand Down
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