Merge pull request #763 from MarenStillger/Update_test

Update Cardinal Version 3.4.3
galaxyproteomics · Jul 4, 2024 · 91e77c1 · 91e77c1
2 parents 17fc7ee + 523c7c8
commit 91e77c1
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diff --git a/tools/cardinal/classification.xml b/tools/cardinal/classification.xml
diff --git a/tools/cardinal/colocalization.xml b/tools/cardinal/colocalization.xml
@@ -1,11 +1,9 @@
-<tool id="cardinal_colocalization" name="MSI colocalization" version="@[email protected]">
+<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[
 

diff --git a/tools/cardinal/combine.xml b/tools/cardinal/combine.xml
@@ -1,25 +1,21 @@
-<tool id="cardinal_combine" name="MSI combine" version="@[email protected]">
+<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_${i}.imzML &&
+                cp '${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
@@ -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
@@ -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)
@@ -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)
@@ -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))
 

diff --git a/tools/cardinal/data_exporter.xml b/tools/cardinal/data_exporter.xml
@@ -1,4 +1,4 @@
-<tool id="cardinal_data_exporter" name="MSI data exporter" version="@[email protected]">
+<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>
@@ -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)
@@ -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)
@@ -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
@@ -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>

diff --git a/tools/cardinal/filtering.xml b/tools/cardinal/filtering.xml
@@ -1,12 +1,9 @@
-<tool id="cardinal_filtering" name="MSI filtering" version="@[email protected]">
+<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[

diff --git a/tools/cardinal/macros.xml b/tools/cardinal/macros.xml
@@ -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>
@@ -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
@@ -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'
@@ -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'
@@ -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

diff --git a/tools/cardinal/mz_images.xml b/tools/cardinal/mz_images.xml
@@ -1,13 +1,11 @@
-<tool id="cardinal_mz_images" name="MSI mz images" version="@[email protected]">
+<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@
@@ -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
@@ -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>
@@ -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"/>
@@ -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"/>
@@ -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"/>
@@ -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"/>
@@ -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"/>