| Previous changeset 6:25b83cbd596a (2020-03-25) Next changeset 8:a69865da6f80 (2020-05-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3" |
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modified:
macros.xml mz_images.xml test-data/112_auto_combined.imzml test-data/112_auto_combined.imzml.txt test-data/112_auto_combined_QC.pdf test-data/123_combined.imzml test-data/123_combined.imzml.txt test-data/123_combined_QC.pdf test-data/123_combined_auto.imzml test-data/123_combined_auto.imzml.txt test-data/123_combined_auto.pdf test-data/12_combined.imzml test-data/12_combined.imzml.txt test-data/12_combined_QC.pdf test-data/2123_auto_combined.imzml test-data/2123_auto_combined.imzml.txt test-data/2123_auto_combined_QC.pdf test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_rdata.pdf test-data/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_imzml.pdf test-data/Plot_rdata.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75.svg test-data/centroids_rdata.pdf test-data/classes_ssc.tabular test-data/cluster_skm.RData test-data/cluster_skm.tabular test-data/features_out1.tabular test-data/features_out3.tabular test-data/features_test6.tabular test-data/int_matrix1.tabular test-data/int_matrix3.tabular test-data/kmeans_analyze.pdf test-data/mean_out2.tabular test-data/pca_imzml.pdf test-data/picked.ibd test-data/picked.imzml test-data/picked.imzml.txt test-data/picked_QC.pdf test-data/pixel_out3.tabular test-data/pixels_test6.tabular test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf test-data/preprocessing_results5.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.imzml.txt test-data/preprocessing_results5.pdf test-data/sd_out2.tabular test-data/test6.pdf test-data/test6.rdata test-data/toplabels_skm.tabular test-data/toplabels_ssc.tabular |
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added:
test-data/Heatmaps_processed.pdf test-data/Plot_picked.pdf test-data/Plot_processed.pdf test-data/centroids_proc.pdf test-data/classes_proc.tabular test-data/features_out4.tabular test-data/pixel_out4.tabular test-data/spectra_1_pixel.tabular test-data/toplabels_proc.tabular |
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removed:
test-data/Plot_empty_spectra.pdf |
| b |
| diff -r 25b83cbd596a -r 5e6f8fb2df07 macros.xml --- a/macros.xml Wed Mar 25 05:31:15 2020 -0400 +++ b/macros.xml Thu Apr 23 08:08:28 2020 -0400 |
| [ |
| @@ -1,10 +1,10 @@ <macros> - <token name="@VERSION@">1.12.1</token> + <token name="@VERSION@">2.4.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> - <requirement type="package" version="3.5.1">r-base</requirement> + <requirement type="package" version="3.6.1">r-base</requirement> <yield/> </requirements> </xml> @@ -32,15 +32,10 @@ <token name="@READING_MSIDATA@"><![CDATA[ ## importing MSI data files - ## function to read RData files independent of filename - loadRData <- function(fileName){ - load(fileName) - get(ls()[ls() != "fileName"]) - } - #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": - msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE) + 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) @@ -50,6 +45,11 @@ msidata = readAnalyze('infile', attach.only=TRUE) centroided(msidata) = $centroids #else + ## function to read RData files independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } msidata = loadRData('infile.RData') #end if @@ -86,34 +86,34 @@ property_df = data.frame(properties, values) ]]></token> - <token name="@READING_MSIDATA_INRAM@"><![CDATA[ + <token name="@READING_MSIDATA_FULLY_COMPATIBLE@"><![CDATA[ ## importing MSI data files - ## function to read RData files independent of filename - loadRData <- function(fileName){ - load(fileName) - get(ls()[ls() != "fileName"]) - } - #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": - msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) centroided(msidata) = $centroids - iData(msidata) = iData(msidata)[] #else - msidata <- readImzML('infile') + msidata <- readImzML('infile', attach.only=TRUE) centroided(msidata) = $centroids #end if #elif $infile.ext == 'analyze75' - msidata = readAnalyze('infile') + msidata = readAnalyze('infile', attach.only=TRUE) centroided(msidata) = $centroids #else + ## function to read RData files independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } msidata = loadRData('infile.RData') + msidata = as(msidata, "MSImagingExperiment") + run(msidata) = "infile" #end if ]]></token> - <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ + <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ ########################### QC numbers ######################## ## including intensity calculations which need data in RAM ## Number of features (mz) @@ -130,17 +130,16 @@ minimumy = min(coord(msidata)[,2]) maximumy = max(coord(msidata)[,2]) ## Range of intensities - minint = round(min(spectra(msidata), na.rm=TRUE), digits=2) - maxint = round(max(spectra(msidata), na.rm=TRUE), digits=2) + minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) + maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) ## Number of intensities > 0, for if conditions - npeaks= sum(spectra(msidata)>0, na.rm=TRUE) + npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE) ## Number of NA in spectra matrix NAcount = sum(is.na(spectra(msidata))) ## Number of NA in spectra matrix - infcount = sum(is.infinite(spectra(msidata))) + infcount = sum(is.infinite(as.matrix(spectra(msidata)))) ## Number of duplicated coordinates dupl_coord = sum(duplicated(coord(msidata))) - properties = c("Number of m/z features", "Range of m/z values", "Number of pixels", @@ -298,6 +297,7 @@ <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/btv146</citation> + <citation type="doi">10.1093/gigascience/giz143</citation> </citations> </xml> <xml name="infile_analyze75"> |
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| diff -r 25b83cbd596a -r 5e6f8fb2df07 mz_images.xml --- a/mz_images.xml Wed Mar 25 05:31:15 2020 -0400 +++ b/mz_images.xml Thu Apr 23 08:08:28 2020 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2">\n+<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0">\n <description>\n mass spectrometry imaging m/z heatmaps\n </description>\n@@ -7,7 +7,6 @@\n </macros>\n <expand macro="requirements">\n <requirement type="package" version="2.3">r-gridextra</requirement>\n- <requirement type="package" version="0.20_35">r-lattice</requirement>\n </expand>\n <command detect_errors="aggressive">\n <![CDATA[\n@@ -23,9 +22,9 @@\n \n library(Cardinal)\n library(gridExtra)\n-library(lattice)\n+##library(lattice)\n \n-@READING_MSIDATA@\n+@READING_MSIDATA_FULLY_COMPATIBLE@\n \n @DATA_PROPERTIES@\n \n@@ -59,52 +58,26 @@\n ############################# II) images ####################################\n \n ### only plot images when file has features and pixels: \n-\n+par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend\n if (ncol(msidata)>0 & nrow(msidata) >0){\n if (length(inputmz) != 0){\n for (mass in 1:length(inputmz)){\n \n- ###standard image\n-\n- #if str($image_type) == "standard_image":\n- print("standard image")\n-\n- print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", \n- smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.2*maximumy,minimumy-1),\n- main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminus_dalton, " Da)")))}\n-\n-\n- ###lattice image\n-\n- #elif str($image_type) == "lattice_image":\n- print("lattice image")\n+ print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", \n+ smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))}\n \n- #if str($strip) =="TRUE": \n-\n- print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),\n- lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", \n- colorkey=$colorkey,ylim=c(maximumy+0.2*maximumy,minimumy-1),\n- main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminus_dalton, " Da)")))}\n-\n- #elif str($strip) =="FALSE": \n-\n- print(image(msidata, mz=inputmz[mass], strip = $strip,\n- lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", \n- colorkey=$colorkey,\n- main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminus_dalton, " Da)")))}\n-\n- #end if\n-\n- #end if \n \n ## optional svg output with original coordinates\n #if $svg_pixelimage:\n print("svg pixel image")\n ## reverse y axis for svg output = correct order and nice svg image\n coord(msidata)\\$y <- max(coord(msidata)\\$y) - coord(msidata)\\$y + 1\n+ ## works only with MSImageSet as expected\n+ msidata = as(msidata, "MSImageSet")\n+\n svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)\n- par(mar=c(0,0,0,0))\n- image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing")\n+ par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg\n+ print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton, colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = '..b'ge_type" value="lattice_image"/>\n <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>\n </test>\n <test>\n@@ -206,6 +193,7 @@\n <param name="name_column" value="1"/>\n <param name="plusminus_dalton" value="0.5"/>\n <param name="filename" value="Testfile_analyze75"/>\n+ <param name="colorscale" value="magma"/>\n <param name="image_smoothing" value="gaussian"/>\n <param name="strip" value="False"/>\n <param name="colorkey" value="True"/>\n@@ -221,7 +209,6 @@\n <param name="plusminus_dalton" value="0.5"/>\n <param name="strip" value="True"/>\n <param name="colorkey" value="True"/>\n- <param name="image_type" value="lattice_image"/>\n <param name="filename" value="Testfile_rdata"/>\n <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>\n </test>\n@@ -231,35 +218,59 @@\n <param name="mz_column" value="1"/>\n <param name="name_column" value="1"/>\n <param name="plusminus_dalton" value="0.5"/>\n+ <param name="colorscale" value="plasma"/>\n <param name="strip" value="True"/>\n <param name="colorkey" value="False"/>\n <param name="filename" value="Testfile_rdata"/>\n <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>\n </test>\n+ <test>\n+ <expand macro="processed_infile_imzml"/>\n+ <conditional name="processed_cond">\n+ <param name="processed_file" value="processed"/>\n+ <param name="accuracy" value="100"/>\n+ <param name="units" value="ppm"/>\n+ </conditional>\n+ <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>\n+ <param name="mz_column" value="1"/>\n+ <param name="name_column" value="2"/>\n+ <conditional name="overlay_cond">\n+ <param name="overlay_selection" value="yes_overlay"/>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#ff00ff"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#1f497d"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#00b050"/>\n+ </repeat>\n+ <param name="legend_position" value="topleft"/>\n+ </conditional>\n+ <output name="plots" file="Heatmaps_processed.pdf" ftype="pdf" compare="sim_size"/>\n+ </test>\n </tests>\n <help><