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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c |
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modified:
macros.xml quality_report.xml 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_empty_spectra.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/analyze75_filtered2.pdf test-data/analyze_filteredoutside.RData test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf test-data/kmeans_analyze.pdf test-data/pca_imzml.pdf test-data/rdata_notfiltered.RData test-data/rdata_notfiltered.pdf test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
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removed:
test-data/imzml_filtered2.RData test-data/imzml_filtered2.pdf |
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| diff -r 5f18275c250a -r ae9ffc7ba261 macros.xml --- a/macros.xml Mon Oct 01 01:07:13 2018 -0400 +++ b/macros.xml Thu Oct 25 07:28:42 2018 -0400 |
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| @@ -4,10 +4,17 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> + <requirement type="package" version="3.5.1">r-base</requirement> <yield/> </requirements> </xml> + <xml name="print_version"> + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + <token name="@INPUT_LINKING@"><![CDATA[ #if $infile.ext == 'imzml' ln -s '${infile.extra_files_path}/imzml' infile.imzML && @@ -33,14 +40,14 @@ #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', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE) centroided(msidata) = $centroids #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 msidata = loadRData('infile.RData') @@ -177,7 +184,8 @@ <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name"> <sanitizer invalid_char=""> <valid initial="string.ascii_letters,string.digits"> - <add value="_" /> + <add value="_"/> + <add value=" "/> </valid> </sanitizer> </param> @@ -198,12 +206,12 @@ <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> </xml> - <xml name="reading_2_column_mz_tabular"> - <param name="calibrant_file" type="data" optional="true" format="tabular" + <xml name="reading_2_column_mz_tabular" token_optional="false"> + <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular" label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/> - <param name="mz_column" data_ref="calibrant_file" label="Column with m/z values" type="data_column"/> - <param name="name_column" data_ref="calibrant_file" label="Column with name of m/z values" type="data_column"/> - <param name="calibrant_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/> + <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/> + <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> </xml> <xml name="reading_pixel_annotations"> |
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| diff -r 5f18275c250a -r ae9ffc7ba261 quality_report.xml --- a/quality_report.xml Mon Oct 01 01:07:13 2018 -0400 +++ b/quality_report.xml Thu Oct 25 07:28:42 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.0">\n+<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.1">\n <description>\n mass spectrometry imaging QC\n </description>\n@@ -6,12 +6,12 @@\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements">\n- <requirement type="package" version="2.2.1">r-ggplot2</requirement>\n <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>\n- <requirement type="package" version="2.2.1">r-gridextra</requirement>\n+ <requirement type="package" version="2.3">r-gridextra</requirement>\n+ <requirement type="package" version="3.0">r-ggplot2</requirement>\n <requirement type="package" version="2.23_15">r-kernsmooth</requirement>\n- <requirement type="package" version="0.5.0">r-scales</requirement>\n- <requirement type="package" version="1.0.8"> r-pheatmap</requirement>\n+ <requirement type="package" version="1.0.0">r-scales</requirement>\n+ <requirement type="package" version="1.0.10"> r-pheatmap</requirement>\n </expand>\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -33,6 +33,7 @@\n library(scales)\n library(pheatmap)\n \n+\n @READING_MSIDATA@\n \n ## remove duplicated coordinates\n@@ -362,7 +363,7 @@\n peaksperpixel = colSums(spectra(msidata)[]> 0, na.rm=TRUE)\n peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel)\n \n- print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)+\n+ print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel))+\n geom_tile() + coord_fixed() +\n ggtitle("Number of peaks per spectrum")+\n theme_bw() +\n@@ -375,9 +376,8 @@\n ############################### 6) TIC image ###############################\n \n TICcoordarray=cbind(coord(msidata)[,1:2], TICs)\n- colo = colorRampPalette(\n- c("blue", "cyan", "green", "yellow","red"))\n- print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)+\n+\n+ print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs))+\n geom_tile() + coord_fixed() +\n ggtitle("Total Ion Chromatogram")+\n theme_bw() +\n@@ -386,6 +386,20 @@\n scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") \n ,space = "Lab", na.value = "black", name = "TIC"))\n \n+ ############################### 6b) median int image ###############################\n+\n+ median_int = apply(spectra(msidata)[],2,median) \n+ median_coordarray=cbind(coord(msidata)[,1:2], median_int)\n+ print(ggplot(median_coordarray, aes(x=x, y=y, fill=median_int))+\n+ geom_tile() + coord_fixed() +\n+ ggtitle("Median intensity per pixel")+\n+ theme_bw() +\n+ theme(plot.title = element_text(hjust = 0.5))+\n+ theme(text=element_text(family="ArialMT", face="bold", size=12))+\n+ scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") \n+ ,space = "Lab", na.value = "black", name = "median\\nintensity"))\n+\n+\n \n ############################### 7) Most abundant m/z image #################\n \n@@ -407,6 +421,7 @@\n \n #if $do_pca:\n \n+ set.seed(1)\n pca = PCA(msidata, ncomp=2) \n par(mfrow = c(2,1))\n plot(pca, col=c("black", "darkgrey"), main="PCA for two components")\n@@ -499,7 +514,6 @@\n ########################## 12) Number of peaks per m/z #####################\n \n peakspermz = rowSums(spectra(msidata)[] > 0, na.rm=TRUE)\n-print(median(peakspermz/pixelcount*100))\n \n par(mfrow = c(2,1), mar=c(5,6,4,4.5))\n ## 12a) scatterplot\n@@ -600,7 +614,7 @@\n \n heatmap.parameters <- list(corr_matrix, \n show_rownames = T, show_colnames = T,\n- main = "Pearson correlation on mean intensities for each annotation group")\n+ main = "Pearson correlation on mean intensities")\n do.call("pheatmap", heatmap.parameters)\n }\n \n@@ -639,8 +653,8 @@\n for (mass in '..b' </conditional>\n <expand macro="pdf_filename"/>\n- <expand macro="reading_2_column_mz_tabular"/>\n+ <expand macro="reading_2_column_mz_tabular" optional="true"/>\n <param name="plusminus_ppm" value="200" type="float" label="ppm range" help="Will be added in both directions to input calibrant m/z"/>\n <param name="do_pca" type="boolean" label="PCA with 2 components"/>\n <repeat name="calibrantratio" title="Plot fold change of two m/z" min="0" max="10">\n@@ -855,9 +872,6 @@\n <conditional name="tabular_annotation">\n <param name="load_annotation" value="no_annotation"/>\n </conditional>\n- <param name="calibrant_file" value="inputcalibrantfile2.txt"/>\n- <param name="mz_column" value="1"/>\n- <param name="name_column" value="2"/>\n <param name="filename" value="Testfile_analyze75"/>\n <param name="do_pca" value="True"/>\n <output name="QC_report" file="QC_analyze75.pdf" compare="sim_size"/>\n@@ -946,6 +960,7 @@\n - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z. The intensities are averaged within the calibrant m/z window (ppm range). \n - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap.\n - Total ion chromatogram: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap. \n+- Median intensity: For each spectrum the median intensity is plotted as heatmap. \n - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted. \n - PCA for two components: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels. \n \n@@ -973,7 +988,7 @@\n **Mass spectra and m/z accuracy**\n \n - Mass spectra over the full m/z range: First plot shows the average intensities over all spectra. The other three mass spectra are from random individual pixels (spectra). \n-- (cal) For each calibrant four zoomed in mass spectrum are drawn: The first shows the average intensities over all spectra and the other three are single mass spectra. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window.\n+- (cal) For each calibrant four zoomed in mass spectrum are drawn: The first two mass spectra show the average intensities over all spectra and the other two specra are from random individual pixels. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window. In the second average spectra plot each blue plot indicates one data point.\n - (annot) Average spectrum per annotation group: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each annotation group separately. \n - (cal) Difference m/z with max. average intensity vs. theor. calibrant m/z: The difference in ppm between the m/z with the highest average intensity and the theoretical m/z are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the red line in the zoomed in mass spectra. \n - (cal) Difference closest measured m/z vs. theor. calibrant m/z: The difference in ppm between the closest m/z value and the theoretical m/z values are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the green line in the zoomed in mass spectra. \n' |
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| diff -r 5f18275c250a -r ae9ffc7ba261 test-data/analyze75.svg --- a/test-data/analyze75.svg Mon Oct 01 01:07:13 2018 -0400 +++ b/test-data/analyze75.svg Thu Oct 25 07:28:42 2018 -0400 |
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