Mercurial > repos > galaxyp > cardinal_preprocessing
changeset 10:5abc3ab4792c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a"
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--- a/macros.xml Thu Sep 24 11:43:31 2020 +0000 +++ b/macros.xml Sun Sep 27 11:10:30 2020 +0000 @@ -117,6 +117,13 @@ <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 @@ -131,14 +138,12 @@ minimumy = min(coord(msidata)[,2]) maximumy = max(coord(msidata)[,2]) ## Range of intensities - minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) - maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) + minint = round(min(int_matrix), digits=2) + maxint = round(max(int_matrix), digits=2) ## Number of intensities > 0, for if conditions - npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE) + npeaks= sum(int_matrix>0) ## Number of NA in spectra matrix - NAcount = sum(is.na(spectra(msidata))) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(as.matrix(spectra(msidata)))) + infcount = sum(is.infinite(int_matrix)) ## Number of duplicated coordinates dupl_coord = sum(duplicated(coord(msidata))) properties = c("Number of m/z features",
--- a/preprocessing.xml Thu Sep 24 11:43:31 2020 +0000 +++ b/preprocessing.xml Sun Sep 27 11:10:30 2020 +0000 @@ -74,7 +74,7 @@ ## Choose random spectra for QC plots random_spectra = sample(pixels(msidata), 4, replace=FALSE) par(oma=c(0,0,2,0)) - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Input spectra", outer=TRUE, line=0) ############################### Preprocessing steps ########################### @@ -88,10 +88,6 @@ print('Normalization') ##normalization - if (class(msidata) == "MSProcessedImagingExperiment"){ - msidata = as(msidata, "MSContinuousImagingExperiment") - } - msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method") msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) @@ -105,7 +101,7 @@ normalized = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, normalized) vectorofactions = append(vectorofactions, "normalized") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after normalization", outer=TRUE, line=0) ############################### Baseline reduction ########################### @@ -114,10 +110,6 @@ print('Baseline_reduction') ##baseline reduction - if (class(msidata) == "MSProcessedImagingExperiment"){ - msidata = as(msidata, "MSContinuousImagingExperiment") - } - msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline) msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) @@ -130,7 +122,7 @@ baseline = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, baseline) vectorofactions = append(vectorofactions, "baseline red.") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after baseline reduction", outer=TRUE, line=0) ############################### Smoothing ########################### @@ -139,11 +131,6 @@ print('Smoothing') ## Smoothing - if (class(msidata) == "MSProcessedImagingExperiment"){ - msidata = as(msidata, "MSContinuousImagingExperiment") - } - - #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian': print('gaussian smoothing') @@ -176,7 +163,7 @@ smoothed = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, smoothed) vectorofactions = append(vectorofactions, "smoothed") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after smoothing", outer=TRUE, line=0) @@ -211,7 +198,7 @@ mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, mz_aligned) vectorofactions = append(vectorofactions, "mz aligned") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after m/z alignment", outer=TRUE, line=0) @@ -240,10 +227,6 @@ #end if msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) - #if str($method.methods_conditional.imzml_output) == "cont_format": - #set $continuous_format = True - #end if - ############################### QC ########################### @@ -254,7 +237,7 @@ picked = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, picked) vectorofactions = append(vectorofactions, "picked") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after peak picking", outer=TRUE, line=0) ############################### Peak alignment ########################### @@ -285,9 +268,6 @@ msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) - #if str($method.methods_conditional.imzml_output) == "cont_format": - #set $continuous_format = True - #end if ############################### QC ########################### @@ -298,7 +278,7 @@ aligned = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, aligned) vectorofactions = append(vectorofactions, "aligned") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after alignment", outer=TRUE, line=0) ############################### Peak filtering ########################### @@ -318,7 +298,7 @@ filtered = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, filtered) vectorofactions = append(vectorofactions, "filtered") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after filtering", outer=TRUE, line=0) ############################### Peak binning ########################### @@ -343,7 +323,7 @@ peak_binned = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, peak_binned) vectorofactions = append(vectorofactions, "peak binned") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after peak binning", outer=TRUE, line=0) @@ -387,7 +367,7 @@ reduced = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, reduced) vectorofactions = append(vectorofactions, "reduced") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after m/z binning", outer=TRUE, line=0) ############################### Transformation ########################### @@ -430,7 +410,7 @@ transformed = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, transformed) vectorofactions = append(vectorofactions, "transformed") - print(plot(msidata, pixel=random_spectra)) + print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after transformation", outer=TRUE, line=0) #end if @@ -440,6 +420,10 @@ ################################################################################ ## save msidata as imzML file, will only work if there is at least 1 m/z left + + #if str($imzml_output) == "cont_format": + #set $continuous_format = True + #end if if (nrow(msidata) > 0){ ## make sure that coordinates are integers @@ -578,7 +562,6 @@ <when value="mad"/> <when value="simple"/> </conditional> - <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/> </when> <when value="Peak_alignment"> <param name="value_diffalignment" type="float" value="200" @@ -597,7 +580,6 @@ <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/> </when> </conditional> - <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format" help= "Processed imzML works only in MALDIquant tools, not yet in MSI tools (Cardinal)"/> </when> <when value="Peak_filtering"> <param name="frequ_filtering" type="float" value="0.01" max="1" min="0" label="Minimum frequency" help="Peaks that occur in the dataset in lesser proportion than this will be dropped (0.01 --> filtering for 1% of spectra)"/> @@ -661,6 +643,7 @@ </when> </conditional> </repeat> + <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/> </inputs> <outputs> <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/> @@ -696,13 +679,11 @@ <param name="blocks_picking" value="3"/> <param name="window_picking" value="3"/> <param name="SNR_picking_method" value="3"/> - <param name="imzml_output" value="cont_format"/> </conditional> </repeat> <repeat name="methods"> <conditional name="methods_conditional"> <param name="preprocessing_method" value="Peak_alignment"/> - <param name="imzml_output" value="cont_format"/> </conditional> </repeat> <repeat name="methods"> @@ -719,6 +700,7 @@ </conditional> </conditional> </repeat> + <param name="imzml_output" value="cont_format"/> <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size"> <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/> @@ -736,15 +718,14 @@ <conditional name="methods_for_picking"> <param name="picking_method" value="adaptive"/> </conditional> - <param name="imzml_output" value="cont_format"/> </conditional> </repeat> <repeat name="methods"> <conditional name="methods_conditional"> <param name="preprocessing_method" value="Peak_alignment"/> - <param name="imzml_output" value="cont_format"/> </conditional> </repeat> + <param name="imzml_output" value="cont_format"/> <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size"> <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>
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--- a/test-data/out8.imzml.txt Thu Sep 24 11:43:31 2020 +0000 +++ b/test-data/out8.imzml.txt Sun Sep 27 11:10:30 2020 +0000 @@ -1,4 +1,4 @@ imzML file: -total 348 --rw-rw-r-- 1 meli meli 335976 Aug 23 17:42 ibd --rw-rw-r-- 1 meli meli 12402 Aug 23 17:42 imzml +total 260 +-rw-rw-r-- 1 meli meli 248824 Sep 27 11:44 ibd +-rw-rw-r-- 1 meli meli 12397 Sep 27 11:44 imzml