# HG changeset patch # User galaxyp # Date 1534952946 14400 # Node ID e2aa05746a6981c9b94416ef030ce774ad53b3b1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 diff -r 000000000000 -r e2aa05746a69 maldi_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maldi_macros.xml Wed Aug 22 11:49:06 2018 -0400 @@ -0,0 +1,26 @@ + + + + + + + bioconductor-cardinal + r-maldiquantforeign + r-maldiquant + r-ggplot2 + + + + + + 10.1093/bioinformatics/bts447 + + + diff -r 000000000000 -r e2aa05746a69 maldi_quant_preprocessing.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maldi_quant_preprocessing.xml Wed Aug 22 11:49:06 2018 -0400 @@ -0,0 +1,509 @@ + + + Preprocessing of mass-spectrometry imaging data + + + maldi_macros.xml + + + + $outfile_imzml && + ls -l "$outfile_imzml.files_path" >> $outfile_imzml + ]]> + + + 20 && number_combined<40){ + legend_size = 9 + }else if (number_combined>40 && number_combined<60){ + legend_size = 8 + }else if (number_combined>60 && number_combined<100){ + legend_size = 7 + }else{ + legend_size = 6 + } + + combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+ + geom_tile() + + coord_fixed()+ + ggtitle("Spatial orientation of annotated data")+ + theme_bw()+ + theme(plot.title = element_text(hjust = 0.5))+ + theme(text=element_text(family="ArialMT", face="bold", size=12))+ + theme(legend.position="bottom",legend.direction="vertical")+ + theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ + guides(fill=guide_legend(ncol=5,byrow=TRUE)) + + print(combine_plot) + +#end if + +#################### Preprocessing methods ##################################### + +## QC plot +avgSpectra = averageMassSpectra(maldi_data,method="mean") +plot(avgSpectra, main="Average spectrum for input file") + +#for $method in $methods: + + #if str( $method.methods_conditional.method ) == 'Transformation': + + print('transforming') + ##transformation + maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method") + ## QC plot + avgSpectra = averageMassSpectra(maldi_data,method="mean") + plot(avgSpectra, main="Average spectrum after transformation") + + + #elif str( $method.methods_conditional.method ) == 'Smoothing': + + print('smoothing') + ##smoothing + + #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay': + print('SavitzkyGolay') + + maldi_data = smoothIntensity(maldi_data, + method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial, + halfWindowSize=$method.methods_conditional.halfWindowSize) + + #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage': + print('MovingAverage') + + maldi_data = smoothIntensity(maldi_data, + method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted, + halfWindowSize=$method.methods_conditional.halfWindowSize) + + #end if + + ## QC plot + avgSpectra = averageMassSpectra(maldi_data,method="mean") + plot(avgSpectra, main="Average spectrum after smoothing") + + + #elif str( $method.methods_conditional.method ) == 'Baseline': + + print('baseline removing') + ## Remove baseline + + maldi_data = removeBaseline(maldi_data, + method="$method.methods_conditional.baseline_method", + iterations=$method.methods_conditional.iterations) + ## QC plot + avgSpectra = averageMassSpectra(maldi_data,method="mean") + plot(avgSpectra, main="Average spectrum after baseline removal") + + + #elif str( $method.methods_conditional.method ) == 'Calibrate': + + print('calibrate') + ##calibrate + + #if $method.methods_conditional.mass_start != 0 and $method.methods_conditional.mass_end != 0: + ## calibrate only given m/z range + maldi_data = calibrateIntensity(maldi_data, + method="$method.methods_conditional.calibrate_method", + range=c($method.methods_conditional.mass_start, $method.methods_conditional.mass_end)) + #else: + maldi_data = calibrateIntensity(maldi_data, + method="$method.methods_conditional.calibrate_method") + #end if + ## QC plot + avgSpectra = averageMassSpectra(maldi_data,method="mean") + plot(avgSpectra, main="Average spectrum after normalization") + + + #elif str( $method.methods_conditional.method ) == 'Align': + + print('align') + ##align spectra + + #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference': + + maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize, + SNR=$method.methods_conditional.snr, + tolerance=$method.methods_conditional.tolerance, + warpingMethod="$method.methods_conditional.warping_method") + + #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference': + + ## create reference mass_vector from tabular file + mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = FALSE, stringsAsFactors = FALSE)[,1] + int_vector = rep(1,length(mass_vector)) + mass_list = createMassPeaks(mass_vector, int_vector) + + maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize, + SNR=$method.methods_conditional.snr, + tolerance=$method.methods_conditional.tolerance, + warpingMethod="$method.methods_conditional.warping_method", + reference = mass_list, allowNoMatches =$method.methods_conditional.reference_for_alignment.allow_nomatch, emptyNoMatches = $method.methods_conditional.reference_for_alignment.empty_nomatch) + + #if $method.methods_conditional.reference_for_alignment.remove_empty: + + #if $infile.ext == 'rdata' + cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),] ## remove coordinates of empty spectra for Cardinal RData input + #end if + #if str($tabular_annotation.load_annotation) == 'yes_annotation': + merged_annotation = merged_annotation[-findEmptyMassObjects(maldi_data),] ## remove coordinate annotations for empty spectra + #end if + maldi_data = removeEmptyMassObjects(maldi_data) + #end if + #end if + + ## QC plot + + if (length(maldi_data)>0){ + avgSpectra = averageMassSpectra(maldi_data,method="mean") + plot(avgSpectra, main="Average spectrum after alignment") + }else{"All spectra are empty"} + + #end if +#end for + +dev.off() + +## export imzML file +if (length(maldi_data)>0){ + #if $infile.ext == 'rdata' + MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates) + #else + MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed) + #end if + + ## export annotation tabular file + #if str($tabular_annotation.load_annotation) == 'yes_annotation': + write.table(merged_annotation, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") + #end if +}else{"All spectra are empty, outputfiles will be empty,too."} + + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tabular_annotation["load_annotation"] == 'yes_annotation' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_ +- optinal tabular file with pixel coordinates to restrict reading of imzML file to coordinates of interest + +Options: + +- Transformation: transformation of intensities with log, log2, log10 and squareroot +- Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are SavitzkyGolay and Moving Average +- Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets). Available methods are SNIP, TopHat,ConvexHull and median. +- Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN) +- Spectra alignment (warping):alignment for (re)calibration of m/z values + + +Output: + +- imzML file (imzML format can be continuous or processed) +- pdf with average mass spectra after each preprocessing step + +.. _MALDIquant: http://strimmerlab.org/software/maldiquant/ + + ]]> + + + diff -r 000000000000 -r e2aa05746a69 test-data/Analyze75.hdr Binary file test-data/Analyze75.hdr has changed diff -r 000000000000 -r e2aa05746a69 test-data/Analyze75.img Binary file test-data/Analyze75.img has changed diff -r 000000000000 -r e2aa05746a69 test-data/Analyze75.t2m Binary file test-data/Analyze75.t2m has changed diff -r 000000000000 -r e2aa05746a69 test-data/Example_Continuous.ibd Binary file test-data/Example_Continuous.ibd has changed diff -r 000000000000 -r e2aa05746a69 test-data/Example_Continuous.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Wed Aug 22 11:49:06 2018 -0400 @@ -0,0 +1,313 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r e2aa05746a69 test-data/Preprocessing1_QC.pdf Binary file test-data/Preprocessing1_QC.pdf has changed diff -r 000000000000 -r e2aa05746a69 test-data/Preprocessing2_QC.pdf Binary file test-data/Preprocessing2_QC.pdf has changed diff -r 000000000000 -r e2aa05746a69 test-data/Preprocessing3_QC.pdf Binary file test-data/Preprocessing3_QC.pdf has changed diff -r 000000000000 -r e2aa05746a69 test-data/align_reference_test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align_reference_test2.tabular Wed Aug 22 11:49:06 2018 -0400 @@ -0,0 +1,2 @@ +350 +340 diff -r 000000000000 -r e2aa05746a69 test-data/annotations_output3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_output3.tabular Wed Aug 22 11:49:06 2018 -0400 @@ -0,0 +1,4 @@ +x y pixel_index annotation +3 1 3 col3 +2 2 5 col2 +1 3 7 col1 diff -r 000000000000 -r e2aa05746a69 test-data/int1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int1.tabular Wed Aug 22 11:49:06 2018 -0400 @@ -0,0 +1,91 @@ +mz | spectra col1 col2 col3 +300.083343505859 0 0.0878976186116536 0 +304 9.438736829163e-11 0.137228806813558 0.203098436196645 +304.166687011719 0.104457606871923 0.0169352528949116 0.00765286510187286 +304.666687011719 0.00242311644190166 0.15201666439801 0.269343495368958 +305 0.238949338595072 0 0 +305.75 6.17044061804064e-07 0.155222187439613 1.2719295986822e-09 +305.916687011719 4.33073489900975e-15 0.20923868753016 0.186377684291186 +306.25 0.133792817751516 3.32863570899159e-06 0.00443744411071142 +306.666687011719 0.232789536317284 4.21300777966646e-07 0.00672620768781245 +306.916687011719 0.322907487551371 0.0935481031580518 0.012873843312233 +307.083343505859 0.146026631196443 0.151374835480731 0.218145370482365 +307.166687011719 0.0322767967978232 0.0595835944471799 0.48292171999357 +307.75 4.47047947697381e-07 0.14276859164238 2.35246092014329e-05 +308 4.74193198607586e-31 0.0105287345747153 0.107646773258845 +308.25 1.31886150149067e-10 0.34317347407341 2.12085331600466e-18 +309.833343505859 1.04017844226842e-22 8.99523714516626e-14 0.161644687255224 +311.5 8.2674876717639e-36 0.126103460788727 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0.170605540275574 2.68065472318023e-19 4.58339070400444e-10 +397.083343505859 0.0962067842483521 5.10727327656766e-39 1.3634908830594e-18 +398.166687011719 4.69207117603236e-10 0 0.142847468455633 +398.75 0.214157521724701 0 0.0781838993231456 diff -r 000000000000 -r e2aa05746a69 test-data/int2.tabular diff -r 000000000000 -r e2aa05746a69 test-data/intensity_matrix3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/intensity_matrix3.tabular Wed Aug 22 11:49:06 2018 -0400 @@ -0,0 +1,61 @@ +mz | spectra x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3 +304.595254080636 1.76512676262064e-05 0 0.327420804051165 1.17177887401856e-13 2.65423709869989e-05 0 0.279548346996307 0.256212419994475 0.226718190873036 +305.119057791574 1.62699820283052e-09 0 1.36897748140363e-05 5.69736818276873e-18 1.71781823336396e-09 0 0.716848015785217 1.44706262158933e-05 9.11607707771881e-06 +305.66667175293 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306.25 0.133792817751516 x = 1, y = 1 +11.9239943102966 306.666687011719 0.232789536317284 x = 1, y = 1 +16.7672721943661 306.916687011719 0.322907487551371 x = 1, y = 1 +14.5727405573344 315.916687011719 0.134740673005581 x = 1, y = 1 +12.6587975530526 316.25 0.117780188719432 x = 1, y = 1 +15.5891513371263 320.916687011719 0.0873032609621684 x = 1, y = 1 +8.28066653191209 322.75 0.107258200645447 x = 1, y = 1 +8.64305080588796 327.083343505859 0.593451981743177 x = 1, y = 1 +22.5976205263238 329 1.80600585540136 x = 1, y = 1 +6.62986417925206 343.083343505859 0.319934318463008 x = 1, y = 1 +5.76872573536526 343.75 0.314895849686906 x = 1, y = 1 +7.23012875909998 344 0.41009783744812 x = 1, y = 1 +12.5923211364761 345 0.777459700902303 x = 1, y = 1 +5.61154187261139 346.083343505859 0.311080597071943 x = 1, y = 1 +11.6128628366043 353.083343505859 0.0853602389494578 x = 1, y = 1 +8.93926402677033 355.166687011719 0.093819797039032 x = 1, y = 1 +11.4518402499656 355.916687011719 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367.083343505859 1.29202726295574e-09 x = 1, y = 3 +Inf 367.645835876465 1.26925610321495e-13 x = 1, y = 3 +Inf 368.222229003906 6.86202649112451e-18 x = 1, y = 3 +Inf 368.666680908203 6.0804923995715e-22 x = 1, y = 3 +Inf 369.216674804688 3.92168363149906e-26 x = 1, y = 3 +Inf 369.766680908203 2.87628364894794e-30 x = 1, y = 3 +Inf 370.523821149554 2.11079916033934e-34 x = 1, y = 3 +Inf 306.32292175293 2.58914169535274e-05 x = 2, y = 3 +Inf 307.031265258789 0.2786685526371 x = 2, y = 3 +Inf 307.614593505859 2.96689468086697e-05 x = 2, y = 3 +Inf 308.266668701172 0.630028009414673 x = 2, y = 3 +Inf 308.718757629395 3.5055691114394e-05 x = 2, y = 3 +Inf 309.250011444092 3.4764433554102e-09 x = 2, y = 3 +Inf 309.833347865513 2.08417769262566e-13 x = 2, y = 3 +Inf 310.361124674479 1.65365266219334e-17 x = 2, y = 3 +Inf 310.902786254883 1.14908291585848e-21 x = 2, y = 3 +Inf 311.430557250977 7.77481833182232e-26 x = 2, y = 3 +Inf 311.986119588216 6.04272858040201e-30 x = 2, y = 3 +Inf 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349.44445461697 6.95620575449764e-22 x = 2, y = 3 +Inf 349.96297539605 5.08223484114241e-26 x = 2, y = 3 +Inf 351.069458007812 2.63284561467787e-34 x = 2, y = 3 +Inf 370.523821149554 0.38996833562851 x = 2, y = 3 +Inf 328.937515258789 1.43404459953308 x = 3, y = 3 +Inf 329.697925567627 6.18351987213828e-05 x = 3, y = 3 +Inf 330.712968614366 3.4482751940304e-13 x = 3, y = 3 +Inf 331.259270562066 2.93395139921047e-17 x = 3, y = 3 +Inf 331.796308729384 1.94369975414076e-21 x = 3, y = 3 +Inf 332.342600504557 1.38486306848585e-25 x = 3, y = 3 +Inf 332.879638671875 1.03717248235199e-29 x = 3, y = 3 +Inf 333.44445461697 6.46787389371651e-34 x = 3, y = 3 +Inf 334.020843505859 5.33374608969737e-38 x = 3, y = 3 +Inf 345.629638671875 0.000100398268841673 x = 3, y = 3 +Inf 346.120378282335 0.700047612190247 x = 3, y = 3 +Inf 347.296308729384 0.290130436420441 x = 3, y = 3 +Inf 347.814826117622 1.69061459018849e-05 x = 3, y = 3 +Inf 348.361117892795 1.38276745609289e-09 x = 3, y = 3 +Inf 348.888895670573 9.4092654945744e-14 x = 3, y = 3 +Inf 349.44445461697 6.51254681822392e-18 x = 3, y = 3 +Inf 349.96297539605 4.97919259365601e-22 x = 3, y = 3 +Inf 387.850006103516 4.42154814663809e-05 x = 3, y = 3 +Inf 388.895843505859 2.20461995013854e-13 x = 3, y = 3 +Inf 389.854179382324 1.07776605300705e-21 x = 3, y = 3 +Inf 391.083335876465 5.18557991695755e-30 x = 3, y = 3 +Inf 391.972229003906 2.46211811583847e-38 x = 3, y = 3 +Inf 394.083351135254 0.225453585386276 x = 3, y = 3 +Inf 394.791679382324 0.310508847236633 x = 3, y = 3 +Inf 395.270843505859 2.11353399208747e-05 x = 3, y = 3 +Inf 395.816680908203 1.37501721120259e-09 x = 3, y = 3 +Inf 396.383337402344 9.99066823194339e-14 x = 3, y = 3 +Inf 396.916674804687 7.3794850397387e-18 x = 3, y = 3 diff -r 000000000000 -r e2aa05746a69 test-data/msidata_1.RData Binary file test-data/msidata_1.RData has changed diff -r 000000000000 -r e2aa05746a69 test-data/outfile1.ibd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ 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