Mercurial > repos > galaxyp > maldi_quant_peak_detection

comparison maldi_quant_peakdetection.xml @ 6:8431b33e6989 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
author galaxyp
date Thu, 16 Apr 2020 21:48:53 +0000
parents af766257766e
children 4bd085117204
comparison
equal deleted inserted replaced
5:af766257766e 6:8431b33e6989
1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.5"> 1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.6">
2 <description> 2 <description>
3 Peak detection, binning and filtering for mass-spectrometry imaging data 3 Peak detection, binning and filtering for mass-spectrometry imaging data
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>maldi_macros.xml</import> 6 <import>maldi_macros.xml</import>
377 #if $infile.ext == 'rdata' 377 #if $infile.ext == 'rdata'
378 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(peaks),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input 378 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(peaks),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
379 #end if 379 #end if
380 380
381 peaks = removeEmptyMassObjects(peaks) 381 peaks = removeEmptyMassObjects(peaks)
382 pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")
382 } 383 }
383 #end if 384 #end if
384 385
385 ## QC plot and numbers 386 ## QC plot and numbers
386 par(mfrow = c(2, 2), oma=c(0,0,2,0)) 387 par(mfrow = c(2, 2), oma=c(0,0,2,0))
387 388
388 for (random_sample in random_spectra){ 389 for (random_sample in random_spectra){
389 390
390 391 tryCatch(
391 tryCatch( 392 {
392 { 393 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
393 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}, 394 },error=function(cond)
394 error=function(cond) { 395 {
395 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z") 396 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
396 } 397 }
397 ) 398 )
398 } 399 }
399 400
400 title("Aligned spectra", outer=TRUE, line=0) 401 title("Aligned spectra", outer=TRUE, line=0)
401 minmz = round(min(unlist(lapply(peaks,mass))), digits=4) 402 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
402 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4) 403 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
403 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2) 404 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
413 #if $infile.ext == 'imzml' 414 #if $infile.ext == 'imzml'
414 #if str($centroids) == "FALSE" 415 #if str($centroids) == "FALSE"
415 featureMatrix <- intensityMatrix(peaks, maldi_data) 416 featureMatrix <- intensityMatrix(peaks, maldi_data)
416 #end if 417 #end if
417 #end if 418 #end if
419
418 featureMatrix2 =cbind(pixelnames, featureMatrix) 420 featureMatrix2 =cbind(pixelnames, featureMatrix)
419 colnames(featureMatrix2)[1] = c("mz") 421 colnames(featureMatrix2)[1] = c("mz")
420 featureMatrix2 = t(featureMatrix2) 422 featureMatrix2 = t(featureMatrix2)
421 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t") 423 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
422 }else{print("There are no spectra with peaks left")} 424 }else{print("There are no spectra with peaks left")}
423 425
426
424 #elif str( $method.methods_conditional.method ) == 'Binning': 427 #elif str( $method.methods_conditional.method ) == 'Binning':
425 428
426 print('binning') 429 print('binning')
427 ##m/z binning 430 ##m/z binning
428 431
429 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance, method="$method.methods_conditional.bin_method") 432 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance, method="$method.methods_conditional.bin_method")
430 433
431 ## QC plot and numbers 434 ## QC plot and numbers
432 par(mfrow = c(2, 2), oma=c(0,0,2,0)) 435 par(mfrow = c(2, 2), oma=c(0,0,2,0))
436
433 for (random_sample in random_spectra){ 437 for (random_sample in random_spectra){
434 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))} 438
439 tryCatch(
440 {
441 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
442 },error=function(cond)
443 {
444 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
445 }
446 )
447 }
448
435 title("Binned spectra", outer=TRUE, line=0) 449 title("Binned spectra", outer=TRUE, line=0)
436 minmz = round(min(unlist(lapply(peaks,mass))), digits=4) 450 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
437 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4) 451 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
438 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2) 452 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
439 medint =round( median(unlist(lapply(peaks,intensity))), digits=2) 453 medint =round( median(unlist(lapply(peaks,intensity))), digits=2)
479 mergeWhitelists=$method.methods_conditional.mergeWhitelists, label = samples) 493 mergeWhitelists=$method.methods_conditional.mergeWhitelists, label = samples)
480 #end if 494 #end if
481 495
482 ##QC plot and numbers 496 ##QC plot and numbers
483 par(mfrow = c(2, 2), oma=c(0,0,2,0)) 497 par(mfrow = c(2, 2), oma=c(0,0,2,0))
498
484 for (random_sample in random_spectra){ 499 for (random_sample in random_spectra){
485 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))} 500
501 tryCatch(
502 {
503 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
504 },error=function(cond)
505 {
506 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
507 }
508 )
509 }
510
486 title("Filtered spectra", outer=TRUE, line=0) 511 title("Filtered spectra", outer=TRUE, line=0)
487 minmz = round(min(unlist(lapply(peaks,mass))), digits=4) 512 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
488 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4) 513 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
489 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2) 514 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
490 medint = round(median(unlist(lapply(peaks,intensity))), digits=2) 515 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)