Mercurial > repos > galaxyp > maldi_quant_peak_detection

comparison maldi_quant_peakdetection.xml @ 5:e66f552a3c47 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
author galaxyp
date Thu, 19 Mar 2020 18:09:47 -0400
parents e9300ef37403
children d286ff4600dd
comparison
equal deleted inserted replaced
4:e9300ef37403 5:e66f552a3c47
1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.4"> 1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.5">
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>
14 #elif $infile.ext == 'analyze75' 14 #elif $infile.ext == 'analyze75'
15 cp '${infile.extra_files_path}/hdr' infile.hdr && 15 cp '${infile.extra_files_path}/hdr' infile.hdr &&
16 cp '${infile.extra_files_path}/img' infile.img && 16 cp '${infile.extra_files_path}/img' infile.img &&
17 cp '${infile.extra_files_path}/t2m' infile.t2m && 17 cp '${infile.extra_files_path}/t2m' infile.t2m &&
18 #else 18 #else
19 ln -s $infile infile.RData && 19 ln -s '$infile' infile.RData &&
20 #end if 20 #end if
21 Rscript '${maldi_quant_peak_detection}'&& 21 cat '${maldi_quant_peak_detection}' &&
22 Rscript '${maldi_quant_peak_detection}' &&
22 mkdir $outfile_imzml.files_path && 23 mkdir $outfile_imzml.files_path &&
23 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true && 24 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
24 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true && 25 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
25 echo "imzML file:" > $outfile_imzml && 26 echo "imzML file:" > $outfile_imzml &&
26 ls -l "$outfile_imzml.files_path" >> $outfile_imzml 27 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
357 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method", 358 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
358 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list) 359 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
359 ## 2) warp spectra: 360 ## 2) warp spectra:
360 peaks_new_list = warpMassPeaks(list(peaks[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch) 361 peaks_new_list = warpMassPeaks(list(peaks[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
361 } 362 }
362 peaks_new = peaks_new_list 363 peaks = peaks_new_list
363 364
364 #end if 365 #end if
365 366
367 #end if
368
369 #if $method.methods_conditional.remove_empty:
370 print(paste(length(findEmptyMassObjects(peaks)), " empty spectra were removed", sep=" "))
371
372 ## only if there are empty spectra to remove
373
374 if (length(findEmptyMassObjects(peaks))>0)
375
376 {
377 #if $infile.ext == 'rdata'
378 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(peaks),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
379 #end if
380
381 peaks = removeEmptyMassObjects(peaks)
382 }
366 #end if 383 #end if
367 384
368 ## QC plot and numbers 385 ## QC plot and numbers
369 par(mfrow = c(2, 2), oma=c(0,0,2,0)) 386 par(mfrow = c(2, 2), oma=c(0,0,2,0))
387
370 for (random_sample in random_spectra){ 388 for (random_sample in random_spectra){
371 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))} 389
390
391 tryCatch(
392 {
393 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))},
394 error=function(cond) {
395 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
396 }
397 )
398 }
399
372 title("Aligned spectra", outer=TRUE, line=0) 400 title("Aligned spectra", outer=TRUE, line=0)
373 minmz = round(min(unlist(lapply(peaks,mass))), digits=4) 401 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
374 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4) 402 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
375 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2) 403 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
376 medint = round(median(unlist(lapply(peaks,intensity))), digits=2) 404 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)