Mercurial > repos > galaxyp > maldi_quant_preprocessing

comparison maldi_quant_preprocessing.xml @ 4:60ee8c592b13 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
author galaxyp
date Sat, 04 Mar 2023 19:14:31 +0000
parents 71411ac28268
children
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3:71411ac28268 4:60ee8c592b13
1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.3"> 1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.0">
2 <description> 2 <description>
3 Preprocessing of mass-spectrometry imaging data 3 Preprocessing of mass-spectrometry imaging data
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>maldi_macros.xml</import> 6 <import>maldi_macros.xml</import>
17 cp '${infile.extra_files_path}/img' infile.img && 17 cp '${infile.extra_files_path}/img' infile.img &&
18 cp '${infile.extra_files_path}/t2m' infile.t2m && 18 cp '${infile.extra_files_path}/t2m' infile.t2m &&
19 du infile.hdr && 19 du infile.hdr &&
20 du infile.img && 20 du infile.img &&
21 du -s -B1 infile.hdr && 21 du -s -B1 infile.hdr &&
22 #else
23 ln -s $infile infile.RData &&
24 #end if 22 #end if
25 Rscript "${maldi_quant_preprocessing}" && 23 Rscript "${maldi_quant_preprocessing}" &&
26 24
27 mkdir $outfile_imzml.files_path && 25 mkdir $outfile_imzml.files_path &&
28 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true && 26 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
57 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data))) 55 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
58 #elif $infile.ext == 'analyze75' 56 #elif $infile.ext == 'analyze75'
59 ## Import analyze7.5 file 57 ## Import analyze7.5 file
60 maldi_data = importAnalyze( 'infile.hdr' ) 58 maldi_data = importAnalyze( 'infile.hdr' )
61 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data))) 59 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
62 #else
63 loadRData <- function(fileName){
64 ##loads an RData file, and returns it
65 load(fileName)
66 get(ls()[ls() != "fileName"])
67 }
68 msidata = loadRData('infile.RData')
69 ## save coordinates
70 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
71 ## save mz values
72 cardinal_mzs = Cardinal::mz(msidata)
73 ## create MALDIquant MassSpectrum object, order of pixels in iData is same as in coord(msidata):
74 maldi_data = list()
75 for(number_spectra in 1:ncol(msidata)){
76 maldi_data[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
77 }
78 #end if 60 #end if
79 61
80 #end if 62 #end if
81 63
82 ## Quality control plots during preprocessing 64 ## Quality control plots during preprocessing
342 ## only if there are empty spectra to remove 324 ## only if there are empty spectra to remove
343 325
344 if (length(findEmptyMassObjects(maldi_data))>0) 326 if (length(findEmptyMassObjects(maldi_data))>0)
345 327
346 { 328 {
347 #if $infile.ext == 'rdata'
348 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
349 #end if
350
351 maldi_data = removeEmptyMassObjects(maldi_data) 329 maldi_data = removeEmptyMassObjects(maldi_data)
352 } 330 }
353 #end if 331 #end if
354 332
355 ## QC plot 333 ## QC plot
384 362
385 dev.off() 363 dev.off()
386 364
387 ## export imzML file 365 ## export imzML file
388 if (length(maldi_data)>0){ 366 if (length(maldi_data)>0){
389 #if $infile.ext == 'rdata'
390 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
391 #else
392 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed) 367 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
393 #end if
394 368
395 }else{"All spectra are empty, outputfiles will be empty,too."} 369 }else{"All spectra are empty, outputfiles will be empty,too."}
396 370
397 ]]> 371 ]]>
398 </configfile> 372 </configfile>
399 </configfiles> 373 </configfiles>
400 <inputs> 374 <inputs>
401 <param name="infile" type="data" format="imzml,rdata,analyze75" label="MSI data" help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload). The file must be in profile mode, not centroided."/> 375 <param name="infile" type="data" format="imzml,analyze75" label="MSI data" help="Input file as imzML (composite upload). The file must be in profile mode, not centroided."/>
402 <conditional name="restriction_conditional"> 376 <conditional name="restriction_conditional">
403 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files"> 377 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
404 <option value="no_restriction" selected="True">No, calculate on entire file</option> 378 <option value="no_restriction" selected="True">No, calculate on entire file</option>
405 <option value="restrict">Yes, restrict to spectra of interest</option> 379 <option value="restrict">Yes, restrict to spectra of interest</option>
406 </param> 380 </param>
527 </param> 501 </param>
528 502
529 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/> 503 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/>
530 <param name="allow_nomatch" type="boolean" label="Allow no matches" help="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/> 504 <param name="allow_nomatch" type="boolean" label="Allow no matches" help="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/>
531 <param name="empty_nomatch" type="boolean" label="Empty no matches" help="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/> 505 <param name="empty_nomatch" type="boolean" label="Empty no matches" help="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
532 <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/> 506 <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE"/>
533 507
534 <conditional name="reference_for_alignment"> 508 <conditional name="reference_for_alignment">
535 <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration"> 509 <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration">
536 <option value="no_reference" selected="True">no reference</option> 510 <option value="no_reference" selected="True">no reference</option>
537 <option value="yes_reference">reference from tabular file</option> 511 <option value="yes_reference">reference from tabular file</option>
577 <param name="smooth_method" value="SavitzkyGolay"/> 551 <param name="smooth_method" value="SavitzkyGolay"/>
578 <param name="method" value="Basline"/> 552 <param name="method" value="Basline"/>
579 <param name="baseline_method" value ="TopHat"/> 553 <param name="baseline_method" value ="TopHat"/>
580 </conditional> 554 </conditional>
581 <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4"> 555 <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4">
582 <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="6"/> 556 <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="8"/>
583 <extra_files type="file" file="outfile1.ibd" name="ibd" compare="sim_size"/> 557 <extra_files type="file" file="outfile1.ibd" name="ibd" compare="sim_size"/>
584 </output> 558 </output>
585 <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/> 559 <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/>
586 </test>
587 <test>
588 <param name="infile" value="msidata_1.RData" ftype="rdata"/>
589 <conditional name="methods_conditional">
590 <param name="method" value="Align"/>
591 <param name="warping_method" value="lowess"/>
592 <param name="halfWindowSize" value="5"/>
593 <param name="tolerance" value="0.001"/>
594 <param name="allow_nomatch" value="TRUE"/>
595 <param name="remove_empty" value="TRUE"/>
596 <param name="empty_nomatch" value="TRUE"/>
597 <conditional name="reference_for_alignment">
598 <param name="align_ref" value="yes_reference"/>
599 <param name="reference_file" value="inputpeptides.tabular" ftype="tabular"/>
600 </conditional>
601 </conditional>
602 <output name="outfile_imzml" ftype="imzml" file="preprocessing2.imzml.txt" lines_diff="4">
603 <extra_files type="file" file="outfile2.imzml" name="imzml" lines_diff="6"/>
604 <extra_files type="file" file="outfile2.ibd" name="ibd" compare="sim_size"/>
605 </output>
606 <output name="plots" file="Preprocessing2_QC.pdf" compare="sim_size"/>
607 </test> 560 </test>
608 <test> 561 <test>
609 <param name="infile" value="" ftype="imzml"> 562 <param name="infile" value="" ftype="imzml">
610 <composite_data value="Example_Continuous.imzML"/> 563 <composite_data value="Example_Continuous.imzML"/>
611 <composite_data value="Example_Continuous.ibd"/> 564 <composite_data value="Example_Continuous.ibd"/>
613 <conditional name="methods_conditional"> 566 <conditional name="methods_conditional">
614 <param name="method" value="Calibrate"/> 567 <param name="method" value="Calibrate"/>
615 <param name="calibrate_method" value="median"/> 568 <param name="calibrate_method" value="median"/>
616 </conditional> 569 </conditional>
617 <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4"> 570 <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4">
618 <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="6"/> 571 <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="8"/>
619 <extra_files type="file" file="outfile3.ibd" name="ibd" compare="sim_size"/> 572 <extra_files type="file" file="outfile3.ibd" name="ibd" compare="sim_size"/>
620 </output> 573 </output>
621 <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/> 574 <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/>
622 </test> 575 </test>
623 </tests> 576 </tests>
629 582
630 **Input data** 583 **Input data**
631 584
632 - MSI data: 2 types of input data can be used: 585 - MSI data: 2 types of input data can be used:
633 586
634 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ 587 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_
635 - Cardinal "MSImageSet" data saved as .RData
636 588
637 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported. 589 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported.
638 590
639 :: 591 ::
640 592