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comparison preprocessing.xml @ 7:173070dafe95 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
author galaxyp
date Thu, 23 Apr 2020 11:57:53 +0000
parents cbd9e4df377d
children 413a1b74f496
comparison
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6:cbd9e4df377d 7:173070dafe95
1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="2.4.0.0"> 1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">
2 <description> 2 <description>
3 mass spectrometry imaging preprocessing 3 mass spectrometry imaging preprocessing
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <expand macro="requirements">
9 <requirement type="package" version="2.4.0">bioconductor-cardinal</requirement>
10 <requirement type="package" version="3.6.1">r-base</requirement>
11 <requirement type="package" version="2.3">r-gridextra</requirement> 9 <requirement type="package" version="2.3">r-gridextra</requirement>
12 <requirement type="package" version="3.2.1">r-ggplot2</requirement> 10 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
13 <requirement type="package" version="0.20_38">r-lattice</requirement> 11 </expand>
14 </requirements>
15 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
16 <![CDATA[ 13 <![CDATA[
17 14
18 @INPUT_LINKING@ 15 @INPUT_LINKING@
19 cat '${cardinal_preprocessing}' && 16 cat '${cardinal_preprocessing}' &&
30 <configfiles> 27 <configfiles>
31 <configfile name="cardinal_preprocessing"><![CDATA[ 28 <configfile name="cardinal_preprocessing"><![CDATA[
32 29
33 ################################# load libraries and read file ################# 30 ################################# load libraries and read file #################
34 31
32 ## set CPU, default = 1
33
34 if (Sys.getenv("GALAXY_SLOTS")!="")
35 {
36 number_cpu = 1 ## default = 1
37 }else{
38 number_cpu = as.numeric(Sys.getenv("GALAXY_SLOTS")) ##cpu set by Galaxy
39 }
40
35 library(Cardinal) 41 library(Cardinal)
36 library(gridExtra) 42 library(gridExtra)
37 library(lattice)
38 library(ggplot2) 43 library(ggplot2)
39 44
40 45
41 ## function to read RData files independent of filename 46 @READING_MSIDATA_FULLY_COMPATIBLE@
42 loadRData <- function(fileName){
43 load(fileName)
44 get(ls()[ls() != "fileName"])
45 }
46
47 #if $infile.ext == 'imzml'
48 #if str($processed_cond.processed_file) == "processed":
49 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units")
50 centroided(msidata) = $centroids
51 #else
52 msidata <- readImzML('infile')
53 centroided(msidata) = $centroids
54 #end if
55 #elif $infile.ext == 'analyze75'
56 msidata = readAnalyze('infile')
57 centroided(msidata) = $centroids
58 #else
59 msidata = loadRData('infile.RData')
60 msidata = as(msidata, "MSImagingExperiment")
61 #end if
62 47
63 48
64 ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail 49 ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail
65 msidata <- msidata[,!duplicated(coord(msidata)[,1:2])] 50 msidata <- msidata[,!duplicated(coord(msidata)[,1:2])]
66 51
106 if (class(msidata) == "MSProcessedImagingExperiment"){ 91 if (class(msidata) == "MSProcessedImagingExperiment"){
107 msidata = as(msidata, "MSContinuousImagingExperiment") 92 msidata = as(msidata, "MSContinuousImagingExperiment")
108 } 93 }
109 94
110 msidata = normalize(msidata, method="tic") 95 msidata = normalize(msidata, method="tic")
111 msidata <- process(msidata, BPPARAM=MulticoreParam()) 96 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
112 97
113 98
114 ############################### QC ########################### 99 ############################### QC ###########################
115 100
116 maxfeatures =nrow(msidata) 101 maxfeatures =nrow(msidata)
132 if (class(msidata) == "MSProcessedImagingExperiment"){ 117 if (class(msidata) == "MSProcessedImagingExperiment"){
133 msidata = as(msidata, "MSContinuousImagingExperiment") 118 msidata = as(msidata, "MSContinuousImagingExperiment")
134 } 119 }
135 120
136 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline) 121 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline)
137 msidata <- process(msidata, BPPARAM=MulticoreParam()) 122 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
138 123
139 ############################### QC ########################### 124 ############################### QC ###########################
140 125
141 maxfeatures =nrow(msidata) 126 maxfeatures =nrow(msidata)
142 pixelcount = ncol(msidata) 127 pixelcount = ncol(msidata)
178 print('moving average smoothing') 163 print('moving average smoothing')
179 164
180 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter) 165 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter)
181 166
182 #end if 167 #end if
183 msidata <- process(msidata, BPPARAM=MulticoreParam()) 168 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
184 169
185 ############################### QC ########################### 170 ############################### QC ###########################
186 171
187 maxfeatures =nrow(msidata) 172 maxfeatures =nrow(msidata)
188 pixelcount = ncol(msidata) 173 pixelcount = ncol(msidata)
215 print('simple peakpicking') 200 print('simple peakpicking')
216 201
217 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method) 202 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method)
218 203
219 #end if 204 #end if
220 msidata <- process(msidata, BPPARAM=MulticoreParam()) 205 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
221 206
222 #if str($method.methods_conditional.imzml_output) == "cont_format": 207 #if str($method.methods_conditional.imzml_output) == "cont_format":
223 #set $continuous_format = True 208 #set $continuous_format = True
224 #end if 209 #end if
225 210
260 245
261 msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment") 246 msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment")
262 247
263 #end if 248 #end if
264 249
265 msidata <- process(msidata, BPPARAM=MulticoreParam()) 250 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
266 251
267 #if str($method.methods_conditional.imzml_output) == "cont_format": 252 #if str($method.methods_conditional.imzml_output) == "cont_format":
268 #set $continuous_format = True 253 #set $continuous_format = True
269 #end if 254 #end if
270 255
284 269
285 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering': 270 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
286 print('Peak_filtering') 271 print('Peak_filtering')
287 272
288 msidata = peakFilter(msidata, freq.min = $method.methods_conditional.frequ_filtering) 273 msidata = peakFilter(msidata, freq.min = $method.methods_conditional.frequ_filtering)
289 msidata <- process(msidata, BPPARAM=MulticoreParam()) 274 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
290 275
291 ############################### QC ########################### 276 ############################### QC ###########################
292 277
293 maxfeatures =nrow(msidata) 278 maxfeatures =nrow(msidata)
294 pixelcount = ncol(msidata) 279 pixelcount = ncol(msidata)
298 QC_numbers= cbind(QC_numbers, filtered) 283 QC_numbers= cbind(QC_numbers, filtered)
299 vectorofactions = append(vectorofactions, "filtered") 284 vectorofactions = append(vectorofactions, "filtered")
300 print(plot(msidata, pixel=random_spectra)) 285 print(plot(msidata, pixel=random_spectra))
301 title("Spectra after filtering", outer=TRUE, line=0) 286 title("Spectra after filtering", outer=TRUE, line=0)
302 287
288 ############################### Peak binning ###########################
289
290 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_binning':
291 print('Peak_binning')
292
293 ## reading reference file
294 reference_table = read.delim("$method.methods_conditional.mz_tabular", header = $method.methods_conditional.feature_header, stringsAsFactors = FALSE)
295 reference_column = reference_table[,$method.methods_conditional.feature_column]
296 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
297
298 msidata = peakBin(msidata, ref = peak_reference, tolerance = $method.methods_conditional.peakbin_tol, units = "$method.methods_conditional.peakbin_units", type="$method.methods_conditional.peaks_type")
299 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
300
301 ############################### QC ###########################
302
303 maxfeatures =nrow(msidata)
304 pixelcount = ncol(msidata)
305 minmz = round(min(mz(msidata)), digits=2)
306 maxmz = round(max(mz(msidata)), digits=2)
307 peak_binned = c(minmz, maxmz,maxfeatures, pixelcount)
308 QC_numbers= cbind(QC_numbers, peak_binned)
309 vectorofactions = append(vectorofactions, "peak binned")
310 print(plot(msidata, pixel=random_spectra))
311 title("Spectra after peak binning", outer=TRUE, line=0)
312
313
303 ############################### Data reduction ########################### 314 ############################### Data reduction ###########################
304 315
305 #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction': 316 #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction':
306 print('Data_reduction') 317 print('Data_reduction')
307 318
322 333
323 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample': 334 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample':
324 print('resample reduction') 335 print('resample reduction')
325 336
326 msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step) 337 msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step)
327
328 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'peaks':
329 print('peaks reduction')
330
331 #if str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'table':
332
333 reference_table = read.delim("$method.methods_conditional.methods_for_reduction.ref_type.mz_tabular", header = $method.methods_conditional.methods_for_reduction.ref_type.feature_header, stringsAsFactors = FALSE)
334 reference_column = reference_table[,$method.methods_conditional.methods_for_reduction.ref_type.feature_column]
335 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
336
337 #elif str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'msidata_ref':
338
339 peak_reference = loadRData('$method.methods_conditional.methods_for_reduction.ref_type.peaks_msidata')
340
341 #end if
342
343 msidata = reduceDimension(msidata, method="peaks", ref=peak_reference, type="$method.methods_conditional.methods_for_reduction.peaks_type")
344 #end if 338 #end if
345 339
346 ## coercition into new format 340 ## coercition into new format
347 msidata = as(msidata, "MSImagingExperiment") 341 msidata = as(msidata, "MSImagingExperiment")
348 342
445 <option value="Baseline_reduction">Baseline Reduction</option> 439 <option value="Baseline_reduction">Baseline Reduction</option>
446 <option value="Smoothing">Peak smoothing</option> 440 <option value="Smoothing">Peak smoothing</option>
447 <option value="Peak_picking">Peak picking</option> 441 <option value="Peak_picking">Peak picking</option>
448 <option value="Peak_alignment">Peak alignment</option> 442 <option value="Peak_alignment">Peak alignment</option>
449 <option value="Peak_filtering">Peak filtering</option> 443 <option value="Peak_filtering">Peak filtering</option>
444 <option value="Peak_binning">Peak binning to reference peaks</option>
450 <option value="Data_reduction">Data reduction</option> 445 <option value="Data_reduction">Data reduction</option>
451 <option value="Transformation">Transformation</option> 446 <option value="Transformation">Transformation</option>
452 </param> 447 </param>
453 <when value="Normalization"> 448 <when value="Normalization">
454 <conditional name="methods_for_normalization"> 449 <conditional name="methods_for_normalization">
462 </when> 457 </when>
463 <when value="Baseline_reduction"> 458 <when value="Baseline_reduction">
464 <param name="blocks_baseline" type="integer" value="500" 459 <param name="blocks_baseline" type="integer" value="500"
465 label="Blocks"/> 460 label="Blocks"/>
466 <param name="spar_baseline" type="float" value="1.0" label="Spar value" 461 <param name="spar_baseline" type="float" value="1.0" label="Spar value"
467 help = "Smoothing parameter for the spline smoothing 462 help="Smoothing parameter for the spline smoothing
468 applied to the spectrum in order to decide the cutoffs 463 applied to the spectrum in order to decide the cutoffs
469 for throwing away false noise spikes that might occur inside peaks"/> 464 for throwing away false noise spikes that might occur inside peaks"/>
470 </when> 465 </when>
471 <when value="Smoothing"> 466 <when value="Smoothing">
472 <conditional name="methods_for_smoothing"> 467 <conditional name="methods_for_smoothing">
513 for throwing away false noise spikes that might occur inside peaks"/> 508 for throwing away false noise spikes that might occur inside peaks"/>
514 </when> 509 </when>
515 <when value="mad"/> 510 <when value="mad"/>
516 <when value="simple"/> 511 <when value="simple"/>
517 </conditional> 512 </conditional>
518 <param name="imzml_output" type="boolean" label="imzML output in processed format" truevalue="proc_format" falsevalue="cont_format" help= "Processed imzML works only in MALDIquant tools, not yet in MSI tools (Cardinal)"/> 513 <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>
519 </when> 514 </when>
520 <when value="Peak_alignment"> 515 <when value="Peak_alignment">
521 <param name="value_diffalignment" type="float" value="200" 516 <param name="value_diffalignment" type="float" value="200"
522 label="tolerance" help="Peaks that differ less than this value will be aligned together"/> 517 label="tolerance" help="Peaks that differ less than this value will be aligned together"/>
523 <param name="units_diffalignment" type="select" display="radio" optional="False" label="units"> 518 <param name="units_diffalignment" type="select" display="radio" optional="False" label="units">
532 <when value="align_noref"/> 527 <when value="align_noref"/>
533 <when value="align_table"> 528 <when value="align_table">
534 <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."/> 529 <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."/>
535 </when> 530 </when>
536 </conditional> 531 </conditional>
537 <param name="imzml_output" type="boolean" label="imzML output in processed format" truevalue="proc_format" falsevalue="cont_format" help= "Processed imzML works only in MALDIquant tools, not yet in MSI tools (Cardinal)"/> 532 <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)"/>
538 </when> 533 </when>
539 <when value="Peak_filtering"> 534 <when value="Peak_filtering">
540 <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)"/> 535 <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)"/>
536 </when>
537 <when value="Peak_binning">
538 <expand macro="reading_1_column_mz_tabular" label="A reference to which the peaks are binned." help="Tabular file with m/z features to extract from input file"/>
539 <param name="peakbin_tol" value="NA" type="text" label="The tolerance to be used when matching the m/z features in the dataset to the reference. If this is NA, then automatically guess a resolution from the data." >
540 <sanitizer invalid_char="">
541 <valid initial="string.digits">
542 <add value="NA" />
543 </valid>
544 </sanitizer>
545 </param>
546 <param name="peakbin_units" display="radio" type="select" label="The units to use for the tolerance.">
547 <option value="mz" >mz</option>
548 <option value="ppm" selected="True" >ppm</option>
549 </param>
550 <param name="peaks_type" type="select" display="radio"
551 label="Should the peak height or area under the curve be taken as the intensity value?">
552 <option value="height" selected="True">height</option>
553 <option value="area">area</option>
554 </param>
541 </when> 555 </when>
542 <when value="Data_reduction"> 556 <when value="Data_reduction">
543 <conditional name="methods_for_reduction"> 557 <conditional name="methods_for_reduction">
544 <param name="reduction_method" type="select" label="Reduction method"> 558 <param name="reduction_method" type="select" label="Reduction method">
545 <option value="bin" selected="True">bin</option> 559 <option value="bin" selected="True">bin</option>
546 <option value="resample">resample</option> 560 <option value="resample">resample</option>
547 <option value="peaks">peaks</option>
548 </param> 561 </param>
549 <when value="bin"> 562 <when value="bin">
550 <param name="bin_width" type="float" value="1" 563 <param name="bin_width" type="float" value="1"
551 label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/> 564 label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/>
552 <param name="bin_units" type="select" display="radio" 565 <param name="bin_units" type="select" display="radio"
563 </when> 576 </when>
564 <when value="resample"> 577 <when value="resample">
565 <param name="resample_step" type="float" value="1" 578 <param name="resample_step" type="float" value="1"
566 label="The step size in m/z" help="Step size must be greater than range of m/z values divided by number of m/z features"/> 579 label="The step size in m/z" help="Step size must be greater than range of m/z values divided by number of m/z features"/>
567 </when> 580 </when>
568 <when value="peaks">
569 <param name="peaks_type" type="select" display="radio"
570 label="Should the peak height or area under the curve be taken as the intensity value?">
571 <option value="height" selected="True">height</option>
572 <option value="area">area</option>
573 </param>
574 <conditional name="ref_type">
575 <param name="reference_datatype" type="select" label="Choose reference datatype">
576 <option value="table" selected="True">tabular file</option>
577 <option value="msidata_ref">msidata file</option>
578 </param>
579 <when value="table">
580 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to extract from input file"/>
581 </when>
582 <when value="msidata_ref">
583 <param name="peaks_msidata" type="data" format="rdata" label="Picked and aligned Cardinal MSImageSet saved as RData"/>
584 </when>
585 </conditional>
586 </when>
587 </conditional> 581 </conditional>
588 </when> 582 </when>
589 <when value="Transformation"> 583 <when value="Transformation">
590 <conditional name="transf_conditional"> 584 <conditional name="transf_conditional">
591 <param name="trans_type" type="select" label="Intensity transformations" help="logarithm base 2 (log2) or squareroot (sqrt)"> 585 <param name="trans_type" type="select" label="Intensity transformations" help="logarithm base 2 (log2) or squareroot (sqrt)">
633 <param name="picking_method" value="adaptive"/> 627 <param name="picking_method" value="adaptive"/>
634 </conditional> 628 </conditional>
635 <param name="blocks_picking" value="3"/> 629 <param name="blocks_picking" value="3"/>
636 <param name="window_picking" value="3"/> 630 <param name="window_picking" value="3"/>
637 <param name="SNR_picking_method" value="3"/> 631 <param name="SNR_picking_method" value="3"/>
632 <param name="imzml_output" value="cont_format"/>
638 </conditional> 633 </conditional>
639 </repeat> 634 </repeat>
640 <repeat name="methods"> 635 <repeat name="methods">
641 <conditional name="methods_conditional"> 636 <conditional name="methods_conditional">
642 <param name="preprocessing_method" value="Peak_alignment"/> 637 <param name="preprocessing_method" value="Peak_alignment"/>
638 <param name="imzml_output" value="cont_format"/>
643 </conditional> 639 </conditional>
644 </repeat> 640 </repeat>
645 <repeat name="methods"> 641 <repeat name="methods">
646 <conditional name="methods_conditional"> 642 <conditional name="methods_conditional">
647 <param name="preprocessing_method" value="Peak_filtering"/> 643 <param name="preprocessing_method" value="Peak_filtering"/>
671 <param name="window_picking" value="5"/> 667 <param name="window_picking" value="5"/>
672 <param name="SNR_picking_method" value="2"/> 668 <param name="SNR_picking_method" value="2"/>
673 <conditional name="methods_for_picking"> 669 <conditional name="methods_for_picking">
674 <param name="picking_method" value="adaptive"/> 670 <param name="picking_method" value="adaptive"/>
675 </conditional> 671 </conditional>
672 <param name="imzml_output" value="cont_format"/>
676 </conditional> 673 </conditional>
677 </repeat> 674 </repeat>
678 <repeat name="methods"> 675 <repeat name="methods">
679 <conditional name="methods_conditional"> 676 <conditional name="methods_conditional">
680 <param name="preprocessing_method" value="Peak_alignment"/> 677 <param name="preprocessing_method" value="Peak_alignment"/>
678 <param name="imzml_output" value="cont_format"/>
681 </conditional> 679 </conditional>
682 </repeat> 680 </repeat>
683 <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/> 681 <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>
684 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size"> 682 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">
685 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/> 683 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>
697 </conditional> 695 </conditional>
698 </repeat> 696 </repeat>
699 <repeat name="methods"> 697 <repeat name="methods">
700 <conditional name="methods_conditional"> 698 <conditional name="methods_conditional">
701 <param name="preprocessing_method" value="Peak_picking"/> 699 <param name="preprocessing_method" value="Peak_picking"/>
702 <param name="blocks_picking" value="100"/> 700 <param name="blocks_picking" value="20"/>
703 <param name="window_picking" value="5"/> 701 <param name="window_picking" value="5"/>
704 <param name="SNR_picking_method" value="3"/> 702 <param name="SNR_picking_method" value="2"/>
705 <conditional name="methods_for_picking"> 703 <conditional name="methods_for_picking">
706 <param name="picking_method" value="mad"/> 704 <param name="picking_method" value="mad"/>
707 </conditional> 705 </conditional>
708 </conditional>
709 <param name="imzml_output" value="proc_format"/> 706 <param name="imzml_output" value="proc_format"/>
707 </conditional>
710 </repeat> 708 </repeat>
711 <repeat name="methods"> 709 <repeat name="methods">
712 <conditional name="methods_conditional"> 710 <conditional name="methods_conditional">
713 <param name="preprocessing_method" value="Peak_alignment"/> 711 <param name="preprocessing_method" value="Peak_alignment"/>
714 </conditional> 712 <param name="imzml_output" value="proc_format"/>
715 <param name="imzml_output" value="proc_format"/>
716 </repeat>
717 <repeat name="methods">
718 <conditional name="methods_conditional">
719 <param name="preprocessing_method" value="Transformation"/>
720 <conditional name="transf_conditional">
721 <param name="trans_type" value="log2"/>
722 </conditional>
723 </conditional> 713 </conditional>
724 </repeat> 714 </repeat>
725 <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/> 715 <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/>
726 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results3.imzml.txt" compare="sim_size"> 716 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results3.imzml.txt" compare="sim_size">
727 <extra_files type="file" file="preprocessing_results3.imzml" name="imzml" lines_diff="6"/> 717 <extra_files type="file" file="preprocessing_results3.imzml" name="imzml" lines_diff="6"/>
760 </conditional> 750 </conditional>
761 <repeat name="methods"> 751 <repeat name="methods">
762 <conditional name="methods_conditional"> 752 <conditional name="methods_conditional">
763 <param name="preprocessing_method" value="Transformation"/> 753 <param name="preprocessing_method" value="Transformation"/>
764 <conditional name="transf_conditional"> 754 <conditional name="transf_conditional">
765 <param name="trans_type" value="sqrt"/> 755 <param name="trans_type" value="log2"/>
766 </conditional> 756 </conditional>
767 </conditional> 757 </conditional>
768 </repeat> 758 </repeat>
769 <repeat name="methods"> 759 <repeat name="methods">
770 <conditional name="methods_conditional"> 760 <conditional name="methods_conditional">
797 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets) 787 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets)
798 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection 788 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection
799 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards) 789 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
800 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value; if no reference is given the peaks are aligned to the local maxima of the mean spectrum of the current dataset; external reference data can be used from another MSI data file or a tabular file with m/z values, but then only the m/z from the reference will be kept 790 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value; if no reference is given the peaks are aligned to the local maxima of the mean spectrum of the current dataset; external reference data can be used from another MSI data file or a tabular file with m/z values, but then only the m/z from the reference will be kept
801 - Peak filtering: removes peaks that occur only in a small proportion of pixels. If not sure which cut off to choose run quality control tool first and decide according to the number of peaks per m/z plot 791 - Peak filtering: removes peaks that occur only in a small proportion of pixels. If not sure which cut off to choose run quality control tool first and decide according to the number of peaks per m/z plot
802 - Data reduction: binning, resampling or peak filtering to reduce data 792 - Peak binning: extracts peaks intensities (from a profile dataset) for a list of m/z (reference) values
793 - Data reduction: binning or resampling to reduce data
803 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 794 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems.
804 795
805 **Output** 796 **Output**
806 797
807 - MSI data as continuous imzML file (option to output processed imzML file only after peak picking/peak alignment; but is not yet compatible with other MSI tools) 798 - MSI data as continuous or processed imzML file
808 - pdf with key values and four random mass spectra after each processing step 799 - pdf with key values and four random mass spectra after each processing step
809 800
810 ]]> 801 ]]>
811 </help> 802 </help>
812 <expand macro="citations"/> 803 <expand macro="citations"/>