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comparison preprocessing.xml @ 10:aa479a0cfb43 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
author galaxyp
date Sun, 29 Aug 2021 07:20:07 +0000
parents e0bbaf9f7da0
children 274e81434593
comparison
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9:e0bbaf9f7da0 10:aa479a0cfb43
1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1"> 1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0">
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 <expand macro="requirements"> 8 <expand macro="requirements">
9 <requirement type="package" version="2.3">r-gridextra</requirement> 9 <requirement type="package" version="2.3">r-gridextra</requirement>
10 <requirement type="package" version="3.3.2">r-ggplot2</requirement> 10 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
11 </expand> 11 </expand>
12 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
13 <![CDATA[ 13 <![CDATA[
14 14
15 @INPUT_LINKING@ 15 @INPUT_LINKING@
45 45
46 @READING_MSIDATA_FULLY_COMPATIBLE@ 46 @READING_MSIDATA_FULLY_COMPATIBLE@
47 47
48 48
49 ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail 49 ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail
50 msidata <- msidata[,!duplicated(coord(msidata)[,1:2])]
51 50
52 ## set variable to False 51 ## set variable to False
53 #set $used_peak_picking = False 52 #set $used_peak_picking = False
54 #set $used_peak_alignment = False 53 #set $used_peak_alignment = False
55 #set $continuous_format = False 54 #set $continuous_format = False
133 132
134 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian': 133 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
135 print('gaussian smoothing') 134 print('gaussian smoothing')
136 135
137 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian) 136 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
137 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
138 138
139 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay': 139 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
140 print('sgolay smoothing') 140 print('sgolay smoothing')
141 141
142 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters) 142 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
143 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
143 144
144 ## if selected replace negative intensities with zero 145 ## if selected replace negative intensities with zero
145 #if $method.methods_conditional.methods_for_smoothing.replace_negatives: 146 #if $method.methods_conditional.methods_for_smoothing.replace_negatives:
146 spectra(msidata)[spectra(msidata)<0] = 0 147 ## bring spectra matrix to disk
148 spectra_df = as.matrix(spectra(msidata))
149 spectra_df[spectra_df<0] = 0
150 spectra(msidata) = spectra_df
147 #end if 151 #end if
148 152
149 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma': 153 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
150 print('moving average smoothing') 154 print('moving average smoothing')
151 155
152 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter) 156 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter)
157 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
153 158
154 #end if 159 #end if
155 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
156 160
157 ############################### QC ########################### 161 ############################### QC ###########################
158 162
159 maxfeatures =nrow(msidata) 163 maxfeatures =nrow(msidata)
160 pixelcount = ncol(msidata) 164 pixelcount = ncol(msidata)
168 172
169 173
170 ############################### Mz alignment ########################### 174 ############################### Mz alignment ###########################
171 175
172 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_alignment': 176 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_alignment':
173 print('M/z alignment') 177 print('m/z alignment')
174 ## M/z alignment 178 ## M/z alignment
175 179
176 #if str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_table': 180 #if str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_table':
177 181
178 reference_mz = read.delim("$method.methods_conditional.mzalign_ref_type.mz_tabular", header = $method.methods_conditional.mzalign_ref_type.feature_header, stringsAsFactors = FALSE) 182 reference_mz = read.delim("$method.methods_conditional.mzalign_ref_type.mz_tabular", header = $method.methods_conditional.mzalign_ref_type.feature_header, stringsAsFactors = FALSE)
181 msidata = mzAlign(msidata, ref=reference_mz, tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span) 185 msidata = mzAlign(msidata, ref=reference_mz, tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
182 186
183 187
184 #elif str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_noref': 188 #elif str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_noref':
185 189
186 msidata = mzAlign(msidata,tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", , quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span) 190 msidata = mzAlign(msidata,tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
187 191
188 #end if 192 #end if
189 193
190 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) 194 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
191 195
198 mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount) 202 mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount)
199 QC_numbers= cbind(QC_numbers, mz_aligned) 203 QC_numbers= cbind(QC_numbers, mz_aligned)
200 vectorofactions = append(vectorofactions, "mz aligned") 204 vectorofactions = append(vectorofactions, "mz aligned")
201 print(plot(msidata, pixel=random_spectra, col="black")) 205 print(plot(msidata, pixel=random_spectra, col="black"))
202 title("Spectra after m/z alignment", outer=TRUE, line=0) 206 title("Spectra after m/z alignment", outer=TRUE, line=0)
207
208
209 ############################### Mz recalibration ###########################
210
211 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_recalibration':
212 print('m/z recalibration')
213 ## M/z recalibration
214
215 reference_mz = read.delim("$method.methods_conditional.mz_tabular", header = $method.methods_conditional.feature_header, stringsAsFactors = FALSE)
216 reference_mz = reference_mz[,$method.methods_conditional.feature_column]
217
218 msidata = mzAlign(msidata, ref=reference_mz, tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
219
220 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
221
222 ## remove the reference peaks data to allow proper peak alignment afterwards
223 metadata(featureData(msidata))['reference peaks'] <- NULL
224
225 ############################### QC ###########################
226
227 maxfeatures =nrow(msidata)
228 pixelcount = ncol(msidata)
229 minmz = round(min(mz(msidata)), digits=2)
230 maxmz = round(max(mz(msidata)), digits=2)
231 mz_recal = c(minmz, maxmz,maxfeatures, pixelcount)
232 QC_numbers= cbind(QC_numbers, mz_recal)
233 vectorofactions = append(vectorofactions, "mz recalibrated")
234 print(plot(msidata, pixel=random_spectra, col="black"))
235 title("Spectra after m/z recalibration", outer=TRUE, line=0)
203 236
204 237
205 ############################### Peak picking ########################### 238 ############################### Peak picking ###########################
206 239
207 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking': 240 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
330 ############################### Mass binning ########################### 363 ############################### Mass binning ###########################
331 364
332 #elif str( $method.methods_conditional.preprocessing_method) == 'Mass_binning': 365 #elif str( $method.methods_conditional.preprocessing_method) == 'Mass_binning':
333 print('mass binning') 366 print('mass binning')
334 367
335 #if str( $method.methods_conditional.mz_range.features_filtering) == 'change_mz_range': 368 #if str($method.methods_conditional.mz_range.features_filtering) == 'change_mz_range':
336
337 #if str($processed_cond.processed_file) == "processed":
338 369
339 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun") 370 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
340
341 #else
342 ## continuous file cannot be binned from m/z to m/z, therefore first cut m/z range and then do mzbin:
343 msidata = msidata[mz(msidata) >= $method.methods_conditional.mz_range.min_mz & mz(msidata) <= $method.methods_conditional.mz_range.max_mz,]
344 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
345 #end if
346 371
347 372
348 #elif str( $method.methods_conditional.mz_range.features_filtering) == 'none': 373 #elif str($method.methods_conditional.mz_range.features_filtering) == 'none':
349 374
350 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) 375 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
376
377 #elif str($method.methods_conditional.mz_range.features_filtering) == 'bin_to_reference':
378
379 bin_reference_mz = read.delim("$method.methods_conditional.mz_range.mz_tabular", header = $method.methods_conditional.mz_range.feature_header, stringsAsFactors = FALSE)
380 bin_reference_mz = bin_reference_mz[,$method.methods_conditional.mz_range.feature_column]
381
382 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun,
383 ref=bin_reference_mz)
351 384
352 #end if 385 #end if
353 386
354 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) 387 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
355 388
383 416
384 #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2': 417 #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2':
385 print('log2 transformation') 418 print('log2 transformation')
386 419
387 ## replace 0 with NA to prevent Inf 420 ## replace 0 with NA to prevent Inf
388 spectra_df = spectra(msidata) ## convert into R matrix 421 spectra_df = as.matrix(spectra(msidata)) ## convert into R matrix
389 spectra_df[spectra_df ==0] = NA 422 spectra_df[spectra_df ==0] = NA
390 print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra_df)))) 423 print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra_df))))
391 spectra(msidata) = spectra_df 424 spectra(msidata) = spectra_df
392 ## log transformation 425 ## log transformation
393 spectra(msidata) = log2(spectra(msidata)) 426 spectra(msidata) = log2(spectra(msidata))
420 453
421 ############# Outputs: RData, imzml and QC report ############# 454 ############# Outputs: RData, imzml and QC report #############
422 ################################################################################ 455 ################################################################################
423 456
424 ## save msidata as imzML file, will only work if there is at least 1 m/z left 457 ## save msidata as imzML file, will only work if there is at least 1 m/z left
425
426 #if str($imzml_output) == "cont_format":
427 #set $continuous_format = True
428 #end if
429 458
430 if (nrow(msidata) > 0){ 459 if (nrow(msidata) > 0){
431 ## make sure that coordinates are integers 460 ## make sure that coordinates are integers
432 coord(msidata)\$y = as.integer(coord(msidata)\$y) 461 coord(msidata)\$y = as.integer(coord(msidata)\$y)
433 coord(msidata)\$x = as.integer(coord(msidata)\$x) 462 coord(msidata)\$x = as.integer(coord(msidata)\$x)
434 #if $used_peak_picking: 463 ## only continuous files can currently be exported
435 #if $continuous_format: 464 msidata = as(msidata, "MSContinuousImagingExperiment")
436 msidata = as(msidata, "MSContinuousImagingExperiment") 465 writeImzML(msidata, "out")
437 #end if
438 #elif $used_peak_alignment
439 #if $continuous_format:
440 msidata = as(msidata, "MSContinuousImagingExperiment")
441 #end if
442 #end if
443 writeImzML(msidata, "out")
444 } 466 }
445 467
446 plot(0,type='n',axes=FALSE,ann=FALSE) 468 plot(0,type='n',axes=FALSE,ann=FALSE)
447 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "# spectra") 469 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "# spectra")
448 grid.table(t(QC_numbers)) 470 grid.table(t(QC_numbers))
461 <param name="preprocessing_method" type="select" label="Preprocessing methods"> 483 <param name="preprocessing_method" type="select" label="Preprocessing methods">
462 <option value="Normalization" selected="True">Intensity Normalization</option> 484 <option value="Normalization" selected="True">Intensity Normalization</option>
463 <option value="Baseline_reduction">Baseline Reduction</option> 485 <option value="Baseline_reduction">Baseline Reduction</option>
464 <option value="Smoothing">Peak smoothing</option> 486 <option value="Smoothing">Peak smoothing</option>
465 <option value="mz_alignment">m/z alignment</option> 487 <option value="mz_alignment">m/z alignment</option>
488 <option value="mz_recalibration">m/z recalibration</option>
466 <option value="Peak_picking">Peak picking</option> 489 <option value="Peak_picking">Peak picking</option>
467 <option value="Peak_alignment">Peak alignment</option> 490 <option value="Peak_alignment">Peak alignment</option>
468 <option value="Peak_filtering">Peak filtering</option> 491 <option value="Peak_filtering">Peak filtering</option>
469 <option value="Peak_binning">Peak binning to reference peaks</option> 492 <option value="Peak_binning">Peak binning to reference peaks</option>
470 <option value="Mass_binning">m/z binning</option> 493 <option value="Mass_binning">m/z binning</option>
539 <param name="quantile" type="float" value="0.2" 562 <param name="quantile" type="float" value="0.2"
540 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/> 563 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/>
541 <param name="span" type="float" value="0.75" 564 <param name="span" type="float" value="0.75"
542 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/> 565 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/>
543 </when> 566 </when>
567 <when value="mz_recalibration">
568 <param name="alignment_tol" type="text" value="NA"
569 label="tolerance" help="The tolerance to be used when matching the peaks in the unaligned spectra to the reference spectrum. If this is NA, then automatically guess a tolerance from the data.">
570 <sanitizer>
571 <valid initial="string.digits">
572 <add value="N" />
573 <add value="A" />
574 </valid>
575 </sanitizer>
576 </param>
577 <param name="alignment_units" type="select" display="radio" optional="False" label="The units to use for the tolerance.">
578 <option value="ppm" selected="True">ppm</option>
579 <option value="mz">m/z</option>
580 </param>
581 <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."/>
582 <param name="quantile" type="float" value="0.2"
583 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/>
584 <param name="span" type="float" value="0.75"
585 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/>
586 </when>
544 <when value="Peak_picking"> 587 <when value="Peak_picking">
545 <param name="SNR_picking_method" type="float" value="6" 588 <param name="SNR_picking_method" type="float" value="6"
546 label="Signal to noise ratio" 589 label="Signal to noise ratio"
547 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/> 590 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
548 <param name="blocks_picking" type="integer" value="100" label = "Number of blocks" 591 <param name="blocks_picking" type="integer" value="100" label = "Number of blocks"
618 <option value="mean" selected="True">mean</option> 661 <option value="mean" selected="True">mean</option>
619 <option value="sum">sum</option> 662 <option value="sum">sum</option>
620 </param> 663 </param>
621 <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/> 664 <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/>
622 <conditional name="mz_range"> 665 <conditional name="mz_range">
623 <param name="features_filtering" type="select" label="Select m/z feature filtering option"> 666 <param name="features_filtering" type="select" label="Select m/z options">
624 <option value="none" selected="True">none</option> 667 <option value="none" selected="True">none</option>
625 <option value="change_mz_range">change m/z range</option> 668 <option value="change_mz_range">change m/z range</option>
669 <option value="bin_to_reference">bin m/z to reference</option>
626 </param> 670 </param>
627 <when value="none"/> 671 <when value="none"/>
628 <when value="change_mz_range"> 672 <when value="change_mz_range">
629 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/> 673 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
630 <param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/> 674 <param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/>
631 </when> 675 </when>
676 <when value="bin_to_reference">
677 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features as reference for binning. Only the m/z values from the tabular file will be kept."/>
678 </when>
632 </conditional> 679 </conditional>
633 </when> 680 </when>
634 <when value="Transformation"> 681 <when value="Transformation">
635 <conditional name="transf_conditional"> 682 <conditional name="transf_conditional">
636 <param name="trans_type" type="select" label="Intensity transformations" help="logarithm base 2 (log2) or squareroot (sqrt)"> 683 <param name="trans_type" type="select" label="Intensity transformations" help="logarithm base 2 (log2) or squareroot (sqrt)">
643 <when value="sqrt"/> 690 <when value="sqrt"/>
644 </conditional> 691 </conditional>
645 </when> 692 </when>
646 </conditional> 693 </conditional>
647 </repeat> 694 </repeat>
648 <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>
649 </inputs> 695 </inputs>
650 <outputs> 696 <outputs>
651 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/> 697 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
652 <data format="pdf" name="QC_overview" from_work_dir="Preprocessing.pdf" label = "${tool.name} on ${on_string}: QC"/> 698 <data format="pdf" name="QC_overview" from_work_dir="Preprocessing.pdf" label = "${tool.name} on ${on_string}: QC"/>
653 </outputs> 699 </outputs>
664 </repeat> 710 </repeat>
665 <repeat name="methods"> 711 <repeat name="methods">
666 <conditional name="methods_conditional"> 712 <conditional name="methods_conditional">
667 <param name="preprocessing_method" value="Smoothing"/> 713 <param name="preprocessing_method" value="Smoothing"/>
668 <conditional name="methods_for_smoothing"> 714 <conditional name="methods_for_smoothing">
669 <param name="smoothing_method" value="gaussian"/> 715 <param name="smoothing_method" value="sgolay"/>
670 <param name="sd_gaussian" value="4"/> 716 </conditional>
671 </conditional>
672 <param name="window_smoothing" value="9"/>
673 </conditional> 717 </conditional>
674 </repeat> 718 </repeat>
675 <repeat name="methods"> 719 <repeat name="methods">
676 <conditional name="methods_conditional"> 720 <conditional name="methods_conditional">
677 <param name="preprocessing_method" value="Peak_picking"/> 721 <param name="preprocessing_method" value="Peak_picking"/>
700 <conditional name="transf_conditional"> 744 <conditional name="transf_conditional">
701 <param name="trans_type" value="sqrt"/> 745 <param name="trans_type" value="sqrt"/>
702 </conditional> 746 </conditional>
703 </conditional> 747 </conditional>
704 </repeat> 748 </repeat>
705 <param name="imzml_output" value="cont_format"/>
706 <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/> 749 <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>
707 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size"> 750 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size">
708 <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/> 751 <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/>
709 <extra_files type="file" file="preprocessing_results1.ibd" name="ibd" compare="sim_size"/> 752 <extra_files type="file" file="preprocessing_results1.ibd" name="ibd" compare="sim_size"/>
710 </output> 753 </output>
725 <repeat name="methods"> 768 <repeat name="methods">
726 <conditional name="methods_conditional"> 769 <conditional name="methods_conditional">
727 <param name="preprocessing_method" value="Peak_alignment"/> 770 <param name="preprocessing_method" value="Peak_alignment"/>
728 </conditional> 771 </conditional>
729 </repeat> 772 </repeat>
730 <param name="imzml_output" value="cont_format"/>
731 <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/> 773 <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>
732 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size"> 774 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">
733 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/> 775 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>
734 <extra_files type="file" file="preprocessing_results2.ibd" name="ibd" compare="sim_size"/> 776 <extra_files type="file" file="preprocessing_results2.ibd" name="ibd" compare="sim_size"/>
735 </output> 777 </output>
751 <param name="window_picking" value="5"/> 793 <param name="window_picking" value="5"/>
752 <param name="SNR_picking_method" value="2"/> 794 <param name="SNR_picking_method" value="2"/>
753 <conditional name="methods_for_picking"> 795 <conditional name="methods_for_picking">
754 <param name="picking_method" value="mad"/> 796 <param name="picking_method" value="mad"/>
755 </conditional> 797 </conditional>
756 <param name="imzml_output" value="proc_format"/>
757 </conditional> 798 </conditional>
758 </repeat> 799 </repeat>
759 <repeat name="methods"> 800 <repeat name="methods">
760 <conditional name="methods_conditional"> 801 <conditional name="methods_conditional">
761 <param name="preprocessing_method" value="Peak_alignment"/> 802 <param name="preprocessing_method" value="Peak_alignment"/>
762 <param name="imzml_output" value="proc_format"/>
763 </conditional> 803 </conditional>
764 </repeat> 804 </repeat>
765 <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/> 805 <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/>
766 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results3.imzml.txt" compare="sim_size"> 806 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results3.imzml.txt" compare="sim_size">
767 <extra_files type="file" file="preprocessing_results3.imzml" name="imzml" lines_diff="6"/> 807 <extra_files type="file" file="preprocessing_results3.imzml" name="imzml" lines_diff="6"/>
777 </conditional> 817 </conditional>
778 </repeat> 818 </repeat>
779 <repeat name="methods"> 819 <repeat name="methods">
780 <conditional name="methods_conditional"> 820 <conditional name="methods_conditional">
781 <param name="preprocessing_method" value="mz_alignment"/> 821 <param name="preprocessing_method" value="mz_alignment"/>
822 </conditional>
823 </repeat>
824 <repeat name="methods">
825 <conditional name="methods_conditional">
826 <param name="preprocessing_method" value="mz_recalibration"/>
827 <param name="alignment_tol" value="2"/>
828 <param name="alignment_units" value="ppm"/>
829 <param name="mz_tabular" value="inputcalibrantfile2.txt" ftype="tabular"/>
830 <param name="feature_column" value="1"/>
831 <param name="feature_header" value="TRUE"/>
782 </conditional> 832 </conditional>
783 </repeat> 833 </repeat>
784 <repeat name="methods"> 834 <repeat name="methods">
785 <conditional name="methods_conditional"> 835 <conditional name="methods_conditional">
786 <param name="preprocessing_method" value="Mass_binning"/> 836 <param name="preprocessing_method" value="Mass_binning"/>
848 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 898 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems.
849 899
850 900
851 **Output** 901 **Output**
852 902
853 - MSI data as continuous or processed imzML file 903 - MSI data as continuous imzML file
854 - pdf with key values and four random mass spectra after each processing step 904 - pdf with key values and four random mass spectra after each processing step
855 905
856 ]]> 906 ]]>
857 </help> 907 </help>
858 <expand macro="citations"/> 908 <expand macro="citations"/>