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comparison preprocessing.xml @ 8:87bb011a4ee8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
author galaxyp
date Wed, 13 May 2020 14:21:48 -0400
parents 44a4b31fcbf3
children ca727a6dede6
comparison
equal deleted inserted replaced
7:44a4b31fcbf3 8:87bb011a4ee8
1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1"> 1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.2">
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>
90 90
91 if (class(msidata) == "MSProcessedImagingExperiment"){ 91 if (class(msidata) == "MSProcessedImagingExperiment"){
92 msidata = as(msidata, "MSContinuousImagingExperiment") 92 msidata = as(msidata, "MSContinuousImagingExperiment")
93 } 93 }
94 94
95 msidata = normalize(msidata, method="tic") 95 msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method")
96 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) 96 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
97 97
98 98
99 ############################### QC ########################### 99 ############################### QC ###########################
100 100
176 smoothed = c(minmz, maxmz,maxfeatures, pixelcount) 176 smoothed = c(minmz, maxmz,maxfeatures, pixelcount)
177 QC_numbers= cbind(QC_numbers, smoothed) 177 QC_numbers= cbind(QC_numbers, smoothed)
178 vectorofactions = append(vectorofactions, "smoothed") 178 vectorofactions = append(vectorofactions, "smoothed")
179 print(plot(msidata, pixel=random_spectra)) 179 print(plot(msidata, pixel=random_spectra))
180 title("Spectra after smoothing", outer=TRUE, line=0) 180 title("Spectra after smoothing", outer=TRUE, line=0)
181
182
183 ############################### Mz alignment ###########################
184
185 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_alignment':
186 print('M/z alignment')
187 ## M/z alignment
188
189 #if str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_table':
190
191 reference_mz = read.delim("$method.methods_conditional.mzalign_ref_type.mz_tabular", header = $method.methods_conditional.mzalign_ref_type.feature_header, stringsAsFactors = FALSE)
192 reference_mz = reference_mz[,$method.methods_conditional.mzalign_ref_type.feature_column]
193
194 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)
195
196
197 #elif str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_noref':
198
199 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)
200
201 #end if
202
203 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
204
205 ############################### QC ###########################
206
207 maxfeatures =nrow(msidata)
208 pixelcount = ncol(msidata)
209 minmz = round(min(mz(msidata)), digits=2)
210 maxmz = round(max(mz(msidata)), digits=2)
211 mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount)
212 QC_numbers= cbind(QC_numbers, mz_aligned)
213 vectorofactions = append(vectorofactions, "mz aligned")
214 print(plot(msidata, pixel=random_spectra))
215 title("Spectra after m/z alignment", outer=TRUE, line=0)
216
181 217
182 ############################### Peak picking ########################### 218 ############################### Peak picking ###########################
183 219
184 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking': 220 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
185 #set $used_peak_picking = True 221 #set $used_peak_picking = True
436 <conditional name="methods_conditional"> 472 <conditional name="methods_conditional">
437 <param name="preprocessing_method" type="select" label="Preprocessing methods"> 473 <param name="preprocessing_method" type="select" label="Preprocessing methods">
438 <option value="Normalization" selected="True">Intensity Normalization</option> 474 <option value="Normalization" selected="True">Intensity Normalization</option>
439 <option value="Baseline_reduction">Baseline Reduction</option> 475 <option value="Baseline_reduction">Baseline Reduction</option>
440 <option value="Smoothing">Peak smoothing</option> 476 <option value="Smoothing">Peak smoothing</option>
477 <option value="mz_alignment">m/z alignment</option>
441 <option value="Peak_picking">Peak picking</option> 478 <option value="Peak_picking">Peak picking</option>
442 <option value="Peak_alignment">Peak alignment</option> 479 <option value="Peak_alignment">Peak alignment</option>
443 <option value="Peak_filtering">Peak filtering</option> 480 <option value="Peak_filtering">Peak filtering</option>
444 <option value="Peak_binning">Peak binning to reference peaks</option> 481 <option value="Peak_binning">Peak binning to reference peaks</option>
445 <option value="Data_reduction">Data reduction</option> 482 <option value="Data_reduction">Data reduction</option>
484 label="The coefficients for the moving average filter"/> 521 label="The coefficients for the moving average filter"/>
485 </when> 522 </when>
486 </conditional> 523 </conditional>
487 <param name="window_smoothing" type="float" value="8" 524 <param name="window_smoothing" type="float" value="8"
488 label="Window size"/> 525 label="Window size"/>
526 </when>
527 <when value="mz_alignment">
528 <param name="alignment_tol" type="text" value="NA"
529 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.">
530 <sanitizer>
531 <valid initial="string.digits">
532 <add value="N" />
533 <add value="A" />
534 </valid>
535 </sanitizer>
536 </param>
537 <param name="alignment_units" type="select" display="radio" optional="False" label="The units to use for the tolerance.">
538 <option value="ppm" selected="True">ppm</option>
539 <option value="mz">m/z</option>
540 </param>
541 <conditional name="mzalign_ref_type">
542 <param name="align_reference_datatype" type="select" label="Choose reference">
543 <option value="align_noref" selected="True">use mean spectrum as reference</option>
544 <option value="align_table" >m/z values from tabular file as reference</option>
545 </param>
546 <when value="align_noref"/>
547 <when value="align_table">
548 <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."/>
549 </when>
550 </conditional>
551 <param name="quantile" type="float" value="0.2"
552 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/>
553 <param name="span" type="float" value="0.75"
554 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/>
489 </when> 555 </when>
490 <when value="Peak_picking"> 556 <when value="Peak_picking">
491 <param name="SNR_picking_method" type="float" value="6" 557 <param name="SNR_picking_method" type="float" value="6"
492 label="Signal to noise ratio" 558 label="Signal to noise ratio"
493 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/> 559 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
520 <option value="mz">m/z</option> 586 <option value="mz">m/z</option>
521 </param> 587 </param>
522 <conditional name="align_ref_type"> 588 <conditional name="align_ref_type">
523 <param name="align_reference_datatype" type="select" label="Choose reference"> 589 <param name="align_reference_datatype" type="select" label="Choose reference">
524 <option value="align_noref" selected="True">no reference</option> 590 <option value="align_noref" selected="True">no reference</option>
525 <option value="align_table" >tabular file as reference</option> 591 <option value="align_table" >m/z values from tabular file as reference</option>
526 </param> 592 </param>
527 <when value="align_noref"/> 593 <when value="align_noref"/>
528 <when value="align_table"> 594 <when value="align_table">
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."/> 595 <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."/>
530 </when> 596 </when>
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)"/> 601 <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> 602 </when>
537 <when value="Peak_binning"> 603 <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"/> 604 <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." > 605 <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=""> 606 <sanitizer>
541 <valid initial="string.digits"> 607 <valid initial="string.digits">
542 <add value="NA" /> 608 <add value="N" />
609 <add value="A" />
543 </valid> 610 </valid>
544 </sanitizer> 611 </sanitizer>
545 </param> 612 </param>
546 <param name="peakbin_units" display="radio" type="select" label="The units to use for the tolerance."> 613 <param name="peakbin_units" display="radio" type="select" label="The units to use for the tolerance.">
547 <option value="mz" >mz</option> 614 <option value="mz" >mz</option>
726 <param name="normalization_method" value="tic"/> 793 <param name="normalization_method" value="tic"/>
727 </conditional> 794 </conditional>
728 </repeat> 795 </repeat>
729 <repeat name="methods"> 796 <repeat name="methods">
730 <conditional name="methods_conditional"> 797 <conditional name="methods_conditional">
798 <param name="preprocessing_method" value="mz_alignment"/>
799 </conditional>
800 </repeat>
801 <repeat name="methods">
802 <conditional name="methods_conditional">
731 <param name="preprocessing_method" value="Data_reduction"/> 803 <param name="preprocessing_method" value="Data_reduction"/>
732 <conditional name="methods_for_reduction"> 804 <conditional name="methods_for_reduction">
733 <param name="reduction_method" value="bin"/> 805 <param name="reduction_method" value="bin"/>
734 <param name="bin_width" value="0.1"/> 806 <param name="bin_width" value="0.1"/>
735 </conditional> 807 </conditional>
759 <repeat name="methods"> 831 <repeat name="methods">
760 <conditional name="methods_conditional"> 832 <conditional name="methods_conditional">
761 <param name="preprocessing_method" value="Baseline_reduction"/> 833 <param name="preprocessing_method" value="Baseline_reduction"/>
762 </conditional> 834 </conditional>
763 </repeat> 835 </repeat>
764 <output name="QC_overview" file="preprocessing_results5.pdf" compare="sim_size"/> 836 <output name="QC_overview" file="preprocessing_results5.pdf" compare="sim_size" delta="13000"/>
765 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results5.imzml.txt" compare="sim_size"> 837 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results5.imzml.txt" compare="sim_size">
766 <extra_files type="file" file="preprocessing_results5.imzml" name="imzml" lines_diff="6"/> 838 <extra_files type="file" file="preprocessing_results5.imzml" name="imzml" lines_diff="6"/>
767 <extra_files type="file" file="preprocessing_results5.ibd" name="ibd" compare="sim_size"/> 839 <extra_files type="file" file="preprocessing_results5.ibd" name="ibd" compare="sim_size"/>
768 </output> 840 </output>
769 </test> 841 </test>