Mercurial > repos > galaxyp > cardinal_preprocessing
comparison preprocessing.xml @ 15:accf9fb6ea01 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
| author | galaxyp |
|---|---|
| date | Sun, 29 Aug 2021 07:32:56 +0000 |
| parents | 6b36be80febb |
| children | 611d80c0e29d |
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| 14:f1897eb07081 | 15:accf9fb6ea01 |
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| 1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.2"> | 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@ |
| 202 mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount) | 202 mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount) |
| 203 QC_numbers= cbind(QC_numbers, mz_aligned) | 203 QC_numbers= cbind(QC_numbers, mz_aligned) |
| 204 vectorofactions = append(vectorofactions, "mz aligned") | 204 vectorofactions = append(vectorofactions, "mz aligned") |
| 205 print(plot(msidata, pixel=random_spectra, col="black")) | 205 print(plot(msidata, pixel=random_spectra, col="black")) |
| 206 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) | |
| 207 | 236 |
| 208 | 237 |
| 209 ############################### Peak picking ########################### | 238 ############################### Peak picking ########################### |
| 210 | 239 |
| 211 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking': | 240 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking': |
| 454 <param name="preprocessing_method" type="select" label="Preprocessing methods"> | 483 <param name="preprocessing_method" type="select" label="Preprocessing methods"> |
| 455 <option value="Normalization" selected="True">Intensity Normalization</option> | 484 <option value="Normalization" selected="True">Intensity Normalization</option> |
| 456 <option value="Baseline_reduction">Baseline Reduction</option> | 485 <option value="Baseline_reduction">Baseline Reduction</option> |
| 457 <option value="Smoothing">Peak smoothing</option> | 486 <option value="Smoothing">Peak smoothing</option> |
| 458 <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> | |
| 459 <option value="Peak_picking">Peak picking</option> | 489 <option value="Peak_picking">Peak picking</option> |
| 460 <option value="Peak_alignment">Peak alignment</option> | 490 <option value="Peak_alignment">Peak alignment</option> |
| 461 <option value="Peak_filtering">Peak filtering</option> | 491 <option value="Peak_filtering">Peak filtering</option> |
| 462 <option value="Peak_binning">Peak binning to reference peaks</option> | 492 <option value="Peak_binning">Peak binning to reference peaks</option> |
| 463 <option value="Mass_binning">m/z binning</option> | 493 <option value="Mass_binning">m/z binning</option> |
| 532 <param name="quantile" type="float" value="0.2" | 562 <param name="quantile" type="float" value="0.2" |
| 533 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."/> |
| 534 <param name="span" type="float" value="0.75" | 564 <param name="span" type="float" value="0.75" |
| 535 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."/> |
| 536 </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> | |
| 537 <when value="Peak_picking"> | 587 <when value="Peak_picking"> |
| 538 <param name="SNR_picking_method" type="float" value="6" | 588 <param name="SNR_picking_method" type="float" value="6" |
| 539 label="Signal to noise ratio" | 589 label="Signal to noise ratio" |
| 540 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."/> |
| 541 <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" |
| 771 <param name="preprocessing_method" value="mz_alignment"/> | 821 <param name="preprocessing_method" value="mz_alignment"/> |
| 772 </conditional> | 822 </conditional> |
| 773 </repeat> | 823 </repeat> |
| 774 <repeat name="methods"> | 824 <repeat name="methods"> |
| 775 <conditional name="methods_conditional"> | 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"/> | |
| 832 </conditional> | |
| 833 </repeat> | |
| 834 <repeat name="methods"> | |
| 835 <conditional name="methods_conditional"> | |
| 776 <param name="preprocessing_method" value="Mass_binning"/> | 836 <param name="preprocessing_method" value="Mass_binning"/> |
| 777 <param name="bin_width" value="0.1"/> | 837 <param name="bin_width" value="0.1"/> |
| 778 <param name="bin_units" value="mz"/> | 838 <param name="bin_units" value="mz"/> |
| 779 </conditional> | 839 </conditional> |
| 780 </repeat> | 840 </repeat> |