| Previous changeset 14:f1897eb07081 (2020-12-23) Next changeset 16:798da6bdff3d (2022-02-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f" |
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modified:
macros.xml preprocessing.xml test-data/pixels_test6.tabular test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/test1.pdf test-data/test2.pdf test-data/test3.pdf test-data/test4.pdf test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
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added:
test-data/QC_imzml_shortreport.pdf |
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| diff -r f1897eb07081 -r accf9fb6ea01 macros.xml --- a/macros.xml Wed Dec 23 22:32:19 2020 +0000 +++ b/macros.xml Sun Aug 29 07:32:56 2021 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.6.0</token> + <token name="@VERSION@">2.10.0</token> <xml name="requirements"> <requirements> |
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| diff -r f1897eb07081 -r accf9fb6ea01 preprocessing.xml --- a/preprocessing.xml Wed Dec 23 22:32:19 2020 +0000 +++ b/preprocessing.xml Sun Aug 29 07:32:56 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.2"> +<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0"> <description> mass spectrometry imaging preprocessing </description> @@ -7,7 +7,7 @@ </macros> <expand macro="requirements"> <requirement type="package" version="2.3">r-gridextra</requirement> - <requirement type="package" version="3.3.2">r-ggplot2</requirement> + <requirement type="package" version="3.3.5">r-ggplot2</requirement> </expand> <command detect_errors="exit_code"> <![CDATA[ @@ -204,6 +204,35 @@ vectorofactions = append(vectorofactions, "mz aligned") print(plot(msidata, pixel=random_spectra, col="black")) title("Spectra after m/z alignment", outer=TRUE, line=0) + + + ############################### Mz recalibration ########################### + + #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_recalibration': + print('m/z recalibration') + ## M/z recalibration + + reference_mz = read.delim("$method.methods_conditional.mz_tabular", header = $method.methods_conditional.feature_header, stringsAsFactors = FALSE) + reference_mz = reference_mz[,$method.methods_conditional.feature_column] + + 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) + + msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) + + ## remove the reference peaks data to allow proper peak alignment afterwards + metadata(featureData(msidata))['reference peaks'] <- NULL + + ############################### QC ########################### + + maxfeatures =nrow(msidata) + pixelcount = ncol(msidata) + minmz = round(min(mz(msidata)), digits=2) + maxmz = round(max(mz(msidata)), digits=2) + mz_recal = c(minmz, maxmz,maxfeatures, pixelcount) + QC_numbers= cbind(QC_numbers, mz_recal) + vectorofactions = append(vectorofactions, "mz recalibrated") + print(plot(msidata, pixel=random_spectra, col="black")) + title("Spectra after m/z recalibration", outer=TRUE, line=0) ############################### Peak picking ########################### @@ -456,6 +485,7 @@ <option value="Baseline_reduction">Baseline Reduction</option> <option value="Smoothing">Peak smoothing</option> <option value="mz_alignment">m/z alignment</option> + <option value="mz_recalibration">m/z recalibration</option> <option value="Peak_picking">Peak picking</option> <option value="Peak_alignment">Peak alignment</option> <option value="Peak_filtering">Peak filtering</option> @@ -534,6 +564,26 @@ <param name="span" type="float" value="0.75" label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/> </when> + <when value="mz_recalibration"> + <param name="alignment_tol" type="text" value="NA" + 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."> + <sanitizer> + <valid initial="string.digits"> + <add value="N" /> + <add value="A" /> + </valid> + </sanitizer> + </param> + <param name="alignment_units" type="select" display="radio" optional="False" label="The units to use for the tolerance."> + <option value="ppm" selected="True">ppm</option> + <option value="mz">m/z</option> + </param> + <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."/> + <param name="quantile" type="float" value="0.2" + label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/> + <param name="span" type="float" value="0.75" + label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/> + </when> <when value="Peak_picking"> <param name="SNR_picking_method" type="float" value="6" label="Signal to noise ratio" @@ -773,6 +823,16 @@ </repeat> <repeat name="methods"> <conditional name="methods_conditional"> + <param name="preprocessing_method" value="mz_recalibration"/> + <param name="alignment_tol" value="2"/> + <param name="alignment_units" value="ppm"/> + <param name="mz_tabular" value="inputcalibrantfile2.txt" ftype="tabular"/> + <param name="feature_column" value="1"/> + <param name="feature_header" value="TRUE"/> + </conditional> + </repeat> + <repeat name="methods"> + <conditional name="methods_conditional"> <param name="preprocessing_method" value="Mass_binning"/> <param name="bin_width" value="0.1"/> <param name="bin_units" value="mz"/> |
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| diff -r f1897eb07081 -r accf9fb6ea01 test-data/QC_imzml_shortreport.pdf |
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| diff -r f1897eb07081 -r accf9fb6ea01 test-data/pixels_test6.tabular --- a/test-data/pixels_test6.tabular Wed Dec 23 22:32:19 2020 +0000 +++ b/test-data/pixels_test6.tabular Sun Aug 29 07:32:56 2021 +0000 |
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| @@ -1,25 +1,25 @@ -pixel names x y predicted condition -xy_1_1 1 1 A -xy_2_1 2 1 A -xy_3_1 3 1 B -xy_4_1 4 1 C -xy_1_2 1 2 C -xy_2_2 2 2 C -xy_3_2 3 2 A -xy_4_2 4 2 A -xy_1_3 1 3 A -xy_2_3 2 3 B -xy_3_3 3 3 C -xy_4_3 4 3 A -xy_10_1 10 1 C -xy_11_1 11 1 C -xy_12_1 12 1 C -xy_13_1 13 1 B -xy_10_2 10 2 C -xy_11_2 11 2 B -xy_12_2 12 2 C -xy_13_2 13 2 C -xy_10_3 10 3 C -xy_11_3 11 3 C -xy_12_3 12 3 B -xy_13_3 13 3 C +pixel names x y predicted condition A B C +xy_1_1 1 1 A 0.434439526064797 0.195646317191818 0.369914156743386 +xy_2_1 2 1 A 0.38219998209377 0.242372158141275 0.375427859764956 +xy_3_1 3 1 B 0.312531499299517 0.385612104162858 0.301856396537625 +xy_4_1 4 1 C 0.393153488582866 0.191107087820634 0.4157394235965 +xy_1_2 1 2 C 0.366986470447772 0.216121568441093 0.416891961111135 +xy_2_2 2 2 C 0.381682206547616 0.213188918797062 0.405128874655322 +xy_3_2 3 2 A 0.376695037169723 0.260689491088564 0.362615471741713 +xy_4_2 4 2 A 0.42305935188829 0.174038449100755 0.402902199010954 +xy_1_3 1 3 A 0.382420991383021 0.249364697048677 0.368214311568302 +xy_2_3 2 3 B 0.272145998315727 0.446525938567718 0.281328063116555 +xy_3_3 3 3 C 0.36296987427851 0.255631013944556 0.381399111776934 +xy_4_3 4 3 A 0.444812272103175 0.132274264153212 0.422913463743613 +xy_10_1 10 1 C 0.376216993893763 0.227584528606788 0.39619847749945 +xy_11_1 11 1 C 0.358430578177403 0.236120068794936 0.405449353027661 +xy_12_1 12 1 C 0.359751662628136 0.218620985552221 0.421627351819643 +xy_13_1 13 1 B 0.101486342705225 0.813997511218961 0.0845161460758142 +xy_10_2 10 2 C 0.354612526523361 0.272635192773437 0.372752280703202 +xy_11_2 11 2 B 0.291635599769993 0.444466545540823 0.263897854689184 +xy_12_2 12 2 C 0.36763798979782 0.203911653614431 0.428450356587749 +xy_13_2 13 2 C 0.344608135177236 0.304026642707691 0.351365222115073 +xy_10_3 10 3 C 0.37046458150651 0.205561286708086 0.423974131785404 +xy_11_3 11 3 C 0.358113833435286 0.262878459144526 0.379007707420187 +xy_12_3 12 3 B 0.180921926305915 0.66902588624642 0.150052187447665 +xy_13_3 13 3 C 0.378266307042675 0.20859472985319 0.413138963104135 |
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| diff -r f1897eb07081 -r accf9fb6ea01 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Wed Dec 23 22:32:19 2020 +0000 +++ b/test-data/preprocessing_results4.imzml Sun Aug 29 07:32:56 2021 +0000 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="48842eaf-40e5-4a3f-831c-2d7a3b7e04b9" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2010ba5b7d44695d891cfe3b6674a5699fa610c0" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="04431b64-9f3d-44b4-9e63-81b9e4924aec" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="38a4fadd32374bdf0e4b2bb7d976f6067d542a29" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.6.0"> + <software id="Cardinal" version="2.10.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r f1897eb07081 -r accf9fb6ea01 test-data/preprocessing_results4.imzml.txt --- a/test-data/preprocessing_results4.imzml.txt Wed Dec 23 22:32:19 2020 +0000 +++ b/test-data/preprocessing_results4.imzml.txt Sun Aug 29 07:32:56 2021 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 84 --rw-rw-r-- 1 meli meli 62696 Oct 5 19:58 ibd --rw-rw-r-- 1 meli meli 18199 Oct 5 19:58 imzml +-rw-rw-r-- 1 meli meli 62696 Aug 28 16:41 ibd +-rw-rw-r-- 1 meli meli 18200 Aug 28 16:41 imzml |
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