Mercurial > repos > galaxyp > cardinal_preprocessing
changeset 8:413a1b74f496 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
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--- a/macros.xml Thu Apr 23 11:57:53 2020 +0000 +++ b/macros.xml Wed May 13 17:56:03 2020 +0000 @@ -32,6 +32,12 @@ <token name="@READING_MSIDATA@"><![CDATA[ ## importing MSI data files + ## read RData files (MSI and other data) independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } + #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units") @@ -45,11 +51,6 @@ msidata = readAnalyze('infile', attach.only=TRUE) centroided(msidata) = $centroids #else - ## function to read RData files independent of filename - loadRData <- function(fileName){ - load(fileName) - get(ls()[ls() != "fileName"]) - } msidata = loadRData('infile.RData') #end if
--- a/preprocessing.xml Thu Apr 23 11:57:53 2020 +0000 +++ b/preprocessing.xml Wed May 13 17:56:03 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1"> +<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.2"> <description> mass spectrometry imaging preprocessing </description> @@ -92,7 +92,7 @@ msidata = as(msidata, "MSContinuousImagingExperiment") } - msidata = normalize(msidata, method="tic") + msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method") msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) @@ -179,6 +179,42 @@ print(plot(msidata, pixel=random_spectra)) title("Spectra after smoothing", outer=TRUE, line=0) + + ############################### Mz alignment ########################### + + #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_alignment': + print('M/z alignment') + ## M/z alignment + + #if str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_table': + + reference_mz = read.delim("$method.methods_conditional.mzalign_ref_type.mz_tabular", header = $method.methods_conditional.mzalign_ref_type.feature_header, stringsAsFactors = FALSE) + reference_mz = reference_mz[,$method.methods_conditional.mzalign_ref_type.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) + + + #elif str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_noref': + + 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) + + #end if + + msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) + + ############################### QC ########################### + + maxfeatures =nrow(msidata) + pixelcount = ncol(msidata) + minmz = round(min(mz(msidata)), digits=2) + maxmz = round(max(mz(msidata)), digits=2) + mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount) + QC_numbers= cbind(QC_numbers, mz_aligned) + vectorofactions = append(vectorofactions, "mz aligned") + print(plot(msidata, pixel=random_spectra)) + title("Spectra after m/z alignment", outer=TRUE, line=0) + + ############################### Peak picking ########################### #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking': @@ -438,6 +474,7 @@ <option value="Normalization" selected="True">Intensity Normalization</option> <option value="Baseline_reduction">Baseline Reduction</option> <option value="Smoothing">Peak smoothing</option> + <option value="mz_alignment">m/z alignment</option> <option value="Peak_picking">Peak picking</option> <option value="Peak_alignment">Peak alignment</option> <option value="Peak_filtering">Peak filtering</option> @@ -487,6 +524,35 @@ <param name="window_smoothing" type="float" value="8" label="Window size"/> </when> + <when value="mz_alignment"> + <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> + <conditional name="mzalign_ref_type"> + <param name="align_reference_datatype" type="select" label="Choose reference"> + <option value="align_noref" selected="True">use mean spectrum as reference</option> + <option value="align_table" >m/z values from tabular file as reference</option> + </param> + <when value="align_noref"/> + <when value="align_table"> + <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."/> + </when> + </conditional> + <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" @@ -522,7 +588,7 @@ <conditional name="align_ref_type"> <param name="align_reference_datatype" type="select" label="Choose reference"> <option value="align_noref" selected="True">no reference</option> - <option value="align_table" >tabular file as reference</option> + <option value="align_table" >m/z values from tabular file as reference</option> </param> <when value="align_noref"/> <when value="align_table"> @@ -537,9 +603,10 @@ <when value="Peak_binning"> <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"/> <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." > - <sanitizer invalid_char=""> + <sanitizer> <valid initial="string.digits"> - <add value="NA" /> + <add value="N" /> + <add value="A" /> </valid> </sanitizer> </param> @@ -728,6 +795,11 @@ </repeat> <repeat name="methods"> <conditional name="methods_conditional"> + <param name="preprocessing_method" value="mz_alignment"/> + </conditional> + </repeat> + <repeat name="methods"> + <conditional name="methods_conditional"> <param name="preprocessing_method" value="Data_reduction"/> <conditional name="methods_for_reduction"> <param name="reduction_method" value="bin"/> @@ -761,7 +833,7 @@ <param name="preprocessing_method" value="Baseline_reduction"/> </conditional> </repeat> - <output name="QC_overview" file="preprocessing_results5.pdf" compare="sim_size"/> + <output name="QC_overview" file="preprocessing_results5.pdf" compare="sim_size" delta="13000"/> <output name="outfile_imzml" ftype="imzml" file="preprocessing_results5.imzml.txt" compare="sim_size"> <extra_files type="file" file="preprocessing_results5.imzml" name="imzml" lines_diff="6"/> <extra_files type="file" file="preprocessing_results5.ibd" name="ibd" compare="sim_size"/>
--- a/test-data/preprocessing_results1.imzml Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Wed May 13 17:56:03 2020 +0000 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="722d404b-4188-40b4-a3b2-3764ebbdecad" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c5aded0bab57fd7317901ff7709f2395fc91152e" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="25fb4349-d529-4b12-8523-a6aa0306ecf4" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7f41f9f5efcb31248caefc91b7d6edce87d7f42c" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription>
--- a/test-data/preprocessing_results1.imzml.txt Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Wed May 13 17:56:03 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 216 Mär 24 10:39 ibd --rw-r--r-- 1 meli meli 18090 Mär 24 10:39 imzml +-rw-r--r-- 1 meli meli 216 Mai 10 17:37 ibd +-rw-r--r-- 1 meli meli 18090 Mai 10 17:37 imzml
--- a/test-data/preprocessing_results2.imzml Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results2.imzml Wed May 13 17:56:03 2020 +0000 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e536d1e2-427b-4c5b-9743-8210ae52a564" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7cea783e9d345946b874fc1f25d40ce90bffd2f9" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="fa59b434-12e0-47fe-b338-814c92daa7d6" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5764be27b51a23d8c23e4c93befb9d8e57161bd9" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription>
--- a/test-data/preprocessing_results2.imzml.txt Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Wed May 13 17:56:03 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 64 --rw-r--r-- 1 meli meli 37404 Mär 24 10:40 ibd --rw-r--r-- 1 meli meli 22796 Mär 24 10:40 imzml +-rw-r--r-- 1 meli meli 37404 Mai 10 17:38 ibd +-rw-r--r-- 1 meli meli 22796 Mai 10 17:38 imzml
--- a/test-data/preprocessing_results3.imzml Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results3.imzml Wed May 13 17:56:03 2020 +0000 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="df9dd256-6485-4954-8338-ddb0c760d4dc" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ea9ad44f2615ef4d24b92d3ceb38dfa8ec47a978" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="d11b7693-3397-4d1f-9e67-29d952701100" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94906879d47bbdcf97126d50c906dfd76e6681e4" /> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" /> </fileContent> </fileDescription>
--- a/test-data/preprocessing_results3.imzml.txt Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results3.imzml.txt Wed May 13 17:56:03 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 960 Apr 22 15:36 ibd --rw-r--r-- 1 meli meli 18112 Apr 22 15:36 imzml +-rw-r--r-- 1 meli meli 960 Mai 10 17:39 ibd +-rw-r--r-- 1 meli meli 18112 Mai 10 17:39 imzml
--- a/test-data/preprocessing_results4.imzml Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results4.imzml Wed May 13 17:56:03 2020 +0000 @@ -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="db79298c-8368-42d7-84fc-18cad6ef1924" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="18bae3cc87b4c9aab2577cffe2fbc7425a93270b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c6122884-ceb5-46b6-9160-5d28e8862946" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="03e4b58b8e63517605164e90b85fe93a851a9c5b" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription>
--- a/test-data/preprocessing_results4.imzml.txt Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results4.imzml.txt Wed May 13 17:56:03 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 84 --rw-r--r-- 1 meli meli 63256 Mär 24 11:35 ibd --rw-r--r-- 1 meli meli 18199 Mär 24 11:35 imzml +-rw-r--r-- 1 meli meli 63256 Mai 10 17:40 ibd +-rw-r--r-- 1 meli meli 18199 Mai 10 17:40 imzml
--- a/test-data/preprocessing_results5.imzml Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results5.imzml Wed May 13 17:56:03 2020 +0000 @@ -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="1cb5b7df-bc82-4588-9a14-1dd58a3983a7" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a16bf7a9d9d4064ce94821e3e7df2681725a497b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="3aff713c-00ec-422d-b63d-efd45fbdd7cc" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9316138c1e7484662943bb206c79c2d074121530" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription>
--- a/test-data/preprocessing_results5.imzml.txt Thu Apr 23 11:57:53 2020 +0000 +++ b/test-data/preprocessing_results5.imzml.txt Wed May 13 17:56:03 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 428 --rw-r--r-- 1 meli meli 415936 Apr 19 21:07 ibd --rw-r--r-- 1 meli meli 18569 Apr 19 21:07 imzml +-rw-r--r-- 1 meli meli 415936 Mai 10 17:40 ibd +-rw-r--r-- 1 meli meli 18569 Mai 10 17:40 imzml