Mercurial > repos > galaxyp > maldi_quant_preprocessing
diff maldi_quant_preprocessing.xml @ 4:82b1de5c142b draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
| author | galaxyp |
|---|---|
| date | Sat, 04 Mar 2023 19:13:31 +0000 |
| parents | aa81463e21ea |
| children |
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--- a/maldi_quant_preprocessing.xml Fri Feb 15 10:13:30 2019 -0500 +++ b/maldi_quant_preprocessing.xml Sat Mar 04 19:13:31 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.3"> +<tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.0"> <description> Preprocessing of mass-spectrometry imaging data </description> @@ -19,8 +19,6 @@ du infile.hdr && du infile.img && du -s -B1 infile.hdr && - #else - ln -s $infile infile.RData && #end if Rscript "${maldi_quant_preprocessing}" && @@ -59,22 +57,6 @@ ## Import analyze7.5 file maldi_data = importAnalyze( 'infile.hdr' ) coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data))) - #else - loadRData <- function(fileName){ - ##loads an RData file, and returns it - load(fileName) - get(ls()[ls() != "fileName"]) - } - msidata = loadRData('infile.RData') - ## save coordinates - cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2]) - ## save mz values - cardinal_mzs = Cardinal::mz(msidata) - ## create MALDIquant MassSpectrum object, order of pixels in iData is same as in coord(msidata): - maldi_data = list() - for(number_spectra in 1:ncol(msidata)){ - maldi_data[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra]) - } #end if #end if @@ -344,10 +326,6 @@ if (length(findEmptyMassObjects(maldi_data))>0) { - #if $infile.ext == 'rdata' - cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input - #end if - maldi_data = removeEmptyMassObjects(maldi_data) } #end if @@ -386,11 +364,7 @@ ## export imzML file if (length(maldi_data)>0){ - #if $infile.ext == 'rdata' - MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates) - #else MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed) - #end if }else{"All spectra are empty, outputfiles will be empty,too."} @@ -398,7 +372,7 @@ </configfile> </configfiles> <inputs> - <param name="infile" type="data" format="imzml,rdata,analyze75" label="MSI data" help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload). The file must be in profile mode, not centroided."/> + <param name="infile" type="data" format="imzml,analyze75" label="MSI data" help="Input file as imzML (composite upload). The file must be in profile mode, not centroided."/> <conditional name="restriction_conditional"> <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files"> <option value="no_restriction" selected="True">No, calculate on entire file</option> @@ -529,7 +503,7 @@ <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/> <param name="allow_nomatch" type="boolean" label="Allow no matches" help="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/> <param name="empty_nomatch" type="boolean" label="Empty no matches" help="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/> - <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/> + <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE"/> <conditional name="reference_for_alignment"> <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration"> @@ -579,33 +553,12 @@ <param name="baseline_method" value ="TopHat"/> </conditional> <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4"> - <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="6"/> + <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="8"/> <extra_files type="file" file="outfile1.ibd" name="ibd" compare="sim_size"/> </output> <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/> </test> <test> - <param name="infile" value="msidata_1.RData" ftype="rdata"/> - <conditional name="methods_conditional"> - <param name="method" value="Align"/> - <param name="warping_method" value="lowess"/> - <param name="halfWindowSize" value="5"/> - <param name="tolerance" value="0.001"/> - <param name="allow_nomatch" value="TRUE"/> - <param name="remove_empty" value="TRUE"/> - <param name="empty_nomatch" value="TRUE"/> - <conditional name="reference_for_alignment"> - <param name="align_ref" value="yes_reference"/> - <param name="reference_file" value="inputpeptides.tabular" ftype="tabular"/> - </conditional> - </conditional> - <output name="outfile_imzml" ftype="imzml" file="preprocessing2.imzml.txt" lines_diff="4"> - <extra_files type="file" file="outfile2.imzml" name="imzml" lines_diff="6"/> - <extra_files type="file" file="outfile2.ibd" name="ibd" compare="sim_size"/> - </output> - <output name="plots" file="Preprocessing2_QC.pdf" compare="sim_size"/> - </test> - <test> <param name="infile" value="" ftype="imzml"> <composite_data value="Example_Continuous.imzML"/> <composite_data value="Example_Continuous.ibd"/> @@ -615,7 +568,7 @@ <param name="calibrate_method" value="median"/> </conditional> <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4"> - <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="6"/> + <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="8"/> <extra_files type="file" file="outfile3.ibd" name="ibd" compare="sim_size"/> </output> <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/> @@ -631,8 +584,7 @@ - MSI data: 2 types of input data can be used: - - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ - - Cardinal "MSImageSet" data saved as .RData + - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_ - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported.