Mercurial > repos > galaxyp > cardinal_preprocessing
diff preprocessing.xml @ 9:ca727a6dede6 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
| author | galaxyp |
|---|---|
| date | Thu, 24 Sep 2020 11:43:31 +0000 |
| parents | 87bb011a4ee8 |
| children | 5abc3ab4792c |
line wrap: on
line diff
--- a/preprocessing.xml Wed May 13 14:21:48 2020 -0400 +++ b/preprocessing.xml Thu Sep 24 11:43:31 2020 +0000 @@ -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="3.2.1">r-ggplot2</requirement> + <requirement type="package" version="3.3.2">r-ggplot2</requirement> </expand> <command detect_errors="exit_code"> <![CDATA[ @@ -347,35 +347,37 @@ title("Spectra after peak binning", outer=TRUE, line=0) - ############################### Data reduction ########################### + ############################### Mass binning ########################### - #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction': - print('Data_reduction') + #elif str( $method.methods_conditional.preprocessing_method) == 'Mass_binning': + print('mass binning') - ## these functions only work on MSImageSet - msidata = as(msidata, "MSImageSet") + #if str( $method.methods_conditional.mz_range.features_filtering) == 'change_mz_range': + + #if str($processed_cond.processed_file) == "processed": - #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'bin': - print('bin reduction') + msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) + + #else + msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) + #end if + + + #elif str( $method.methods_conditional.mz_range.features_filtering) == 'none': - msidata = reduceDimension(msidata, method="bin", width=$method.methods_conditional.methods_for_reduction.bin_width, units="$method.methods_conditional.methods_for_reduction.bin_units", fun=$method.methods_conditional.methods_for_reduction.bin_fun) + msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) + #end if + + msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu)) + ## optional: replace NA with 0 - #if $method.methods_conditional.methods_for_reduction.replace_NA_bin: + #if $method.methods_conditional.replace_NA_bin: ## count and replace NAs print(paste0("Number of NA that were set to zero after binning:",sum(is.na(spectra(msidata))))) spectra(msidata)[is.na(spectra(msidata))] = 0 #end if - - #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample': - print('resample reduction') - - msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step) - #end if - - ## coercition into new format - msidata = as(msidata, "MSImagingExperiment") - + ############################### QC ########################### maxfeatures =nrow(msidata) @@ -386,7 +388,7 @@ QC_numbers= cbind(QC_numbers, reduced) vectorofactions = append(vectorofactions, "reduced") print(plot(msidata, pixel=random_spectra)) - title("Spectra after data reduction", outer=TRUE, line=0) + title("Spectra after m/z binning", outer=TRUE, line=0) ############################### Transformation ########################### @@ -479,7 +481,7 @@ <option value="Peak_alignment">Peak alignment</option> <option value="Peak_filtering">Peak filtering</option> <option value="Peak_binning">Peak binning to reference peaks</option> - <option value="Data_reduction">Data reduction</option> + <option value="Mass_binning">m/z binning</option> <option value="Transformation">Transformation</option> </param> <when value="Normalization"> @@ -620,31 +622,29 @@ <option value="area">area</option> </param> </when> - <when value="Data_reduction"> - <conditional name="methods_for_reduction"> - <param name="reduction_method" type="select" label="Reduction method"> - <option value="bin" selected="True">bin</option> - <option value="resample">resample</option> + <when value="Mass_binning"> + <param name="bin_width" type="float" value="1" label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/> + <param name="bin_units" type="select" display="radio" + label="Unit for bin"> + <option value="mz" selected="True">mz</option> + <option value="ppm">ppm</option> + </param> + <param name="bin_fun" type="select" display="radio" + label="Calculate sum or mean intensity for ions of the same bin"> + <option value="mean" selected="True">mean</option> + <option value="sum">sum</option> + </param> + <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/> + <conditional name="mz_range"> + <param name="features_filtering" type="select" label="Select m/z feature filtering option"> + <option value="none" selected="True">none</option> + <option value="change_mz_range">change m/z range</option> </param> - <when value="bin"> - <param name="bin_width" type="float" value="1" - label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/> - <param name="bin_units" type="select" display="radio" - label="Unit for bin"> - <option value="mz" selected="True">mz</option> - <option value="ppm">ppm</option> - </param> - <param name="bin_fun" type="select" display="radio" - label="Calculate sum or mean intensity for ions of the same bin"> - <option value="mean" selected="True">mean</option> - <option value="sum">sum</option> - </param> - <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/> - </when> - <when value="resample"> - <param name="resample_step" type="float" value="1" - label="The step size in m/z" help="Step size must be greater than range of m/z values divided by number of m/z features"/> - </when> + <when value="none"/> + <when value="change_mz_range"> + <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/> + <param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/> + </when> </conditional> </when> <when value="Transformation"> @@ -800,11 +800,9 @@ </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"/> + <param name="preprocessing_method" value="Mass_binning"/> <param name="bin_width" value="0.1"/> - </conditional> + <param name="bin_units" value="mz"/> </conditional> </repeat> <output name="QC_overview" file="preprocessing_results4.pdf" compare="sim_size"/> @@ -817,7 +815,7 @@ <expand macro="processed_infile_imzml"/> <conditional name="processed_cond"> <param name="processed_file" value="processed"/> - <param name="accuracy" value="100"/> + <param name="accuracy" value="200"/> <param name="units" value="ppm"/> </conditional> <repeat name="methods">