Mercurial > repos > galaxyp > msi_preprocessing
diff msi_preprocessing.xml @ 1:c4abf42419c2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
| author | galaxyp |
|---|---|
| date | Fri, 24 Nov 2017 18:08:19 -0500 |
| parents | 74fcb3c95a53 |
| children | 50ba097d03e0 |
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--- a/msi_preprocessing.xml Tue Oct 31 15:05:05 2017 -0400 +++ b/msi_preprocessing.xml Fri Nov 24 18:08:19 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.7.0"> +<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.7.0.1"> <description> mass spectrometry imaging preprocessing </description> @@ -35,6 +35,7 @@ load('infile.RData') #end if + maxpixel = length(pixels(msidata)) pixelnumber = c(1:maxpixel) @@ -64,6 +65,7 @@ msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter) #end if + #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking': print('Peak_picking') ## Peakpicking @@ -81,6 +83,8 @@ msidata = peakPick(msidata, pixel=pixelnumber, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method) #end if + + #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment': print('Peak_alignment') ## Peakalignment @@ -100,22 +104,31 @@ #end if #end for + ## save as as (.RData) save(msidata, file="$msidata_preprocessed") -## save as intensity matrix (.csv) -csvmatrix = spectra(msidata) -rownames(csvmatrix) = mz(msidata) -newmatrix = rbind(pixels(msidata), csvmatrix) -write.csv(newmatrix[2:nrow(newmatrix),], file="$preprocessed_intensity_matrix") +if (length(features(msidata))> 0) +{ + +## save as intensity matrix +spectramatrix = spectra(msidata) +rownames(spectramatrix) = mz(msidata) +newmatrix = rbind(pixels(msidata), spectramatrix) +write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") + +}else{ + print("file has no features left") +write.table(matrix(rownames(coord(msidata)), ncol=ncol(msidata), nrow=1), file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t") +} + ]]></configfile> </configfiles> <inputs> <param name="infile" type="data" format="imzml,rdata,analyze75" - label="MSI rawdata as imzml or Cardinal MSImageSet saved as RData" - help="load imzml and ibd file by uploading composite datatype imzml"/> - + label="MSI rawdata as imzml or Cardinal MSImageSet saved as RData" + help="load imzml and ibd file by uploading composite datatype imzml"/> <repeat name="methods" title="Preprocessing" min="1" max="50"> <conditional name="methods_conditional"> <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply"> @@ -210,14 +223,14 @@ </repeat> </inputs> <outputs> - <data format="rdata" name="msidata_preprocessed" label="Preprocessed_output"/> - <data format="csv" name="preprocessed_intensity_matrix" label="preprocessed intensity matrix" /> + <data format="rdata" name="msidata_preprocessed" label="${tool.name} on $infile.display_name"/> + <data format="tabular" name="matrixasoutput" label="${tool.name} on $infile.display_name" /> </outputs> <tests> <test> <param name="infile" value="" ftype="imzml"> - <composite_data value="Example_Continuous.imzML" ftype="imzml"/> - <composite_data value="Example_Continuous.ibd" ftype="ibd"/> + <composite_data value="Example_Continuous.imzML"/> + <composite_data value="Example_Continuous.ibd"/> </param> <repeat name="methods"> <conditional name="methods_conditional"> @@ -226,9 +239,15 @@ </repeat> <repeat name="methods"> <conditional name="methods_conditional"> + <param name="preprocessing_method" value="Baseline_reduction" /> + <param name="blocks_baseline" value="100" /> + </conditional> + </repeat> + <repeat name="methods"> + <conditional name="methods_conditional"> <param name="preprocessing_method" value="Smoothing" /> <conditional name="methods_for_smoothing"> - <param name="smoothing_method" value="sgolay" /> + <param name="smoothing_method" value="gaussian" /> </conditional> </conditional> </repeat> @@ -246,26 +265,26 @@ <conditional name="methods_conditional"> <param name="preprocessing_method" value="Peak_alignment" /> <conditional name="methods_for_alignment"> - <param name="alignment_method" value="DP" /> + <param name="alignment_method" value="diff" /> </conditional> </conditional> </repeat> - <repeat name="methods"> + <!--repeat name="methods"> <conditional name="methods_conditional"> <param name="preprocessing_method" value="Peak_filtering" /> </conditional> - </repeat> + </repeat--> <output name="msidata_preprocessed" file="preprocessing_results1.RData" compare="sim_size" /> - <output name="preprocessed_intensity_matrix" file="preprocessing_results1.csv" /> + <output name="matrixasoutput" file="preprocessing_results1.txt" /> </test> <test> - <param name="infile" value="LM5_first68pixel.RData" ftype="rdata"/> - <repeat name="methods"> + <param name="infile" value="example_continous.RData" ftype="rdata"/> + <!--repeat name="methods"> <conditional name="methods_conditional"> <param name="preprocessing_method" value="Baseline_reduction" /> - <param name="blocks_baseline" value="50" /> + <param name="blocks_baseline" value="3" /> </conditional> - </repeat> + </repeat--> <repeat name="methods"> <conditional name="methods_conditional"> <param name="preprocessing_method" value="Peak_picking" /> @@ -281,27 +300,25 @@ </conditional> </repeat> <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size" /> - <output name="preprocessed_intensity_matrix" file="preprocessing_results2.csv" lines_diff="2"/> + <output name="matrixasoutput" file="preprocessing_results2.txt" lines_diff="2" /> </test> <test> <param name="infile" value="" ftype="analyze75"> - <composite_data value="Analyze75.hdr" ftype="hdr"/> - <composite_data value="Analyze75.img" ftype="img"/> - <composite_data value="Analyze75.t2m" ftype="t2m"/> + <composite_data value="Analyze75.hdr"/> + <composite_data value="Analyze75.img"/> + <composite_data value="Analyze75.t2m"/> </param> <repeat name="methods"> <conditional name="methods_conditional"> <param name="preprocessing_method" value="Normalization" /> </conditional> </repeat> - <repeat name="methods"> + <!--repeat name="methods"> <conditional name="methods_conditional"> - <param name="preprocessing_method" value="Smoothing" /> - <conditional name="methods_for_smoothing"> - <param name="smoothing_method" value="gaussian" /> - </conditional> + <param name="preprocessing_method" value="Baseline_reduction" /> + <param name="blocks_baseline" value="50" /> </conditional> - </repeat> + </repeat--> <repeat name="methods"> <conditional name="methods_conditional"> <param name="preprocessing_method" value="Peak_picking" /> @@ -317,11 +334,12 @@ </conditional> </repeat> <output name="msidata_preprocessed" file="preprocessing_results3.RData" compare="sim_size" /> - <output name="preprocessed_intensity_matrix" file="preprocessing_results3.csv" /> + <output name="matrixasoutput" file="preprocessing_results3.txt" /> </test> + </tests> <help> - <![CDATA[ + <![CDATA[ Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. **Preprocessing steps:**