Mercurial > repos > galaxyp > msi_filtering
changeset 4:bf61fc662615 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
| author | galaxyp |
|---|---|
| date | Tue, 19 Jun 2018 18:07:17 -0400 |
| parents | d51c3c814d57 |
| children | 3d5ac78fb2b0 |
| files | msi_filtering.xml test-data/analyze75_filtered2.pdf test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_filteredoutside.RData test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/imzml_filtered2.RData test-data/imzml_filtered2.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf |
| diffstat | 15 files changed, 16 insertions(+), 8 deletions(-) [+] |
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--- a/msi_filtering.xml Mon Jun 11 17:33:40 2018 -0400 +++ b/msi_filtering.xml Tue Jun 19 18:07:17 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.1"> +<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.2"> <description>tool for filtering mass spectrometry imaging data</description> <requirements> <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> @@ -34,7 +34,7 @@ library(gridExtra) #if $infile.ext == 'imzml' - msidata = readImzML('infile') + msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") #elif $infile.ext == 'analyze75' msidata = readAnalyze('infile') #else @@ -284,7 +284,7 @@ medint2 = round(median(TICs2), digits=2) properties = c("Number of m/z features", - "Range of m/z values [Da]", + "Range of m/z values", "Number of pixels", "Range of x coordinates", "Range of y coordinates", @@ -330,10 +330,13 @@ image(msidata, mz=$outputs.inputmz, plusminus = $outputs.plusminus_dalton, contrast.enhance = "none", main= paste0($outputs.inputmz," ± ", $outputs.plusminus_dalton, " Da"), ylim = c(maximumy2+0.2*maximumy2,minimumy2-0.2*minimumy2)) - ### control features which are left - plot(featuresinfile, rep(1,length(featuresinfile)), yaxt="n", ylab=NA, xlab="m/z values", col="red", ylim=c(0.8, 1.1), main="Distribution of m/z values") - lines(mz(msidata),rep(0.9, length(mz(msidata))), col="green", type="p") - legend("top", horiz=TRUE, legend = c("before", "filtered"), fill = c("red", "green")) + ### control features which are removed + hist(mz(msidata), xlab="m/z", main="Kept m/z values") + #if str($features_cond.features_filtering) == "none": + print("no difference histogram as no m/z filtering took place") + #else: + hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values") + #end if }else{ print("file has no features or pixels left")} @@ -362,6 +365,11 @@ <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> + <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> + <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> + <option value="mz" >mz</option> + <option value="ppm" selected="True" >ppm</option> + </param> <conditional name="pixels_cond"> <param name="pixel_filtering" type="select" label="Select pixel filtering option"> <option value="none" selected="True">none</option> @@ -603,7 +611,7 @@ Output: - imzML file filtered for pixels and/or m/z -- optional: pdf with heatmap showing the pixels that are left after filtering and plot of m/z before and after filtering +- optional: pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)