comparison msi_filtering.xml @ 4:bf61fc662615 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5

3:d51c3c814d57

<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.1">
    <description>tool for filtering mass spectrometry imaging data</description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
        <requirement type="package" version="2.2.1">r-gridextra</requirement>
    </requirements>

library(Cardinal)
library(gridExtra)

#if $infile.ext == 'imzml'
    msidata = readImzML('infile')
#elif $infile.ext == 'analyze75'
    msidata = readAnalyze('infile')
#else
    load('infile.RData')
#end if

    NumemptyTIC2 = sum(TICs2 == 0)
    ## median TIC
    medint2 = round(median(TICs2), digits=2)

    properties = c("Number of m/z features",
                   "Range of m/z values [Da]",
                   "Number of pixels", 
                   "Range of x coordinates", 
                   "Range of y coordinates",
                   "Intensities > 0",
                   "Median TIC per pixel",

    ### heatmap image as visual pixel control
    if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
        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"))
    }else{
        print("file has no features or pixels left")}

    dev.off()

    </configfiles>
    <inputs>
        <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)"/>
        <conditional name="pixels_cond">
            <param name="pixel_filtering" type="select" label="Select pixel filtering option">
                <option value="none" selected="True">none</option>
                <option value="single_column">tabular file with single column (x = 1, y = 1)</option>
                <option value="two_columns">tabular file with separate columns for x and y values</option>

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: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)


Tip: 

4:bf61fc662615

<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>
        <requirement type="package" version="2.2.1">r-gridextra</requirement>
    </requirements>

library(Cardinal)
library(gridExtra)

#if $infile.ext == 'imzml'
    msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units")
#elif $infile.ext == 'analyze75'
    msidata = readAnalyze('infile')
#else
    load('infile.RData')
#end if

    NumemptyTIC2 = sum(TICs2 == 0)
    ## median TIC
    medint2 = round(median(TICs2), digits=2)

    properties = c("Number of m/z features",
                   "Range of m/z values",
                   "Number of pixels", 
                   "Range of x coordinates", 
                   "Range of y coordinates",
                   "Intensities > 0",
                   "Median TIC per pixel",

    ### heatmap image as visual pixel control
    if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
        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 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")}

    dev.off()

    </configfiles>
    <inputs>
        <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>
                <option value="single_column">tabular file with single column (x = 1, y = 1)</option>
                <option value="two_columns">tabular file with separate columns for x and y values</option>

Output: 

- imzML file filtered for pixels and/or m/z
- 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)


Tip: