comparison msi_ion_images.xml @ 6:5a5b5a8fa8a0 draft

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

5:2b9fa240e261

<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.1">
    <description>
        mass spectrometry imaging m/z heatmaps
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

library(lattice)

## Read MALDI Imaging dataset

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

title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename"))

############################# I) numbers ####################################

properties = c("Number of m/z features",
               "Range of m/z values [Da]",
               "Number of pixels", 
               "Range of x coordinates", 
               "Range of y coordinates",
               "Range of intensities", 
               "Median of intensities",

#if str($image_cond.image_type) == "standard_image":
    print("standard image")

    print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", 
    smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,
    main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}


###lattice image

    #if str($strip) =="TRUE": 

    print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),
    lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", 
    colorkey=$colorkey,
    main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}

    #elif str($strip) =="FALSE": 

    print(image(msidata, mz=inputmz[mass], strip = $strip,

    ]]></configfile>
    </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="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/>
        <param name="massfile" type="data" format="tabular" label="Tabular file with m/z and names"
            help="first column m/z, second column m/z name, tab separated file"/>
        <param name="image_contrast" type="select" label="Select a contrast enhancement function for the heatmap images" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
            <option value="none" selected="True">none</option>

6:5a5b5a8fa8a0

<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.2">
    <description>
        mass spectrometry imaging m/z heatmaps
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

library(lattice)

## Read MALDI Imaging dataset

#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

title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename"))

############################# I) numbers ####################################

properties = c("Number of m/z features",
               "Range of m/z values",
               "Number of pixels", 
               "Range of x coordinates", 
               "Range of y coordinates",
               "Range of intensities", 
               "Median of intensities",

#if str($image_cond.image_type) == "standard_image":
    print("standard image")

    print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", 
    smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),
    main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}


###lattice image

    #if str($strip) =="TRUE": 

    print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),
    lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", 
    colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),
    main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}

    #elif str($strip) =="FALSE": 

    print(image(msidata, mz=inputmz[mass], strip = $strip,

    ]]></configfile>
    </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>
        <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/>
        <param name="massfile" type="data" format="tabular" label="Tabular file with m/z and names"
            help="first column m/z, second column m/z name, tab separated file"/>
        <param name="image_contrast" type="select" label="Select a contrast enhancement function for the heatmap images" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
            <option value="none" selected="True">none</option>