comparison msi_ion_images.xml @ 8:dd44a98ce32c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 620a469e20836b921b6c0147421c8a4268b66ebd

7:188de53d93f7

<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.3">
    <description>
        mass spectrometry imaging m/z heatmaps
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

### only plot images when file has peaks and valid input m/z: 

if (npeaks > 0){
    if (length(inputmz) != 0){
      for (mass in 1:length(inputmz)){

###standard image

#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

#elif str($image_cond.image_type) == "lattice_image":
    print("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,
    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)")))}

    #end if

#end if 

    } else {print("The input m/z were invalid")}
    dev.off()
}else{
    print("inputfile has no intensities > 0")
dev.off()
}
    ]]></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)"/>

                <option value="lattice_image">lattice</option>
            </param>
        <when value="standard_image"/>
        <when value="lattice_image"/>
        </conditional>
    </inputs>
    <outputs>
        <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label = "$infile.display_name heatmaps"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="" ftype="imzml">
                <composite_data value="Example_Continuous.imzML"/>

            <param name="plusminus_dalton" value="0.5"/>
            <param name="filename" value="Testfile_analyze75"/>
            <param name="image_smoothing" value="gaussian"/>
            <param name="strip" value="False"/>
            <param name="colorkey" value="True"/>
            <output name="plots" file="Heatmaps_analyze75.pdf" compare="sim_size" delta="20000"/>
        </test>
        <test>
            <param name="infile" value="preprocessed.rdata" ftype="rdata"/>
            <param name="massfile" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="plusminus_dalton" value="0.5"/>

- no empty fields or letters are allowed in the first column

Output:

- Pdf with the heatmap images

Troubleshooting:

- no heatmaps are plotted when tabular file doesn't fulfill the criteria described above
- no heatmaps are plotted when the input mass spectrometry imaging file has no intensities > 0

8:dd44a98ce32c

<tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.4">
    <description>
        mass spectrometry imaging m/z heatmaps
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

### only plot images when file has peaks and valid input m/z: 

if (npeaks > 0){
    if (length(inputmz) != 0){
        for (mass in 1:length(inputmz)){

            ###standard image

            #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

            #elif str($image_cond.image_type) == "lattice_image":
                print("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,
                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)")))}

                #end if

            #end if 

        ## optional svg output with original coordinates
        #if str($svg_cond.svg_pixelimage) == "yes_svg":
            print("svg pixel image")

            svg(file="svg_pixel_output.svg")
            par(mar=c(0,0,0,0))
            image(msidata, mz = inputmz[1],strip=FALSE, ylim=c(maximumy, minimumy), plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing")
            dev.off()
        #end if

    } else {print("The input m/z were invalid")}
    dev.off()
}else{
    print("inputfile has no intensities > 0")
dev.off()
}


    ]]></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)"/>

                <option value="lattice_image">lattice</option>
            </param>
        <when value="standard_image"/>
        <when value="lattice_image"/>
        </conditional>
        <conditional name="svg_cond">
            <param name="svg_pixelimage" type="select" label="Do you want to export a heatmap with the original coordinates as svg image, the first valid m/z from tabular file is used">
                <option value="no_svg" selected="True">No svg image export</option>
                <option value="yes_svg">Export svg image</option>
            </param>
        <when value="no_svg"/>
        <when value="yes_svg"/>
        </conditional>
    </inputs>
    <outputs>
        <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label = "$infile.display_name heatmaps"/>
        <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="$infile.display_name svg">
            <filter>svg_cond['svg_pixelimage'] == 'yes_svg'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="" ftype="imzml">
                <composite_data value="Example_Continuous.imzML"/>

            <param name="plusminus_dalton" value="0.5"/>
            <param name="filename" value="Testfile_analyze75"/>
            <param name="image_smoothing" value="gaussian"/>
            <param name="strip" value="False"/>
            <param name="colorkey" value="True"/>
            <conditional name="svg_cond">
                <param name="svg_pixelimage" value="yes_svg"/>
            </conditional>
            <output name="plots" file="Heatmaps_analyze75.pdf" compare="sim_size" delta="20000"/>
            <output name="svg_output" file="analyze75.svg" compare="sim_size" delta="20000"/>
        </test>
        <test>
            <param name="infile" value="preprocessed.rdata" ftype="rdata"/>
            <param name="massfile" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="plusminus_dalton" value="0.5"/>

- no empty fields or letters are allowed in the first column

Output:

- Pdf with the heatmap images
- optional svg file of a mass-spectrometry imaging m/z heatmap

Troubleshooting:

- no heatmaps are plotted when tabular file doesn't fulfill the criteria described above
- no heatmaps are plotted when the input mass spectrometry imaging file has no intensities > 0