comparison mz_images.xml @ 9:08ebd8da780c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

8:a69865da6f80

if (ncol(msidata)>0 & nrow(msidata) >0){
    if (length(inputmz) != 0){
        for (mass in 1:length(inputmz)){

                print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", 
                smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))}


        ## optional svg output with original coordinates
        #if $svg_pixelimage:
            print("svg pixel image")

                  key=FALSE, 
                  ylim= c(maximumy,minimumy)))

             legend("$overlay_cond.legend_position",
                       fill=colourvector,
                      legend=as.numeric(sort(as.character(inputmz))))
        #end if

    } else {print("The input m/z were invalid")}
    dev.off()
}else{

            <option value="viridis" selected="True">viridis</option>
            <option value="magma">magma</option>
            <option value="plasma">plasma</option>
            <option value="inferno">inferno</option>
        </param>
        <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
        <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
        <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
        <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
        <conditional name="overlay_cond">
            <param name="overlay_selection" type="select" label="Overlay image">

            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <param name="plusminus_dalton" value="0.25"/>
            <param name="filename" value="Testfile_imzml"/>
            <param name="image_contrast" value="histogram"/>
            <param name="strip" value="True"/>
            <param name="colorkey" value="True"/>
            <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>
            <expand macro="infile_analyze75"/>

            <param name="name_column" value="1"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="filename" value="Testfile_analyze75"/>
            <param name="colorscale" value="magma"/>
            <param name="image_smoothing" value="gaussian"/>
            <param name="strip" value="False"/>
            <param name="colorkey" value="True"/>
            <param name="svg_pixelimage" value="True"/>
            <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
            <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
        </test>

            <param name="infile" value="preprocessed.RData" ftype="rdata"/>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="strip" value="True"/>
            <param name="colorkey" value="True"/>
            <param name="filename" value="Testfile_rdata"/>
            <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>

            <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="1"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="colorscale" value="plasma"/>
            <param name="strip" value="True"/>
            <param name="colorkey" value="False"/>
            <param name="filename" value="Testfile_rdata"/>
            <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>
            <expand macro="processed_infile_imzml"/>
            <conditional name="processed_cond">
                <param name="processed_file" value="processed"/>
                <param name="accuracy" value="100"/>
                <param name="units" value="ppm"/>
            </conditional>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>

9:08ebd8da780c

if (ncol(msidata)>0 & nrow(msidata) >0){
    if (length(inputmz) != 0){
        for (mass in 1:length(inputmz)){

                print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", 
                smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))
                title(inputnames[mass], adj = 0.5, line = 1)}


        ## optional svg output with original coordinates
        #if $svg_pixelimage:
            print("svg pixel image")

                  key=FALSE, 
                  ylim= c(maximumy,minimumy)))

             legend("$overlay_cond.legend_position",
                       fill=colourvector,
                      legend=as.numeric(inputmz))
        #end if

    } else {print("The input m/z were invalid")}
    dev.off()
}else{

            <option value="viridis" selected="True">viridis</option>
            <option value="magma">magma</option>
            <option value="plasma">plasma</option>
            <option value="inferno">inferno</option>
        </param>
        <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
        <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
        <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
        <conditional name="overlay_cond">
            <param name="overlay_selection" type="select" label="Overlay image">

            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <param name="plusminus_dalton" value="0.25"/>
            <param name="filename" value="Testfile_imzml"/>
            <param name="image_contrast" value="histogram"/>
            <param name="colorkey" value="True"/>
            <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>
            <expand macro="infile_analyze75"/>

            <param name="name_column" value="1"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="filename" value="Testfile_analyze75"/>
            <param name="colorscale" value="magma"/>
            <param name="image_smoothing" value="gaussian"/>
            <param name="colorkey" value="True"/>
            <param name="svg_pixelimage" value="True"/>
            <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
            <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
        </test>

            <param name="infile" value="preprocessed.RData" ftype="rdata"/>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="colorkey" value="True"/>
            <param name="filename" value="Testfile_rdata"/>
            <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>

            <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="1"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="colorscale" value="plasma"/>
            <param name="colorkey" value="False"/>
            <param name="filename" value="Testfile_rdata"/>
            <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>
            <expand macro="processed_infile_imzml"/>
            <conditional name="processed_cond">
                <param name="processed_file" value="processed"/>
                <param name="accuracy" value="200"/>
                <param name="units" value="ppm"/>
            </conditional>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>