comparison msi_filtering.xml @ 8:262db9893c6f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6

7:73b5a754f35c

<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.5">
    <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>
        <requirement type="package" version="2.2.1">r-ggplot2</requirement>

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


########################### QC numbers ########################

## QC report with more than value-table: only when pixels/features/intensities are left
if (npeaks2 > 0)
{
        ### visual pixel control

            pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
                   geom_tile(height = 1, width=1)+
                   coord_fixed()+
                   ggtitle("Spatial orientation of filtered pixels")+
                   theme_bw()+
                   theme(plot.title = element_text(hjust = 0.5))+
                   theme(text=element_text(family="ArialMT", face="bold", size=12))+
                   theme(legend.position="bottom",legend.direction="vertical")+
                   guides(fill=guide_legend(ncol=4,byrow=TRUE))

            print(pixel_image)

            ### control features which are removed
            hist(mz(msidata), xlab="m/z", main="Kept m/z values")

8:262db9893c6f

<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.6">
    <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>
        <requirement type="package" version="2.2.1">r-ggplot2</requirement>

        msidata <- readImzML('infile')
    #end if
#elif $infile.ext == 'analyze75'
    msidata = readAnalyze('infile')
#else
    loadRData <- function(fileName){
    load(fileName)
    get(ls()[ls() != "fileName"])
    }
    msidata = loadRData('infile.RData')

#end if


########################### QC numbers ########################

## QC report with more than value-table: only when pixels/features/intensities are left
if (npeaks2 > 0)
{
        ### visual pixel control

            levels(position_df\$annotation) = factor(paste(1:length(levels(position_df\$annotation)), levels(position_df\$annotation), sep="_"))

            pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
                   geom_tile(height = 1, width=1)+
                   coord_fixed()+
                   ggtitle("Spatial orientation of filtered pixels")+
                   theme_bw()+
                   theme(plot.title = element_text(hjust = 0.5))+
                   theme(text=element_text(family="ArialMT", face="bold", size=12))+
                   theme(legend.position="bottom",legend.direction="vertical")+
                   theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
                   guides(fill=guide_legend(ncol=4,byrow=TRUE))

    coord_labels = aggregate(cbind(x,y)~annotation, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
    coord_labels\$file_number = 1:length(levels(position_df\$annotation))

    for(file_count in 1:nrow(coord_labels))
    {pixel_image = pixel_image + annotate("text",x=coord_labels[file_count,"x"],
    y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}

            print(pixel_image)

            ### control features which are removed
            hist(mz(msidata), xlab="m/z", main="Kept m/z values")