comparison filtering.xml @ 9:c3d2ca5f9dd0 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"

8:f3a77d4c4991

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.3">r-gridextra</requirement>
        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
    </expand>
    <expand macro="print_version"/>
    <command detect_errors="exit_code">
    <![CDATA[

           ggtitle("Spatial orientation of filtered pixels")+
           theme_bw()+
           theme(plot.title = element_text(hjust = 0.5))+
           theme(legend.position="bottom",legend.direction="vertical")+
           guides(fill=guide_legend(ncol=5,byrow=TRUE))
    print(pixel_image)


    ### visual mz feature control

    kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata)))

        geom_histogram()+ theme_bw()+
        theme(plot.title = element_text(hjust = 0.5))+
        theme(legend.position="bottom",legend.direction="vertical")+
        labs(title="Overview of filtered m/z", x="m/z", y = "count") +
        guides(fill=guide_legend(ncol=5,byrow=TRUE))
      print(histogram_mz)


        dev.off()

    ## save msidata as imzML file, will only work if there is at least 1 m/z left

        if (maxfeatures2 > 0){
            ## make sure that coordinates are integers
            coord(msidata)\$y = as.integer(coord(msidata)\$y)
            coord(msidata)\$x = as.integer(coord(msidata)\$x)
        writeImzML(msidata, "out")}


}else{
    print("Inputfile or filtered file has no intensities > 0")

        </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="pixel_filtering" value="two_columns"/>
            <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
            <param name="column_x" value="1"/>

9:c3d2ca5f9dd0

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.3">r-gridextra</requirement>
        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
    </expand>
    <expand macro="print_version"/>
    <command detect_errors="exit_code">
    <![CDATA[

           ggtitle("Spatial orientation of filtered pixels")+
           theme_bw()+
           theme(plot.title = element_text(hjust = 0.5))+
           theme(legend.position="bottom",legend.direction="vertical")+
           guides(fill=guide_legend(ncol=5,byrow=TRUE))
    print(pixel_image + scale_fill_manual(values=c("#00BFC4", "#F8766D")))


    ### visual mz feature control

    kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata)))

        geom_histogram()+ theme_bw()+
        theme(plot.title = element_text(hjust = 0.5))+
        theme(legend.position="bottom",legend.direction="vertical")+
        labs(title="Overview of filtered m/z", x="m/z", y = "count") +
        guides(fill=guide_legend(ncol=5,byrow=TRUE))
      print(histogram_mz + scale_fill_manual(values=c("#00BFC4", "#F8766D")))

    dev.off()

    ## save msidata as imzML file, will only work if there is at least 1 m/z left

        if (maxfeatures2 > 0){
            ## make sure that coordinates are integers
            coord(msidata)\$y = as.integer(coord(msidata)\$y)
            coord(msidata)\$x = as.integer(coord(msidata)\$x)
            msidata = as(msidata, "MSContinuousImagingExperiment")
        writeImzML(msidata, "out")}


}else{
    print("Inputfile or filtered file has no intensities > 0")

        </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="pixel_filtering" value="two_columns"/>
            <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
            <param name="column_x" value="1"/>