comparison spectra_plots.xml @ 9:006fc980af63 draft

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

8:33dcc1606d53

<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0">
    <description>
        mass spectrometry imaging mass spectra plots
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
        <requirement type="package" version="2.3">r-gridextra</requirement>
        <requirement type="package" version="1.0.0">r-scales</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[
        @INPUT_LINKING@
        cat '${MSI_mzplots}' &&

                msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
                colnames(msidata_coordinates) = c("x", "y", "pixel_index")
                merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)
                merged_annotation[is.na(merged_annotation)] = "NA"
                merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
                msidata\$annotation = as.factor(merged_annotation[,4])

                    ## overview plot over annotated samples
                    number_combined = length(levels(msidata\$annotation))

                    ## the more annotation groups a file has the smaller will be the legend

            ##################### I) Sample: plot full mass spectrum ##############

                    #if $fullmz:
                    ## plot full mz for single tabular mz
                        print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable))
                    #end if

                    pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord)

                    input_pixels = paste(x_coord, y_coord, sep="_")

                            maxmasspixel = maxmasspixel+1
                        }
                }

                    ## print single tabular mz; manual zoom
                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))

                #end for

                #elif str($mz_range.mz_range_options) == "tabular_mz":

                                        maxmasspixel = maxmasspixel+1
                                    }
                            }

                                ## print single tabular mz; tabular zoom
                                print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax)))
                            }
                        }

                #end if

        ##################### I) Sample: plot full mass spectrum ##############

                    #if $fullmz:

                        print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable))
                    #end if

        ##################### II) Sample: plot zoom-in mass spectrum ##########

        #if str($mz_range.mz_range_options) == "manual_mz":

                        }else{
                            maxmasspixel = maxmasspixel+1
                        }
                }

                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))

            #end for

        #elif str($mz_range.mz_range_options) == "tabular_mz":

                                    ## if xlimax is outside mz range, use max mz value
                                    return(features(msidata, mz=max(mz(msidata))))
                                    }
                                )   

                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax)))
                }
            }


        #end if

    </configfiles>
    <inputs>
        <expand macro="reading_msidata"/>
        <expand macro="pdf_filename"/>
        <conditional name="pixel_conditional">
            <param name="pixel_type" type="select" label="Choose spectra (pixel)">
                <option value="all_pixel" selected="True" >All spectra</option>
                <option value="tabular_pixel">Single spectra</option>
            </param>
            <when value="tabular_pixel">
                <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"

        </test>
        <test>
            <expand macro="processed_infile_imzml"/>
            <conditional name="processed_cond">
                <param name="processed_file" value="processed"/>
                <param name="accuracy" value="50"/>
                <param name="units" value="ppm"/>
            </conditional>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="all_pixel"/>
            </conditional>

9:006fc980af63

<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1">
    <description>
        mass spectrometry imaging mass spectra plots
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
        <requirement type="package" version="2.3">r-gridextra</requirement>
        <requirement type="package" version="1.1.1">r-scales</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[
        @INPUT_LINKING@
        cat '${MSI_mzplots}' &&

                msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
                colnames(msidata_coordinates) = c("x", "y", "pixel_index")
                merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)
                merged_annotation[is.na(merged_annotation)] = "NA"
                merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
                msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order

                    ## overview plot over annotated samples
                    number_combined = length(levels(msidata\$annotation))

                    ## the more annotation groups a file has the smaller will be the legend

            ##################### I) Sample: plot full mass spectrum ##############

                    #if $fullmz:
                    ## plot full mz for single tabular mz
                        print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable, col="black"))
                    #end if

                    pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord)

                    input_pixels = paste(x_coord, y_coord, sep="_")

                            maxmasspixel = maxmasspixel+1
                        }
                }

                    ## print single tabular mz; manual zoom
                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))

                #end for

                #elif str($mz_range.mz_range_options) == "tabular_mz":

                                        maxmasspixel = maxmasspixel+1
                                    }
                            }

                                ## print single tabular mz; tabular zoom
                                print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax), col="black"))
                            }
                        }

                #end if

        ##################### I) Sample: plot full mass spectrum ##############

                    #if $fullmz:

                        print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable, col="black"))
                    #end if

        ##################### II) Sample: plot zoom-in mass spectrum ##########

        #if str($mz_range.mz_range_options) == "manual_mz":

                        }else{
                            maxmasspixel = maxmasspixel+1
                        }
                }

                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))

            #end for

        #elif str($mz_range.mz_range_options) == "tabular_mz":

                                    ## if xlimax is outside mz range, use max mz value
                                    return(features(msidata, mz=max(mz(msidata))))
                                    }
                                )   

                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax), col="black"))
                }
            }


        #end if

    </configfiles>
    <inputs>
        <expand macro="reading_msidata"/>
        <expand macro="pdf_filename"/>
        <conditional name="pixel_conditional">
            <param name="pixel_type" type="select" label="Choose spectra (pixel) and/or add spectra annotations">
                <option value="all_pixel" selected="True" >All spectra</option>
                <option value="tabular_pixel">Single spectra</option>
            </param>
            <when value="tabular_pixel">
                <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"

        </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>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="all_pixel"/>
            </conditional>