comparison combine.xml @ 6:bb1ac6b47a6c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"

5:b41107d8fe89

<tool id="cardinal_combine" name="MSI combine" version="2.2.6.0">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <macros>
        <import>macros.xml</import>

    ]]>
    </command>
    <configfiles>
        <configfile name="msi_combine"><![CDATA[
#import re

################ 1) load libraries and do preparations #################

library(Cardinal)

    ## read and manipulate MSI data

    #if $infile.ext == 'imzml'
        #if str($processed_cond.processed_file) == "processed":
            msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet"))
            centroided(msidata_$i) = $centroids
        #else
            msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as = c("MSImageSet"))
            centroided(msidata_$i) = $centroids
        #end if

    coordinates_combined = rbind(coordinates_combined, cardinal_coordinates_$i) 

#end for


######################### 6a) combination same mz axis ###################

#if str( $combine_conditional.combine_method ) == 'automatic_combine':
    print("automatic combine")

   #if not $processed_true:

        coordinates_matrix = as.matrix(unique_coordinates[,1:2])

        ## save msidata as imzML file MALDIquant
        MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix)

        ## create x,y,sample_name dataframe for QC pdf
       ## position_df = unique_coordinates ### ! anders
       ## colnames(position_df)[3] = "sample_name"
        ##coordinates_combined = coordinates_combined[pixelsofinterest,] ###! anders
        coordinates_combined = unique_coordinates
##TODO: hier aufräumen kann alles weg?!

    #end if

#end if

       theme(text=element_text(family="ArialMT", face="bold", size=15))+
       theme(legend.position="bottom",legend.direction="vertical")+
       guides(fill=guide_legend(ncol=4,byrow=TRUE))
coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean)
coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)

print(combine_plot)

    #if str($annotation_cond.annotation_tabular) == 'annotation'
        ## annotation plots
        for (inputcolumns in 4:ncol(coordinates_combined)){

            <param name="column_names" value="3"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="123_annotation_output.tabular"/>
            <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="4"/>
                <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="123_combined_picked.rdata,123_combined_picked2.rdata" ftype="rdata"/>

            <param name="column_names" value="3"/>
            <param name="processed_true" value="TRUE"/>
            <output name="pixel_annotations" file="picked.tabular"/>
            <output name="QC_overview" file="picked_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" compare="sim_size">
                <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="6"/>
                <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/>
            <output name="pixel_annotations" file="123_combined_auto.tabular"/>
            <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size">
                <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="4"/>
                <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="12_annotation_output.tabular"/>
            <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="4"/>
                <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="112_annotation_output.tabular"/>
            <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="4"/>
                <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="2123_annotation_output.tabular"/>
            <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="4"/>
                <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
    </tests>
    <help>

- The combine tool puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. 'MSI classification') or useful (e.g. 'MSI spectra plots').


**Output**

- MSI data as imzML file (in continous format when m/z axis were the same; in processed format when m/z axis were different)
- Pdf with pixel positions and annotations of the combined files
- Tabular file with pixel annotations (x,y,column with input file names and annotation columns)


]]>

6:bb1ac6b47a6c

<tool id="cardinal_combine" name="MSI combine" version="2.2.6.1">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <macros>
        <import>macros.xml</import>

    ]]>
    </command>
    <configfiles>
        <configfile name="msi_combine"><![CDATA[

#import re

################ 1) load libraries and do preparations #################

library(Cardinal)

    ## read and manipulate MSI data

    #if $infile.ext == 'imzml'
        #if str($processed_cond.processed_file) == "processed":
            msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet"))
            centroided(msidata_$i) = $centroids
        #else
            msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as = c("MSImageSet"))
            centroided(msidata_$i) = $centroids
        #end if

    coordinates_combined = rbind(coordinates_combined, cardinal_coordinates_$i) 

#end for


######################### 6b) combination same mz axis ###################

#if str( $combine_conditional.combine_method ) == 'automatic_combine':
    print("automatic combine")

   #if not $processed_true:

        coordinates_matrix = as.matrix(unique_coordinates[,1:2])

        ## save msidata as imzML file MALDIquant
        MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix)

        coordinates_combined = unique_coordinates

    #end if

#end if

       theme(text=element_text(family="ArialMT", face="bold", size=15))+
       theme(legend.position="bottom",legend.direction="vertical")+
       guides(fill=guide_legend(ncol=4,byrow=TRUE))
coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean)
coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
print(combine_plot)

    #if str($annotation_cond.annotation_tabular) == 'annotation'
        ## annotation plots
        for (inputcolumns in 4:ncol(coordinates_combined)){

            <param name="column_names" value="3"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="123_annotation_output.tabular"/>
            <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="12"/>
                <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="123_combined_picked.rdata,123_combined_picked2.rdata" ftype="rdata"/>

            <param name="column_names" value="3"/>
            <param name="processed_true" value="TRUE"/>
            <output name="pixel_annotations" file="picked.tabular"/>
            <output name="QC_overview" file="picked_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" compare="sim_size">
                <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="12"/>
                <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/>
            <output name="pixel_annotations" file="123_combined_auto.tabular"/>
            <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size">
                <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="12"/>
                <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="12_annotation_output.tabular"/>
            <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="12"/>
                <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="112_annotation_output.tabular"/>
            <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="12"/>
                <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
        <test>
            <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>

            <param name="combine_method" value="automatic_combine"/>
            <param name="processed_true" value="FALSE"/>
            <output name="pixel_annotations" file="2123_annotation_output.tabular"/>
            <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/>
            <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" compare="sim_size">
                <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="12"/>
                <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/>
            </output>
        </test>
    </tests>
    <help>

- The combine tool puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. 'MSI classification') or useful (e.g. 'MSI spectra plots').


**Output**

- MSI data as imzML file (in continuous format when m/z axis were the same; in processed format when m/z axis were different)
- Pdf with pixel positions and annotations of the combined files
- Tabular file with pixel annotations (x,y,column with input file names and annotation columns)


]]>