comparison msi_combine.xml @ 4:d05bd881af3d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5

3:91bba2486773

<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.1">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

############## reading files and changing pixel coordinates ###################

#for $i, $infile in enumerate($infiles):

    #if $infile.ext == 'imzml'
        msidata_$i <- readImzML('infile_${i}')
    #elif $infile.ext == 'analyze75'
        msidata_$i <- readAnalyze('infile_${i}')
    #else
        msidata_$i = loadRData('infile_${i}.RData')
    #end if

           coord_fixed()+
           ggtitle("Spatial orientation of combined data")+
           theme_bw()+
           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=position_df, mean)
    coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
    for(file_count in 1:nrow(coord_labels))
    {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
    y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}

    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
            label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
            help="load imzml and ibd file by uploading composite datatype imzml"/>
        <conditional name="combine_conditional">
            <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom">
                <option value="automatic_combine" selected="True" >automatic combination</option>
                <option value="xy_shifts">xy shifts by hand</option>
            </param>

4:d05bd881af3d

<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.2">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

############## reading files and changing pixel coordinates ###################

#for $i, $infile in enumerate($infiles):

    #if $infile.ext == 'imzml'
        msidata_$i <- readImzML('infile_${i}', mass.accuracy=$accuracy, units.accuracy = "$units")
    #elif $infile.ext == 'analyze75'
        msidata_$i <- readAnalyze('infile_${i}')
    #else
        msidata_$i = loadRData('infile_${i}.RData')
    #end if

           coord_fixed()+
           ggtitle("Spatial orientation of combined data")+
           theme_bw()+
           theme(text=element_text(family="ArialMT", face="bold", size=15))+
           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=5,byrow=TRUE))
    coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
    coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
    for(file_count in 1:nrow(coord_labels))
    {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
    y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}

    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
            label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
            help="load imzml and ibd file by uploading composite datatype imzml"/>
        <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
        <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm">
            <option value="mz" >mz</option>
            <option value="ppm" selected="True" >ppm</option>
        </param>
        <conditional name="combine_conditional">
            <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom">
                <option value="automatic_combine" selected="True" >automatic combination</option>
                <option value="xy_shifts">xy shifts by hand</option>
            </param>