comparison msi_combine.xml @ 7:19d8eee15959 draft

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

6:f4aafc565aa3

<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.4">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
        #for $i, $infile in enumerate($infiles):
            #if $infile.ext == 'imzml'

    ## read annotation data, up to 5 annotations can be used for now

    ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
    input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE, 
        stringsAsFactors = FALSE)
    colnames(input_annotation)[1:2] = c("x", "y")
    msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
    colnames(msidata_coordinates)[3] = "pixel_index"
    ## only first 5 annotation columns are kept
    if (ncol(input_annotation) > 7){

    #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
        names_vector = character()
        #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy
        if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files
        {
            if (is.null(levels(msidata_$i\$combined_sample))) ### if the file was not combined before use input file name, otherwise keep combined_sample name which was assigned before
            {
            names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
            msidata_$i\$combined_sample = as.factor(names_vector)
            }
        }

                    <option value="ppm" selected="True" >ppm</option>
                </param>
            </when>
        </conditional>
        <param name="annotation_files" type="data" multiple="true" format="tabular"
            label="Pixel annotations as tabular files"
            help="Tabular files should have the same order as input files"/>
        <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">shift xy coordinates with a tabular file</option>
            </param>

            <param name="column_names" value="3"/>
            <param name="output_matrix" value="True"/>
            <output name="matrixasoutput" file="123_combined_matrix.tabular"/>
            <output name="annotation_output" file="123_annotation_output.tabular"/>
            <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
            <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/>
        </test>
        <test expect_num_outputs="4">
            <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
            <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
            <param name="combine_method" value="automatic_combine"/>
            <param name="output_matrix" value="True"/>
            <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
            <output name="annotation_output" file="12_annotation_output.tabular"/>
            <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
            <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/>
        </test>
        <test expect_num_outputs="3">
            <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
            <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
            <param name="combine_method" value="automatic_combine"/>
            <param name="output_matrix" value="False"/>
            <output name="annotation_output" file="112_annotation_output.tabular"/>
            <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
            <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="20000"/>
        </test>
    </tests>
    <help>
<![CDATA[

7:19d8eee15959

<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.5">
    <description>
        combine several mass spectrometry imaging datasets into one
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
        <requirement type="package" version="3.0.0">r-ggplot2</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
        #for $i, $infile in enumerate($infiles):
            #if $infile.ext == 'imzml'

    ## read annotation data, up to 5 annotations can be used for now

    ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
    input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE, 
        stringsAsFactors = FALSE)

    if (class(input_annotation[,1]) == "character"){
        annotation_coordinates = matrix(unlist(strsplit(as.character(input_annotation[,1]), "\\,")), ncol=2, byrow=TRUE)
        annotation_coordinates2 = cbind(as.numeric(substring(annotation_coordinates[,1], 5, last = 1000000L)), as.numeric(substring(annotation_coordinates[,2], 5, last = 1000000L)))
        input_annotation = cbind(annotation_coordinates2, input_annotation[,-1])
    }

    colnames(input_annotation)[1:2] = c("x", "y")
    msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
    colnames(msidata_coordinates)[3] = "pixel_index"
    ## only first 5 annotation columns are kept
    if (ncol(input_annotation) > 7){

    #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
        names_vector = character()
        #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy
        if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files
        {
            if (is.null(levels(msidata_$i\$combined_sample)))
            {
            names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
            msidata_$i\$combined_sample = as.factor(names_vector)
            }
        }

                    <option value="ppm" selected="True" >ppm</option>
                </param>
            </when>
        </conditional>
        <param name="annotation_files" type="data" multiple="true" format="tabular"
            label="Pixel annotations as tabular files, same number and order of files as input files"
            help="Coordinates in column 1 in format x = 1, y = 1 or first column x values, second column y values. Up to 5 columns with pixel annotations"/>
        <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">shift xy coordinates with a tabular file</option>
            </param>

            <param name="column_names" value="3"/>
            <param name="output_matrix" value="True"/>
            <output name="matrixasoutput" file="123_combined_matrix.tabular"/>
            <output name="annotation_output" file="123_annotation_output.tabular"/>
            <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
            <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="2000"/>
        </test>
        <test expect_num_outputs="4">
            <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
            <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
            <param name="combine_method" value="automatic_combine"/>
            <param name="output_matrix" value="True"/>
            <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
            <output name="annotation_output" file="12_annotation_output.tabular"/>
            <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
            <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="2000"/>
        </test>
        <test expect_num_outputs="3">
            <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
            <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
            <param name="combine_method" value="automatic_combine"/>
            <param name="output_matrix" value="False"/>
            <output name="annotation_output" file="112_annotation_output.tabular"/>
            <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
            <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="2000"/>
        </test>
    </tests>
    <help>
<![CDATA[