diff data_exporter.xml @ 0:28ba52c9548c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_exporter.xml	Mon Oct 01 01:05:33 2018 -0400
@@ -0,0 +1,359 @@
+<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.0">
+    <description>
+        exports imzML and Analyze7.5 to tabular files
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+    <![CDATA[
+
+        @INPUT_LINKING@
+        cat '${cardinal_imzml_exporter}' &&
+        Rscript '${cardinal_imzml_exporter}'
+
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="cardinal_imzml_exporter"><![CDATA[
+
+################################# load libraries and read file #################
+
+library(Cardinal)
+
+@READING_MSIDATA@
+
+npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
+
+if (npeaks > 0){
+
+    ###################### Intensity matrix output ################################
+
+    #if "int_matrix" in str($output_options).split(","):
+        print("intensity matrix output")
+
+        spectramatrix = spectra(msidata)[]
+        mz_names = gsub(" = ", "_", names(features(msidata)))
+        mz_names = gsub("/", "", mz_names)
+        pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
+        pixel_names = gsub(" = ", "y_", pixel_names)
+
+        spectramatrix = cbind(mz_names,spectramatrix)
+        newmatrix = rbind(c("mz_name", pixel_names), spectramatrix)
+        write.table(newmatrix, file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
+
+    #end if
+
+
+    ############################## m/z feature output ##########################
+    #if "mz_tabular" in str($output_options).split(","):
+        print("mz feature output")
+
+        mz_names = gsub(" = ", "_", names(features(msidata)))
+        mz_names = gsub("/", "", mz_names)
+
+        ## mean, median, sd and SEM intensity per file and mz
+        full_sample_mean = apply(spectra(msidata)[],1,mean, na.rm=TRUE)
+        full_sample_median = apply(spectra(msidata)[],1,median, na.rm=TRUE)
+        full_sample_sd = apply(spectra(msidata)[],1,sd, na.rm=TRUE)
+        full_sample_sem = full_sample_sd/full_sample_mean*100
+        ## npeaks and sum of all intensities per spectrum and mz
+        mzTIC = rowSums(spectra(msidata)[], na.rm=TRUE) ## calculate intensity sum for each m/z
+        peakspermz = rowSums(spectra(msidata)[] > 0, na.rm=TRUE) ## calculate number of intensities > 0 for each m/z (max = number of spectra)
+
+        ## combine into dataframe, order is the same for all vectors
+        mz_df = data.frame(mz_names, mz(msidata), full_sample_mean, full_sample_median, full_sample_sd, full_sample_sem, mzTIC, peakspermz)
+        colnames(mz_df) = c("mz_names", "mz", "sample_mean", "sample_median", "sample_sd", "sample_sem", "intensity_sum", "number_peaks")
+        write.table(mz_df, file="$feature_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
+    #end if
+
+    ###################### summarized m/z feature output #######################
+
+    #if str($tabular_annotation.load_annotation) == 'yes_annotation':
+        print("summarized annotation output")
+
+        ## read and extract x,y,annotation information
+        input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
+        annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
+        colnames(annotation_input) = c("x", "y", "annotation")
+
+        ## merge with coordinate information of msidata
+        msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
+        colnames(msidata_coordinates)[3] = "pixel_index"
+        merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
+        merged_annotation[is.na(merged_annotation)] = "NA"
+        merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
+        msidata\$annotation = as.factor(merged_annotation[,4])
+
+        ## create m/z feature name
+        mz_names = gsub(" = ", "_", names(features(msidata)))
+        mz_names = gsub("/", "", mz_names)
+
+        #if "mean" in str($tabular_annotation.summary_type).split(","):
+            print("summarized mean")
+
+            ## calculate mean per annotation group
+            sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
+            count = 1
+            for (subsample in levels(msidata\$annotation)){
+                subsample_pixels = msidata[,msidata\$annotation == subsample]
+                subsample_calc = apply(spectra(subsample_pixels)[],1,mean, na.rm=TRUE)
+                sample_matrix = cbind(sample_matrix, subsample_calc)
+                count = count+1}
+            sample_matrix_mean = cbind(mz_names,sample_matrix)
+            sample_matrix_mean = rbind(c("mz_name", levels(msidata\$annotation)), sample_matrix_mean)
+            write.table(sample_matrix_mean, file="$summarized_mean", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
+        #end if
+
+        #if "median" in str($tabular_annotation.summary_type).split(","):
+            print("summarized median")
+
+            sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
+            count = 1
+            for (subsample in levels(msidata\$annotation)){
+                subsample_pixels = msidata[,msidata\$annotation == subsample]
+                subsample_calc = apply(spectra(subsample_pixels)[],1,median, na.rm=TRUE)
+                sample_matrix = cbind(sample_matrix, subsample_calc)
+                count = count+1}
+            sample_matrix_median = cbind(mz_names,sample_matrix)
+            sample_matrix_median = rbind(c("mz name", levels(msidata\$annotation)), sample_matrix_median)
+            write.table(sample_matrix_median, file="$summarized_median", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
+        #end if
+
+        #if "sd" in str($tabular_annotation.summary_type).split(","):
+            print("summarized sd")
+
+            sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
+            count = 1
+            for (subsample in levels(msidata\$annotation)){
+                subsample_pixels = msidata[,msidata\$annotation == subsample]
+                subsample_calc = apply(spectra(subsample_pixels)[],1,sd, na.rm=TRUE)
+                sample_matrix = cbind(sample_matrix, subsample_calc)
+                count = count+1}
+            sample_matrix_sd = cbind(mz_names,sample_matrix)
+            sample_matrix_sd = rbind(c("mz name", levels(msidata\$annotation)), sample_matrix_sd)
+            write.table(sample_matrix_sd, file="$summarized_sd", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
+        #end if
+
+    #end if
+
+
+    ############################ spectra (pixel) output ############################
+    #if "pixel_tabular" in str($output_options).split(","):
+        print("pixel output")
+
+        ## coordinates
+        xycoordinates = coord(msidata)[,1:2]
+
+        ## pixel name
+        pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
+        pixel_names = gsub(" = ", "y_", pixel_names)
+
+        ## pixel order 
+        pixelxyarray=1:length(pixels(msidata))
+
+        ## number of pixels per spectrum: every intensity value > 0 counts as peak
+        peaksperpixel = colSums(spectra(msidata)[]> 0, na.rm=TRUE)
+
+        ## Total ion chromatogram per spectrum
+        TICs = round(colSums(spectra(msidata)[], na.rm=TRUE), digits = 2)
+
+        ## Highest m/z per spectrum
+        highestmz = apply(spectra(msidata)[],2,which.max) 
+        highestmz_data = mz(msidata)[highestmz]
+
+        ## Combine into dataframe; order is the same for all vectors
+        spectra_df = data.frame(pixel_names, xycoordinates, pixelxyarray, peaksperpixel, TICs, highestmz_data)
+        colnames(spectra_df) = c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz")
+
+        #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":
+
+            calibrant_list = read.delim("$counting_calibrants.mz_tabular", header = $counting_calibrants.feature_header, na.strings=c("","NA"), stringsAsFactors = FALSE)
+            calibrant_list = calibrant_list[,$counting_calibrants.feature_column, drop=FALSE]
+            ### calculate how many input calibrant m/z are valid: 
+            inputcalibrants = calibrant_list[calibrant_list[,1]>min(mz(msidata)) & calibrant_list[,1]<max(mz(msidata)),,drop = FALSE]
+            inputcalibrantmasses = inputcalibrants[,1]
+
+            ##QC plot number 2) Number of calibrants per spectrum
+
+            ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
+            pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
+
+            if (length(inputcalibrantmasses) != 0){
+
+                ## calculate plusminus values in m/z for each calibrant
+                plusminusvalues = rep($counting_calibrants.plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
+
+                ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
+
+                for (mass in 1:length(inputcalibrantmasses)){
+                    filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
+                    if (nrow(filtered_data) > 1 & sum(spectra(filtered_data)[],na.rm=TRUE) > 0){
+                        ## intensity of all m/z > 0
+                        intensity_sum = colSums(spectra(filtered_data)[], na.rm=TRUE) > 0
+                    }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data)[], na.rm=TRUE) > 0){
+                        ## intensity of only m/z > 0
+                        intensity_sum = spectra(filtered_data)[] > 0 
+                    }else{
+                        intensity_sum = rep(FALSE, ncol(filtered_data))}
+                    ## for each pixel add sum of intensities > 0 in the given m/z range
+                    pixelmatrix = rbind(pixelmatrix, intensity_sum)
+                }
+                ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
+                countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))
+            }else{countvector = rep(0,ncol(msidata))}
+                countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
+                colnames(countdf) = c("x_values", "y_values", "input m/z count")
+                spectra_df = merge(spectra_df, countdf, by=c("x_values", "y_values"))
+
+                ## sort columns to have spectra_names as rowname in first column
+                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz", "input m/z count")]
+
+        #end if
+        #if str($tabular_annotation.load_annotation) == 'yes_annotation':
+
+            colnames(annotation_input) = c("x_values", "y_values", "annotation")
+            spectra_df = merge(annotation_input,spectra_df, by=c("x_values", "y_values"))
+
+            ## sort columns to have spectra_names as rowname in first column
+            #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":
+                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz", "input m/z count", "annotation")]
+            #else
+                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz", "annotation")]
+            #end if
+
+        #end if
+        ## sort rows according to original pixel order
+        spectra_df = spectra_df[match(pixel_names, spectra_df\$spectra_names),]
+
+        ## Create list and output tabular
+        write.table(spectra_df, file="$pixel_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
+    #end if
+
+
+}else{
+    print("file has no features or pixels left")
+}
+
+
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="reading_msidata"/>
+        <param name="output_options" type="select" display="checkboxes" optional="False" multiple="true" label="Multiple output files can be selected">
+            <option value="int_matrix" selected="True" >intensity matrix</option>
+            <option value="mz_tabular">mz feature output</option>
+            <option value="pixel_tabular">pixel output</option>
+        </param>
+        <conditional name="counting_calibrants">
+            <param name="pixel_with_calibrants" type="select" label="Add number of m/z of interest per spectrum to pixel output">
+                <option value="no_calibrants" selected="True">no</option>
+                <option value="yes_calibrants">yes</option>
+            </param>
+            <when value="no_calibrants"/>
+            <when value="yes_calibrants">
+                <expand macro="reading_1_column_mz_tabular" label="For each spectrum the occurrence of the provided m/z values is counted"/>
+                <param name="plusminus_ppm" value="200" type="float" label="ppm range will be added in both directions to input m/z" help="The m/z window is used to search for peaks, if intensity > 0 found in the window the m/z is considered present, if all intensities are 0 the m/z is considered not present"/>
+            </when>
+        </conditional>
+        <conditional name="tabular_annotation">
+            <param name="load_annotation" type="select" label="Pixel annotation can be used to summarize intensities per annotation group">
+                <option value="no_annotation" selected="True">no</option>
+                <option value="yes_annotation">yes</option>
+            </param>
+            <when value="no_annotation"/>
+            <when value="yes_annotation">
+                <expand macro="reading_pixel_annotations"/>
+                <param name="summary_type" type="select" display="checkboxes" optional="False" multiple="true" label="Calculation for each m/z and all pixels of a annotation group" help="This step will only work if pixel annotations are provided">
+                    <option value="mean">mean</option>
+                    <option value="median">median</option>
+                    <option value="sd">standard deviation</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="intensity_matrix" label="${tool.name} on ${on_string}: intensity_matrix">
+            <filter>"int_matrix" in output_options</filter>
+        </data>
+        <data format="tabular" name="pixel_output" label="${tool.name} on ${on_string}: spectra">
+            <filter>"pixel_tabular" in output_options</filter>
+        </data>
+        <data format="tabular" name="feature_output" label="${tool.name} on ${on_string}: features">
+            <filter>"mz_tabular" in output_options</filter>
+        </data>
+        <data format="tabular" name="summarized_mean" label="${tool.name} on ${on_string}: group_mean">
+            <filter>tabular_annotation['load_annotation'] == 'yes_annotation' and 'mean' in tabular_annotation['summary_type']</filter>
+        </data>
+        <data format="tabular" name="summarized_median" label="${tool.name} on ${on_string}: group_median">
+            <filter>tabular_annotation['load_annotation'] == 'yes_annotation' and 'median' in tabular_annotation['summary_type']</filter>
+        </data>
+        <data format="tabular" name="summarized_sd" label="${tool.name} on ${on_string}: group_sd">
+            <filter>tabular_annotation['load_annotation'] == 'yes_annotation' and 'sd' in tabular_annotation['summary_type']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <expand macro="infile_imzml"/>
+            <param name="output_options" value="int_matrix,mz_tabular"/>
+            <output name="intensity_matrix" file="int_matrix1.tabular"/>
+            <output name="feature_output" file="features_out1.tabular"/>
+        </test>
+        <test expect_num_outputs="3">
+            <expand macro="infile_analyze75"/>
+            <param name="output_options" value="pixel_tabular"/>
+            <conditional name="tabular_annotation">
+                <param name="load_annotation" value="yes_annotation"/>
+                <param name="annotation_file" value="annotations.tabular"/>
+                <param name="column_x" value="1"/>
+                <param name="column_y" value="2"/>
+                <param name="column_names" value="4"/>
+                <param name="tabular_header" value="True"/>
+                <param name="summary_type" value="mean,sd"/>
+            </conditional>
+            <output name="pixel_output" file="pixel_out2.tabular"/>
+            <output name="summarized_mean" file="mean_out2.tabular"/>
+            <output name="summarized_sd" file="sd_out2.tabular"/>
+        </test>
+        <test expect_num_outputs="3">
+            <expand macro="infile_imzml"/>
+            <param name="output_options" value="int_matrix,pixel_tabular,mz_tabular"/>
+            <conditional name="counting_calibrants">
+                <param name="pixel_with_calibrants" value="yes_calibrants"/>
+                <param name="mz_tabular" value="inputcalibrantfile2.txt"/>
+                <param name="feature_column" value="1"/>
+                <param name="feature_header" value="False"/>
+                <param name="plusminus_ppm" value="200"/>
+            </conditional>
+            <output name="intensity_matrix" file="int_matrix3.tabular"/>
+            <output name="feature_output" file="features_out3.tabular"/>
+            <output name="pixel_output" file="pixel_out3.tabular"/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+
+@CARDINAL_DESCRIPTION@
+
+-----
+
+This tool provides multiple tabular output options for mass spectrometry imaging data files. 
+
+@MSIDATA_INPUT_DESCRIPTION@
+
+@SPECTRA_TABULAR_INPUT_DESCRIPTION@
+
+@MZ_TABULAR_INPUT_DESCRIPTION@
+
+**Output options**
+
+- intensity matrix: m/z in rows, spectra in columns, filled with intensity values
+- spectra output: spectra in rows - for each spectrum: name, x and y coordinates,order, number of peaks (intensities > 0), total ion chromatogram (TIC), highest m/z feature per spectrum, optional count of input m/z per spectrum, optional spectrum annotation
+- mz feature output: m/z in rows - for each m/z: name, m/z, mean, median, standard deviation (sd), standard error of the mean (sem), sum of all intensities per m/z, number of peaks (intensity > 0) per m/z
+- summarized intensities: pixel annotations will be used to group spectra into annotation groups and calculate mean, median and sd of the intensities per group
+
+        ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>