msi_combine: msi_combine.xml comparison

comparison msi_combine.xml @ 6:f4aafc565aa3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee

author	galaxyp
date	Tue, 24 Jul 2018 04:52:39 -0400
parents	ff91e78b5c5c
children	19d8eee15959

comparison

equal deleted inserted replaced

-:ff91e78b5c5c
+:f4aafc565aa3
-<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.3">
+<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>
 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
 #else
 ln -s '$infile' infile_${i}.RData &&
 #end if
 #end for
+#for $i, $annotation_file in enumerate($annotation_files):
+ln -s '$annotation_file' annotation_file_${i}.tabular &&
+#end for
 cat '${msi_combine}' &&
 Rscript '${msi_combine}'
 ]]>
 </command>
 ############## reading files and changing pixel coordinates ###################
 #for $i, $infile in enumerate($infiles):
-#if $infile.ext == 'imzml'
+## read MSI data
-#if str($processed_cond.processed_file) == "processed":
-msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
+#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")
+#else
+msidata_$i <- readImzML('infile_${i}')
+#end if
+#elif $infile.ext == 'analyze75'
+msidata_$i <- readAnalyze('infile_${i}')
 #else
-msidata <- readImzML('infile')
+msidata_$i = loadRData('infile_${i}.RData')
 #end if
-#elif $infile.ext == 'analyze75'
-msidata_$i <- readAnalyze('infile_${i}')
-#else
+## read annotation data, up to 5 annotations can be used for now
-msidata_$i = loadRData('infile_${i}.RData')
-#end if
+## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
+input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE,
+stringsAsFactors = FALSE)
-sampleNames(msidata_$i) = "msidata" ## same name necessary to combine data in one single coordinate system
+colnames(input_annotation)[1:2] = c("x", "y")
+msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
+colnames(msidata_coordinates)[3] = "pixel_index"
+## only first 5 annotation columns are kept
+if (ncol(input_annotation) > 7){
+input_annotation = input_annotation[,1:7]}
+annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
+annotation_df_8 = cbind(annotation_df, data.frame(matrix(NA,ncol=8-ncol(annotation_df), nrow=ncol(msidata_$i))))
+annotation_df_8_sorted = annotation_df_8[order(annotation_df_8\$pixel_index),]## orders pixel according to msidata
+## each annotation column is assigned to the pixel in the pData slot of the MSIdata
+msidata_$i\$column1 = annotation_df_8_sorted[,4]
+msidata_$i\$column2 = annotation_df_8_sorted[,5]
+msidata_$i\$column3 = annotation_df_8_sorted[,6]
+msidata_$i\$column4 = annotation_df_8_sorted[,7]
+msidata_$i\$column5 = annotation_df_8_sorted[,8]
+## same name for MSI data files necessary to combine data in one single coordinate system
+sampleNames(msidata_$i) = "msidata"
 ################### preparation xy shifts ##########################
 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
+## shift coordinates according to input tabular file and store file names
 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file
 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file
 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))
 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
 valid_dataset = append(valid_dataset,
 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0))
 #end for
+## extract columnnames from (last) annotation tabular (for QC plot names)
+annotation_colnames = colnames(input_annotation)[-c(1,2)]
 ###################### automatic combination ###################################
 ################################################################################
 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample)
 colnames(position_df)[3] = "sample_name"
 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
 geom_tile() +
 coord_fixed()+
-ggtitle("Spatial orientation of combined data")+
+ggtitle("Spatial orientation of combined data (sample names)")+
 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, na.rm=TRUE, na.action="na.pass")
 ################################################################################
 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
 print("xy_shifts")
-#if str($combine_conditional.combination_true) == "yes_combi":
+## find duplicated coordinates
-print("combination with xy shifts")
+all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#))
+duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE)
-## find duplicated coordinates
-all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#))
-duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE)
 print(paste0("Number of removed duplicated coordinates: ", sum(duplicated_coordinates)/2))
 unique_coordinates = all_coordinates[!duplicated_coordinates,]
 ## remove duplicated coordinates
 datasetlist = list()
 count = 1
 for (usable_dataset in list(#echo ','.join($msidata)#)){
 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(unique_coordinates)]
 filtered_dataset = usable_dataset[,pixelsofinterest]
 if (ncol(filtered_dataset) > 0 ){
 datasetlist[[count]] = filtered_dataset}
 count = count +1}
 msidata_combined = do.call(combine, datasetlist)
 ## save as (.RData)
 msidata = msidata_combined
 save(msidata, file="$msidata_combined")
 ## create x,y,sample_name dataframe for QC pdf
 position_df = cbind(coord(msidata), msidata\$combined_sample)
 colnames(position_df)[3] = "sample_name"
-#else:
+#end if
-print("no combination, only testing xy shifts")
-position_df = do.call(rbind, list(#echo ','.join($pixelcoords)#))
+################################## outputs ####################################
-position_df\$sample_name = as.factor(pixel_vector)
+################################################################################
-print(paste0("Number of duplicated coordinates: ", sum(duplicated(position_df[,1:2]))))
+########### QC with pixels and their annotations ################################
-#end if
+pdf("Combined_qc.pdf", width=15, height=15)
-## create PDF to show all pixels in PDF as QC
+## combined plot
+combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
-pdf("Combined_qc.pdf", width=15, height=15)
+geom_tile() +
-combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
+coord_fixed()+
+ggtitle("Spatial orientation of combined data")+
+theme_bw()+
+theme(text=element_text(family="ArialMT", face="bold", size=15))+
+theme(legend.position="bottom",legend.direction="vertical")+
+guides(fill=guide_legend(ncol=5,byrow=TRUE))
+coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
+coord_labels\$file_number = gsub( "_.*$", "", 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]))}
+print(combine_plot)
+## annotation plots
+## plot 1
+column1_df = cbind(coord(msidata), msidata\$column1)
+colnames(column1_df)[3] = "column1"
+if (sum(is.na(column1_df[3])) < nrow(column1_df)){
+column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
 geom_tile() +
 coord_fixed()+
-ggtitle("Spatial orientation of combined data")+
+ggtitle(paste0(annotation_colnames[1]))+
 theme_bw()+
 theme(text=element_text(family="ArialMT", face="bold", size=15))+
 theme(legend.position="bottom",legend.direction="vertical")+
-guides(fill=guide_legend(ncol=5,byrow=TRUE))
+guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[1]))
-coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
+print(column1_plot)}
-coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
+##rename columnname for output tabular file
-for(file_count in 1:nrow(coord_labels))
+colnames(column1_df)[3] = annotation_colnames[1]
-{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]))}
+## plot 2
-print(combine_plot)
+column2_df = cbind(coord(msidata), msidata\$column2)
+colnames(column2_df)[3] = "column2"
+if (sum(is.na(column2_df[3])) < nrow(column2_df)){
+column2_plot = ggplot(column2_df, aes(x=x, y=y, fill=column2))+
+geom_tile() +
+coord_fixed()+
+ggtitle(paste0(annotation_colnames[2]))+
+theme_bw()+
+theme(text=element_text(family="ArialMT", face="bold", size=15))+
+theme(legend.position="bottom",legend.direction="vertical")+
+guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[2]))
+print(column2_plot)}
+##rename columnname for output tabular file
+colnames(column2_df)[3] = annotation_colnames[2]
+## plot 3
+column3_df = cbind(coord(msidata), msidata\$column3)
+colnames(column3_df)[3] = "column3"
+if (sum(is.na(column3_df[3])) < nrow(column3_df)){
+column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+
+geom_tile() +
+coord_fixed()+
+ggtitle(paste0(annotation_colnames[3]))+
+theme_bw()+
+theme(text=element_text(family="ArialMT", face="bold", size=15))+
+theme(legend.position="bottom",legend.direction="vertical")+
+guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[3]))
+print(column3_plot)}
+##rename columnname for output tabular file
+colnames(column3_df)[3] = annotation_colnames[3]
+## plot 4
+column4_df = cbind(coord(msidata), msidata\$column4)
+colnames(column4_df)[3] = "column4"
+if (sum(is.na(column4_df[3])) < nrow(column4_df)){
+column4_plot = ggplot(column4_df, aes(x=x, y=y, fill=column4))+
+geom_tile() +
+coord_fixed()+
+ggtitle(paste0(annotation_colnames[4]))+
+theme_bw()+
+theme(text=element_text(family="ArialMT", face="bold", size=15))+
+theme(legend.position="bottom",legend.direction="vertical")+
+guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[4]))
+print(column4_plot)}
+##rename columnname for output tabular file
+colnames(column4_df)[3] = annotation_colnames[4]
+## plot5
+column5_df = cbind(coord(msidata), msidata\$column5)
+colnames(column5_df)[3] = "column5"
+if (sum(is.na(column5_df[3])) < nrow(column5_df)){
+column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+
+geom_tile() +
+coord_fixed()+
+ggtitle(paste0(annotation_colnames[5]))+
+theme_bw()+
+theme(text=element_text(family="ArialMT", face="bold", size=15))+
+theme(legend.position="bottom",legend.direction="vertical")+
+guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[5]))
+print(column5_plot)}
+##rename columnname for output tabular file
+colnames(column5_df)[3] = annotation_colnames[5]
 dev.off()
-#end if
+##################### annotation tabular output ################################
-####################### optional matrix output #################################
-#if $output_matrix:
 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
-spectramatrix = spectra(msidata)[]
+annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df)
-spectramatrix = cbind(mz(msidata),spectramatrix)
+combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list)
-newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
+write.table(combined_annotations, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
-write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
 }else{
-print("file has no features or pixels left")
+print("No annotation tabular output because file has no features or pixels left")
 }
-#end if
+####################### optional matrix output #################################
+#if $output_matrix:
+if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
+spectramatrix = spectra(msidata)[]
+spectramatrix = cbind(mz(msidata),spectramatrix)
+newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
+write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
+}else{
+print("No intensity matrix output because file has no features or pixels left")
+}
+#end if
 ]]></configfile>
 </configfiles>
 <inputs>
 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
 <option value="mz" >mz</option>
 <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">xy shifts by hand</option>
+<option value="xy_shifts">shift xy coordinates with a tabular file</option>
 </param>
 <when value="automatic_combine"/>
 <when value="xy_shifts">
-<param name="coordinates_file" type="data" format="tabular" label="datasetnames, X and y values to shift data before combining"
+<param name="coordinates_file" type="data" format="tabular" label="datasetnames, x and y values to shift pixel coordinates before combining"
-help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift"/>
+help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift. Pixels with the same coordinates after shifting will be deleted."/>
 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
-<param name="combination_true" type="boolean" display="radio" truevalue="yes_combi" falsevalue="no_combi" label="Combine datasets" help = "If there are duplicated pixels they will be deleted. If it is not clear if there are duplicated pixels, select No to get an idea about the pixel overlap"/>
 </when>
 </conditional>
 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
 </inputs>
 <outputs>
 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/>
 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/>
+<data format="tabular" name="annotation_output" label="Annotation_tabular"/>
 <data format="tabular" name="matrixasoutput" label="Combined_matrix">
 <filter>output_matrix</filter>
 </data>
 </outputs>
 <tests>
-<test expect_num_outputs="3">
+<test expect_num_outputs="4">
 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
+<param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/>
 <param name="combine_method" value="xy_shifts"/>
 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
 <param name="column_x" value="1"/>
 <param name="column_y" value="2"/>
 <param name="column_names" value="3"/>
-<param name="combination_true" value="yes_combi"/>
 <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="2">
+<test expect_num_outputs="4">
-<param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
-<param name="combine_method" value="xy_shifts"/>
-<param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
-<param name="column_x" value="1"/>
-<param name="column_y" value="2"/>
-<param name="column_names" value="3"/>
-<param name="combination_true" value="no_combi"/>
-<output name="msidata_combined" file="123_no_combi.RData" compare="sim_size" />
-<output name="combining_qc" file="123_no_combi_QC.pdf" compare="sim_size" delta="20000"/>
-</test>
-<test expect_num_outputs="3">
 <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="2">
+<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>
 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
-Prerequisite:
+Input:
-- m/z values need to be the same across all datasets (before using this tool), this can be achieved with the filtering tool (use same m/z range) and the preprocessing tool (use same binning parameter)
+- MSI data files with same m/z values (to obtain same m/z values for different files: filtering tool same m/z range and preprocessing tool same binning width)
+- Tabular files with pixel annotations need to have the x values in the first column, y values in the second column and then up to five annotations in the next columns. The order of the annotations in the columns must be the same for all files (x and y in column 1 and 2; annotation1 in column3, annotation2 in column4,...)
+- The order and the number of MSI data files and annotation tabular files must be the same
+- For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name (see below)
 Options:
-- "automatic combination": files are automatically arranged in a grid, subfiles are named according to input file name
+- "automatic combination": files are automatically arranged in a grid (duplicated pixels are allowed), subfiles are named according to the input file name
-- "xy shifts by hand": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns and the file name in a third column). To test if the pixels are correctly shifted use "combine datasets: No".
+- "xy shifts by hand": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns and the file name in a third column). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates).
-Combine datasets: Yes - Combines all datasets and removes all duplicated pixels (same x and y coordinates).
 Output:
-- imzML file containing multiple subfiles
+- single imzML file
-- pdf that shows the pixel positions of the combined files
+- pdf that shows the pixel positions and annotations of the combined files
+- Tabular file with pixel annotations (x,y,column with input file names, up to five annotation columns)
 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
 ]]>
 </help>

Mercurial > repos > galaxyp > msi_combine

comparison msi_combine.xml @ 6:f4aafc565aa3 draft