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comparison msi_combine.xml @ 8:c6564ddf0744 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
author galaxyp
date Tue, 04 Sep 2018 13:42:57 -0400
parents 19d8eee15959
children
comparison
equal deleted inserted replaced
7:19d8eee15959 8:c6564ddf0744
1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.5"> 1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.6">
2 <description> 2 <description>
3 combine several mass spectrometry imaging datasets into one 3 combine several mass spectrometry imaging datasets into one
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
18 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m && 18 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
19 #else 19 #else
20 ln -s '$infile' infile_${i}.RData && 20 ln -s '$infile' infile_${i}.RData &&
21 #end if 21 #end if
22 #end for 22 #end for
23 #for $i, $annotation_file in enumerate($annotation_files): 23 #if $annotation_cond.annotation_tabular == 'annotation'
24 ln -s '$annotation_file' annotation_file_${i}.tabular && 24 #for $i, $annotation_file in enumerate($annotation_cond.annotation_files):
25 #end for 25 ln -s '$annotation_file' annotation_file_${i}.tabular &&
26 #end for
27 #end if
26 28
27 cat '${msi_combine}' && 29 cat '${msi_combine}' &&
28 Rscript '${msi_combine}' 30 Rscript '${msi_combine}'
29 31
30 ]]> 32 ]]>
38 40
39 library(Cardinal) 41 library(Cardinal)
40 library(ggplot2) 42 library(ggplot2)
41 43
42 ## read tabular file for xy_shift option 44 ## read tabular file for xy_shift option
43
44 #if str( $combine_conditional.combine_method ) == 'xy_shifts': 45 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
45 input_list = read.delim("$combine_conditional.coordinates_file", header = FALSE, 46 input_list = read.delim("$combine_conditional.coordinates_file", header = FALSE,
46 stringsAsFactors = FALSE) 47 stringsAsFactors = FALSE)
47 #end if 48 #end if
48 49
49 ## load RData and store with new variable name 50 ## function to load RData and store with new variable name
50
51 loadRData <- function(fileName){ 51 loadRData <- function(fileName){
52 #loads an RData file, and returns it
53 load(fileName) 52 load(fileName)
54 get(ls()[ls() != "fileName"]) 53 get(ls()[ls() != "fileName"])
55 } 54 }
56 55
57 ## preparations for reading files one by one with for loop 56 ## preparations for reading files one by one with for loop
58
59 pixel_vector = numeric() 57 pixel_vector = numeric()
60 x_shifts = 0 58 x_shifts = 0
61 y_shifts = 0 59 y_shifts = 0
62 max_y = numeric() 60 max_y = numeric()
63 valid_dataset = logical() 61 valid_dataset = logical()
69 67
70 ############## reading files and changing pixel coordinates ################### 68 ############## reading files and changing pixel coordinates ###################
71 69
72 #for $i, $infile in enumerate($infiles): 70 #for $i, $infile in enumerate($infiles):
73 71
74 ## read MSI data 72 ## read and manipulate MSI data
75 73
76 #if $infile.ext == 'imzml' 74 #if $infile.ext == 'imzml'
77 #if str($processed_cond.processed_file) == "processed": 75 #if str($processed_cond.processed_file) == "processed":
78 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") 76 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
79 #else 77 #else
83 msidata_$i <- readAnalyze('infile_${i}') 81 msidata_$i <- readAnalyze('infile_${i}')
84 #else 82 #else
85 msidata_$i = loadRData('infile_${i}.RData') 83 msidata_$i = loadRData('infile_${i}.RData')
86 #end if 84 #end if
87 85
88 86 ## remove duplicated coordinates, otherwise combine will fail
89 ## read annotation data, up to 5 annotations can be used for now 87 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
90 88 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]
91 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
92 input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE,
93 stringsAsFactors = FALSE)
94
95 if (class(input_annotation[,1]) == "character"){
96 annotation_coordinates = matrix(unlist(strsplit(as.character(input_annotation[,1]), "\\,")), ncol=2, byrow=TRUE)
97 annotation_coordinates2 = cbind(as.numeric(substring(annotation_coordinates[,1], 5, last = 1000000L)), as.numeric(substring(annotation_coordinates[,2], 5, last = 1000000L)))
98 input_annotation = cbind(annotation_coordinates2, input_annotation[,-1])
99 }
100
101 colnames(input_annotation)[1:2] = c("x", "y")
102 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
103 colnames(msidata_coordinates)[3] = "pixel_index"
104 ## only first 5 annotation columns are kept
105 if (ncol(input_annotation) > 7){
106 input_annotation = input_annotation[,1:7]}
107
108 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
109 annotation_df_8 = cbind(annotation_df, data.frame(matrix(NA,ncol=8-ncol(annotation_df), nrow=ncol(msidata_$i))))
110 annotation_df_8_sorted = annotation_df_8[order(annotation_df_8\$pixel_index),]## orders pixel according to msidata
111
112 ## each annotation column is assigned to the pixel in the pData slot of the MSIdata
113 msidata_$i\$column1 = annotation_df_8_sorted[,4]
114 msidata_$i\$column2 = annotation_df_8_sorted[,5]
115 msidata_$i\$column3 = annotation_df_8_sorted[,6]
116 msidata_$i\$column4 = annotation_df_8_sorted[,7]
117 msidata_$i\$column5 = annotation_df_8_sorted[,8]
118 89
119 ## same name for MSI data files necessary to combine data in one single coordinate system 90 ## same name for MSI data files necessary to combine data in one single coordinate system
120 sampleNames(msidata_$i) = "msidata" 91 sampleNames(msidata_$i) = "msidata"
92
93
94 ## read and process annotation tabular or automatically use name of infile as annotation
95
96 ## set all pixel annotations to NA, necessary in case files were combined before with different annotations
97 msidata_$i\$column1 = rep(NA, ncol(msidata_$i))
98 msidata_$i\$column2 = rep(NA, ncol(msidata_$i))
99 msidata_$i\$column3 = rep(NA, ncol(msidata_$i))
100 msidata_$i\$column4 = rep(NA, ncol(msidata_$i))
101 msidata_$i\$column5 = rep(NA, ncol(msidata_$i))
102 msidata_$i\$combined_sample = rep(NA, ncol(msidata_$i))
103
104 #if str($annotation_cond.annotation_tabular) == 'annotation'
105 print("annotations")
106
107 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
108 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE)
109
110 ## change format x = 1, y = 2 into two columns
111 if (class(input_annotation[,1]) == "character"){
112 annotation_names = colnames(input_annotation[2:ncol(input_annotation)])
113 annotation_coordinates = matrix(unlist(strsplit(as.character(input_annotation[,1]), "\\,")), ncol=2, byrow=TRUE)
114 annotation_coordinates2 = cbind(as.numeric(substring(annotation_coordinates[,1], 5, last = 1000000L)), as.numeric(substring(annotation_coordinates[,2], 5, last = 1000000L)))
115 input_annotation = cbind(annotation_coordinates2, input_annotation[,-1])
116 colnames(input_annotation) = c("x", "y", annotation_names)
117 }
118
119 colnames(input_annotation)[1:2] = c("x", "y")
120 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
121 colnames(msidata_coordinates)[3] = "pixel_index"
122
123 ## only first 5 annotation columns are kept
124 if (ncol(input_annotation) > 7){
125 input_annotation = input_annotation[,1:7]}
126
127 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
128 annotation_df_8 = cbind(annotation_df, data.frame(matrix(NA,ncol=8-ncol(annotation_df), nrow=ncol(msidata_$i))))
129 annotation_df_8_sorted = annotation_df_8[order(annotation_df_8\$pixel_index),]## orders pixel according to msidata
130
131 ## each annotation column is assigned to the pixel in the pData slot of the MSIdata
132 msidata_$i\$column1 = annotation_df_8_sorted[,4]
133 msidata_$i\$column2 = annotation_df_8_sorted[,5]
134 msidata_$i\$column3 = annotation_df_8_sorted[,6]
135 msidata_$i\$column4 = annotation_df_8_sorted[,7]
136 msidata_$i\$column5 = annotation_df_8_sorted[,8]
137
138 ## extract columnnames from (last) annotation tabular (for QC plot names)
139 annotation_colnames = colnames(input_annotation)[-c(1,2)]
140
141 #end if
142
121 143
122 ################### preparation xy shifts ########################## 144 ################### preparation xy shifts ##########################
123 145
124 #if str( $combine_conditional.combine_method ) == 'xy_shifts': 146 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
125 147
133 colnames(pixelcoords_$i)[3] = "file_number" 155 colnames(pixelcoords_$i)[3] = "file_number"
134 156
135 ################### preparation automatic combination ########################## 157 ################### preparation automatic combination ##########################
136 158
137 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': 159 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
160
161 ## use name of Galaxy inputfile as combined sample annotation
138 names_vector = character() 162 names_vector = character()
139 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy 163 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))
140 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files 164 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files
141 { 165 {
142 if (is.null(levels(msidata_$i\$combined_sample))) 166 if (is.null(levels(msidata_$i\$combined_sample)))
143 { 167 {
144 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i))) 168 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
168 valid_dataset = append(valid_dataset, 192 valid_dataset = append(valid_dataset,
169 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0)) 193 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0))
170 194
171 #end for 195 #end for
172 196
173 ## extract columnnames from (last) annotation tabular (for QC plot names)
174 annotation_colnames = colnames(input_annotation)[-c(1,2)]
175 197
176 ###################### automatic combination ################################### 198 ###################### automatic combination ###################################
177 ################################################################################ 199 ################################################################################
178 200
179 #if str( $combine_conditional.combine_method ) == 'automatic_combine': 201 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
210 ## save as (.RData) 232 ## save as (.RData)
211 233
212 msidata = msidata_combined 234 msidata = msidata_combined
213 save(msidata, file="$msidata_combined") 235 save(msidata, file="$msidata_combined")
214 236
215
216 ################################## xy shifts ################################### 237 ################################## xy shifts ###################################
217 ################################################################################ 238 ################################################################################
218 239
219 #elif str( $combine_conditional.combine_method ) == 'xy_shifts': 240 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
220 print("xy_shifts") 241 print("xy_shifts")
221 242
222 ## find duplicated coordinates 243 ## in case user made mistake with xy shifts: find duplicated coordinates
223 all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#)) 244 all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#))
224 duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE) 245 duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE)
225 print(paste0("Number of removed duplicated coordinates: ", sum(duplicated_coordinates)/2)) 246 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)/2))
226 unique_coordinates = all_coordinates[!duplicated_coordinates,] 247 unique_coordinates = all_coordinates[!duplicated_coordinates,]
227 248
228 ## remove duplicated coordinates 249 ## remove duplicated coordinates
229 datasetlist = list() 250 datasetlist = list()
230 count = 1 251 count = 1
267 theme(legend.position="bottom",legend.direction="vertical")+ 288 theme(legend.position="bottom",legend.direction="vertical")+
268 guides(fill=guide_legend(ncol=5,byrow=TRUE)) 289 guides(fill=guide_legend(ncol=5,byrow=TRUE))
269 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) 290 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
270 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) 291 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
271 for(file_count in 1:nrow(coord_labels)) 292 for(file_count in 1:nrow(coord_labels))
272 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], 293 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
273 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} 294 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
274 print(combine_plot) 295 print(combine_plot)
275 296
276 297 #if str($annotation_cond.annotation_tabular) == 'annotation'
277 ## annotation plots 298
278 299 ## annotation plots
279 ## plot 1 300
280 301 ## plot 1
281 column1_df = cbind(coord(msidata), msidata\$column1) 302
282 colnames(column1_df)[3] = "column1" 303 column1_df = cbind(coord(msidata), msidata\$column1)
283 304 colnames(column1_df)[3] = "column1"
284 if (sum(is.na(column1_df[3])) < nrow(column1_df)){ 305
285 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+ 306 if (sum(is.na(column1_df[3])) < nrow(column1_df)){
286 geom_tile() + 307 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
287 coord_fixed()+ 308 geom_tile() +
288 ggtitle(paste0(annotation_colnames[1]))+ 309 coord_fixed()+
289 theme_bw()+ 310 ggtitle(paste0(annotation_colnames[1]))+
290 theme(text=element_text(family="ArialMT", face="bold", size=15))+ 311 theme_bw()+
291 theme(legend.position="bottom",legend.direction="vertical")+ 312 theme(text=element_text(family="ArialMT", face="bold", size=15))+
292 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[1])) 313 theme(legend.position="bottom",legend.direction="vertical")+
293 print(column1_plot)} 314 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[1]))
294 ##rename columnname for output tabular file 315 print(column1_plot)}
295 colnames(column1_df)[3] = annotation_colnames[1] 316 ##rename columnname for output tabular file
296 317 colnames(column1_df)[3] = annotation_colnames[1]
297 ## plot 2 318
298 column2_df = cbind(coord(msidata), msidata\$column2) 319 ## plot 2
299 colnames(column2_df)[3] = "column2" 320 column2_df = cbind(coord(msidata), msidata\$column2)
300 321 colnames(column2_df)[3] = "column2"
301 if (sum(is.na(column2_df[3])) < nrow(column2_df)){ 322
302 column2_plot = ggplot(column2_df, aes(x=x, y=y, fill=column2))+ 323 if (sum(is.na(column2_df[3])) < nrow(column2_df)){
303 geom_tile() + 324 column2_plot = ggplot(column2_df, aes(x=x, y=y, fill=column2))+
304 coord_fixed()+ 325 geom_tile() +
305 ggtitle(paste0(annotation_colnames[2]))+ 326 coord_fixed()+
306 theme_bw()+ 327 ggtitle(paste0(annotation_colnames[2]))+
307 theme(text=element_text(family="ArialMT", face="bold", size=15))+ 328 theme_bw()+
308 theme(legend.position="bottom",legend.direction="vertical")+ 329 theme(text=element_text(family="ArialMT", face="bold", size=15))+
309 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[2])) 330 theme(legend.position="bottom",legend.direction="vertical")+
310 print(column2_plot)} 331 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[2]))
311 ##rename columnname for output tabular file 332 print(column2_plot)}
312 colnames(column2_df)[3] = annotation_colnames[2] 333 ##rename columnname for output tabular file
313 334 colnames(column2_df)[3] = annotation_colnames[2]
314 ## plot 3 335
315 column3_df = cbind(coord(msidata), msidata\$column3) 336 ## plot 3
316 colnames(column3_df)[3] = "column3" 337 column3_df = cbind(coord(msidata), msidata\$column3)
317 if (sum(is.na(column3_df[3])) < nrow(column3_df)){ 338 colnames(column3_df)[3] = "column3"
318 column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+ 339 if (sum(is.na(column3_df[3])) < nrow(column3_df)){
319 geom_tile() + 340 column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+
320 coord_fixed()+ 341 geom_tile() +
321 ggtitle(paste0(annotation_colnames[3]))+ 342 coord_fixed()+
322 theme_bw()+ 343 ggtitle(paste0(annotation_colnames[3]))+
323 theme(text=element_text(family="ArialMT", face="bold", size=15))+ 344 theme_bw()+
324 theme(legend.position="bottom",legend.direction="vertical")+ 345 theme(text=element_text(family="ArialMT", face="bold", size=15))+
325 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[3])) 346 theme(legend.position="bottom",legend.direction="vertical")+
326 print(column3_plot)} 347 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[3]))
327 ##rename columnname for output tabular file 348 print(column3_plot)}
328 colnames(column3_df)[3] = annotation_colnames[3] 349 ##rename columnname for output tabular file
329 350 colnames(column3_df)[3] = annotation_colnames[3]
330 ## plot 4 351
331 column4_df = cbind(coord(msidata), msidata\$column4) 352 ## plot 4
332 colnames(column4_df)[3] = "column4" 353 column4_df = cbind(coord(msidata), msidata\$column4)
333 354 colnames(column4_df)[3] = "column4"
334 if (sum(is.na(column4_df[3])) < nrow(column4_df)){ 355
335 column4_plot = ggplot(column4_df, aes(x=x, y=y, fill=column4))+ 356 if (sum(is.na(column4_df[3])) < nrow(column4_df)){
336 geom_tile() + 357 column4_plot = ggplot(column4_df, aes(x=x, y=y, fill=column4))+
337 coord_fixed()+ 358 geom_tile() +
338 ggtitle(paste0(annotation_colnames[4]))+ 359 coord_fixed()+
339 theme_bw()+ 360 ggtitle(paste0(annotation_colnames[4]))+
340 theme(text=element_text(family="ArialMT", face="bold", size=15))+ 361 theme_bw()+
341 theme(legend.position="bottom",legend.direction="vertical")+ 362 theme(text=element_text(family="ArialMT", face="bold", size=15))+
342 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[4])) 363 theme(legend.position="bottom",legend.direction="vertical")+
343 print(column4_plot)} 364 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[4]))
344 ##rename columnname for output tabular file 365 print(column4_plot)}
345 colnames(column4_df)[3] = annotation_colnames[4] 366 ##rename columnname for output tabular file
346 367 colnames(column4_df)[3] = annotation_colnames[4]
347 ## plot5 368
348 369 ## plot5
349 column5_df = cbind(coord(msidata), msidata\$column5) 370
350 colnames(column5_df)[3] = "column5" 371 column5_df = cbind(coord(msidata), msidata\$column5)
351 if (sum(is.na(column5_df[3])) < nrow(column5_df)){ 372 colnames(column5_df)[3] = "column5"
352 column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+ 373 if (sum(is.na(column5_df[3])) < nrow(column5_df)){
353 geom_tile() + 374 column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+
354 coord_fixed()+ 375 geom_tile() +
355 ggtitle(paste0(annotation_colnames[5]))+ 376 coord_fixed()+
356 theme_bw()+ 377 ggtitle(paste0(annotation_colnames[5]))+
357 theme(text=element_text(family="ArialMT", face="bold", size=15))+ 378 theme_bw()+
358 theme(legend.position="bottom",legend.direction="vertical")+ 379 theme(text=element_text(family="ArialMT", face="bold", size=15))+
359 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[5])) 380 theme(legend.position="bottom",legend.direction="vertical")+
360 print(column5_plot)} 381 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[5]))
361 ##rename columnname for output tabular file 382 print(column5_plot)}
362 colnames(column5_df)[3] = annotation_colnames[5] 383 ##rename columnname for output tabular file
384 colnames(column5_df)[3] = annotation_colnames[5]
385
386 #end if
363 387
364 dev.off() 388 dev.off()
365 389
366 ##################### annotation tabular output ################################ 390 ##################### annotation tabular output ################################
367 391
368 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){ 392 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
369 annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df) 393
370 combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list) 394 #if str($annotation_cond.annotation_tabular) == 'no_annotation':
371 write.table(combined_annotations, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") 395 write.table(position_df, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
396
397 #else
398 annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df)
399 combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list)
400 write.table(combined_annotations, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
401
402 #end if
403
372 }else{ 404 }else{
373 print("No annotation tabular output because file has no features or pixels left") 405 print("No annotation tabular output because file has no features or pixels left")
374 } 406 }
375 407
376 ####################### optional matrix output ################################# 408 ####################### optional matrix output #################################
378 #if $output_matrix: 410 #if $output_matrix:
379 411
380 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){ 412 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
381 spectramatrix = spectra(msidata)[] 413 spectramatrix = spectra(msidata)[]
382 spectramatrix = cbind(mz(msidata),spectramatrix) 414 spectramatrix = cbind(mz(msidata),spectramatrix)
383 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix) 415 newmatrix = rbind(c("mz", names(pixels(msidata))), spectramatrix)
384 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t") 416 write.table(newmatrix, file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
385 }else{ 417 }else{
386 print("No intensity matrix output because file has no features or pixels left") 418 print("No intensity matrix output because file has no features or pixels left")
387 } 419 }
388 420
389 #end if 421 #end if
406 <option value="mz" >mz</option> 438 <option value="mz" >mz</option>
407 <option value="ppm" selected="True" >ppm</option> 439 <option value="ppm" selected="True" >ppm</option>
408 </param> 440 </param>
409 </when> 441 </when>
410 </conditional> 442 </conditional>
411 <param name="annotation_files" type="data" multiple="true" format="tabular" 443 <conditional name="annotation_cond">
412 label="Pixel annotations as tabular files, same number and order of files as input files" 444 <param name="annotation_tabular" type="select" label="Optional annotation of pixels with tabular files">
413 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"/> 445 <option value="no_annotation" selected="True">no annotation</option>
446 <option value="annotation">pixel annotations</option>
447 </param>
448 <when value="no_annotation"/>
449 <when value="annotation">
450 <param name="annotation_files" type="data" multiple="true" format="tabular"
451 label="Pixel annotations tabular files"
452 help="Same number and order of files as input files. 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"/>
453 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
454 </when>
455 </conditional>
414 <conditional name="combine_conditional"> 456 <conditional name="combine_conditional">
415 <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"> 457 <param name="combine_method" type="select" label="Way of combining multiple files">
416 <option value="automatic_combine" selected="True" >automatic combination</option> 458 <option value="automatic_combine" selected="True" >automatic combination</option>
417 <option value="xy_shifts">shift xy coordinates with a tabular file</option> 459 <option value="xy_shifts">shift xy coordinates with a tabular file</option>
418 </param> 460 </param>
419 <when value="automatic_combine"/> 461 <when value="automatic_combine"/>
420 <when value="xy_shifts"> 462 <when value="xy_shifts">
427 </conditional> 469 </conditional>
428 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/> 470 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
429 </inputs> 471 </inputs>
430 <outputs> 472 <outputs>
431 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/> 473 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/>
432 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/> 474 <data format="pdf" name="QC_overview" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/>
433 <data format="tabular" name="annotation_output" label="Annotation_tabular"/> 475 <data format="tabular" name="pixel_annotations" label="Combined_pixel_annotations"/>
434 <data format="tabular" name="matrixasoutput" label="Combined_matrix"> 476 <data format="tabular" name="intensity_matrix" label="Combined_matrix">
435 <filter>output_matrix</filter> 477 <filter>output_matrix</filter>
436 </data> 478 </data>
437 </outputs> 479 </outputs>
438 <tests> 480 <tests>
439 <test expect_num_outputs="4"> 481 <test expect_num_outputs="4">
440 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/> 482 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
441 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/> 483 <conditional name="annotation_cond">
484 <param name="annotation_tabular" value="annotation"/>
485 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/>
486 <param name="tabular_header" value="TRUE"/>
487 </conditional>
442 <param name="combine_method" value="xy_shifts"/> 488 <param name="combine_method" value="xy_shifts"/>
443 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/> 489 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
444 <param name="column_x" value="1"/> 490 <param name="column_x" value="1"/>
445 <param name="column_y" value="2"/> 491 <param name="column_y" value="2"/>
446 <param name="column_names" value="3"/> 492 <param name="column_names" value="3"/>
447 <param name="output_matrix" value="True"/> 493 <param name="output_matrix" value="True"/>
448 <output name="matrixasoutput" file="123_combined_matrix.tabular"/> 494 <output name="intensity_matrix" file="123_combined_matrix.tabular"/>
449 <output name="annotation_output" file="123_annotation_output.tabular"/> 495 <output name="pixel_annotations" file="123_annotation_output.tabular"/>
450 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" /> 496 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
451 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="2000"/> 497 <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size" delta="2000"/>
452 </test> 498 </test>
453 <test expect_num_outputs="4"> 499 <test expect_num_outputs="4">
454 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> 500 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
455 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/> 501 <conditional name="annotation_cond">
502 <param name="annotation_tabular" value="annotation"/>
503 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
504 <param name="tabular_header" value="TRUE"/>
505 </conditional>
456 <param name="combine_method" value="automatic_combine"/> 506 <param name="combine_method" value="automatic_combine"/>
457 <param name="output_matrix" value="True"/> 507 <param name="output_matrix" value="True"/>
458 <output name="matrixasoutput" file="12_combined_matrix.tabular"/> 508 <output name="intensity_matrix" file="12_combined_matrix.tabular"/>
459 <output name="annotation_output" file="12_annotation_output.tabular"/> 509 <output name="pixel_annotations" file="12_annotation_output.tabular"/>
460 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" /> 510 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
461 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="2000"/> 511 <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size" delta="2000"/>
462 </test> 512 </test>
463 <test expect_num_outputs="3"> 513 <test expect_num_outputs="3">
464 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/> 514 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
465 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/> 515 <conditional name="annotation_cond">
516 <param name="annotation_tabular" value="annotation"/>
517 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
518 <param name="tabular_header" value="TRUE"/>
519 </conditional>
466 <param name="combine_method" value="automatic_combine"/> 520 <param name="combine_method" value="automatic_combine"/>
467 <param name="output_matrix" value="False"/> 521 <param name="output_matrix" value="False"/>
468 <output name="annotation_output" file="112_annotation_output.tabular"/> 522 <output name="pixel_annotations" file="112_annotation_output.tabular"/>
469 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" /> 523 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
470 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="2000"/> 524 <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size" delta="2000"/>
525 </test>
526 <test expect_num_outputs="3">
527 <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>
528 <conditional name="annotation_cond">
529 <param name="annotation_tabular" value="no_annotation"/>
530 </conditional>
531 <param name="combine_method" value="automatic_combine"/>
532 <param name="output_matrix" value="False"/>
533 <output name="pixel_annotations" file="2123_annotation_output.tabular"/>
534 <output name="msidata_combined" file="2123_auto_combined.RData" compare="sim_size" />
535 <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size" delta="2000"/>
471 </test> 536 </test>
472 </tests> 537 </tests>
473 <help> 538 <help>
474 <![CDATA[ 539 <![CDATA[
475 540