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comparison filtering.xml @ 6:97fdb0ce4dd3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
author galaxyp
date Wed, 25 Mar 2020 09:24:18 +0000
parents b045ba419ac6
children 5aaea231da6b
comparison
equal deleted inserted replaced
5:44dfff9c268f 6:97fdb0ce4dd3
1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.3"> 1 <tool id="cardinal_filtering" name="MSI filtering" version="2.4.0.0">
2 <description>tool for filtering mass spectrometry imaging data</description> 2 <description>tool for filtering mass spectrometry imaging data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <requirements>
7 <requirement type="package" version="2.4.0">bioconductor-cardinal</requirement>
8 <requirement type="package" version="3.6.1">r-base</requirement>
7 <requirement type="package" version="2.3">r-gridextra</requirement> 9 <requirement type="package" version="2.3">r-gridextra</requirement>
8 <requirement type="package" version="3.0">r-ggplot2</requirement> 10 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
9 </expand> 11 </requirements>
10 <expand macro="print_version"/> 12 <expand macro="print_version"/>
11 <command detect_errors="exit_code"> 13 <command detect_errors="exit_code">
12 <![CDATA[ 14 <![CDATA[
13 15
14 @INPUT_LINKING@ 16 @INPUT_LINKING@
15 cat '${MSI_subsetting}' && 17 cat '${MSI_subsetting}' &&
16 Rscript '${MSI_subsetting}' && 18 Rscript '${MSI_subsetting}' &&
17 19 mkdir $outfile_imzml.files_path &&
18 #if str($imzml_output) == "imzml_format": 20 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
19 mkdir $outfile_imzml.files_path && 21 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
20 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
21 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
22 #end if
23 echo "imzML file:" > $outfile_imzml && 22 echo "imzML file:" > $outfile_imzml &&
24 ls -l "$outfile_imzml.files_path" >> $outfile_imzml 23 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
25 ]]> 24 ]]>
26 </command> 25 </command>
27 26
35 34
36 library(Cardinal) 35 library(Cardinal)
37 library(ggplot2) 36 library(ggplot2)
38 library(gridExtra) 37 library(gridExtra)
39 38
40 @READING_MSIDATA@ 39
40
41 ## function to read RData files independent of filename
42 loadRData <- function(fileName){
43 load(fileName)
44 get(ls()[ls() != "fileName"])
45 }
46
47 #if $infile.ext == 'imzml'
48 #if str($processed_cond.processed_file) == "processed":
49 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
50 centroided(msidata) = $centroids
51 #else
52 msidata <- readImzML('infile', attach.only=TRUE)
53 centroided(msidata) = $centroids
54 #end if
55 #elif $infile.ext == 'analyze75'
56 msidata = readAnalyze('infile', attach.only=TRUE)
57 centroided(msidata) = $centroids
58 #else
59 msidata = loadRData('infile.RData')
60 msidata = as(msidata, "MSImagingExperiment")
61 #end if
41 62
42 63
43 ########################### QC numbers ######################## 64 ########################### QC numbers ########################
44 65
45 ## Number of features (m/z) 66 ## Number of features (m/z)
46 maxfeatures = length(features(msidata)) 67 maxfeatures = nrow(msidata)
47 ## Range m/z 68 ## Range m/z
48 minmz = round(min(mz(msidata)), digits=2) 69 minmz = round(min(mz(msidata)), digits=2)
49 maxmz = round(max(mz(msidata)), digits=2) 70 maxmz = round(max(mz(msidata)), digits=2)
50 ## Number of spectra (pixels) 71 ## Number of spectra (pixels)
51 pixelcount = length(pixels(msidata)) 72 pixelcount = ncol(msidata)
52 ## Range x coordinates 73 ## Range x coordinates
53 minimumx = min(coord(msidata)[,1]) 74 minimumx = min(coord(msidata)\$x)
54 maximumx = max(coord(msidata)[,1]) 75 maximumx = max(coord(msidata)\$x)
55 ## Range y coordinates 76 ## Range y coordinates
56 minimumy = min(coord(msidata)[,2]) 77 minimumy = min(coord(msidata)\$y)
57 maximumy = max(coord(msidata)[,2]) 78 maximumy = max(coord(msidata)\$y)
58 ## Store features for QC plot 79 ## Store features for QC plot
59 featuresinfile = mz(msidata) 80 featuresinfile = mz(msidata)
60 81
61 all_df = cbind(coord(msidata)[,1:2], rep("removed pixels", times=ncol(msidata))) 82 all_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, rep("removed pixels", times=ncol(msidata)))
62 colnames(all_df)[3] = "annotation" 83 colnames(all_df) = c("x", "y", "annotation")
63 84
64 ## Next steps will only run if there are more than 0 pixels/features in the file 85 ## Next steps will only run if there are more than 0 pixels/features in the file
65 86
66 if (ncol(msidata)>0 & nrow(msidata) >0) 87 if (ncol(msidata)>0 & nrow(msidata) >0)
67 { 88 {
90 } 111 }
91 }, 112 },
92 error=function(cond) { 113 error=function(cond) {
93 ## in case all coordinates were outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data 114 ## in case all coordinates were outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data
94 message("Error during pixel filtering") 115 message("Error during pixel filtering")
95 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool)") 116 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool")
96 stop(call.=FALSE) 117 stop(call.=FALSE)
97 } 118 }
98 ) 119 )
99 120
100 ## QC values: 121 ## QC values:
140 161
141 ############################# QC data ##################################### 162 ############################# QC data #####################################
142 163
143 ## dataframe for QC of pixel distribution 164 ## dataframe for QC of pixel distribution
144 165
145 remaining_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata))) 166 remaining_df = data.frame(as.numeric(coord(msidata)\$x), as.numeric(coord(msidata)\$y), rep("remaining pixels", times=ncol(msidata)))
146 colnames(remaining_df)[3] = "annotation" 167 colnames(remaining_df) = c("x", "y", "annotation")
147 position_df = rbind(all_df, remaining_df) 168 position_df = rbind(all_df, remaining_df)
148 position_df[row.names(unique(position_df[,c("x", "y")])),] 169 position_df[row.names(unique(position_df[,c("x", "y")])),]
149 position_df\$annotation = factor(position_df\$annotation) 170 position_df\$annotation = factor(position_df\$annotation)
150 gc() 171 gc()
151 172
152 }else{ 173 }else{
203 }, 224 },
204 error=function(cond) { 225 error=function(cond) {
205 ## in case all provided m/z values were outside the m/z range 226 ## in case all provided m/z values were outside the m/z range
206 ## tool is stopped to avoid continuing with wrong data 227 ## tool is stopped to avoid continuing with wrong data
207 message("Error during m/z filtering") 228 message("Error during m/z filtering")
208 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)") 229 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset (this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)")
209 stop(call.=FALSE) 230 stop(call.=FALSE)
210 } 231 }
211 ) 232 )
212 233
213 234
260 #if str($features_cond.units_removal) == "ppm": 281 #if str($features_cond.units_removal) == "ppm":
261 plusminus = masses * $features_cond.removal_plusminus/1000000 282 plusminus = masses * $features_cond.removal_plusminus/1000000
262 #end if 283 #end if
263 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus)) 284 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
264 mass_to_remove = append(mass_to_remove, current_mass)} 285 mass_to_remove = append(mass_to_remove, current_mass)}
265 msidata= msidata[-mass_to_remove, ] 286 mass_to_keep = setdiff(1:nrow(msidata),mass_to_remove)
266 validmz = numberfeatures - nrow(msidata) 287
288 msidata= msidata[mass_to_keep, ]
289 validmz = maxfeatures - nrow(msidata)
290
267 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data 291 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
268 if (nrow(msidata) == 0) 292 if (nrow(msidata) == 0)
269 { 293 {
270 stop(call.=FALSE) 294 stop(call.=FALSE)
271 } 295 }
276 } 300 }
277 ) 301 )
278 302
279 303
280 304
281
282 ######################## No m/z filtering ############################## 305 ######################## No m/z filtering ##############################
283 306
284 #elif str($features_cond.features_filtering) == "none": 307 #elif str($features_cond.features_filtering) == "none":
285 308
286 print("no feature filtering") 309 print("no feature filtering")
302 gc() 325 gc()
303 326
304 #################### QC numbers ####################### 327 #################### QC numbers #######################
305 328
306 ## Number of features (m/z) 329 ## Number of features (m/z)
307 maxfeatures2 = length(features(msidata)) 330 maxfeatures2 = nrow(msidata)
308 ## Range m/z 331 ## Range m/z
309 minmz2 = round(min(mz(msidata)), digits=2) 332 minmz2 = round(min(mz(msidata)), digits=2)
310 maxmz2 = round(max(mz(msidata)), digits=2) 333 maxmz2 = round(max(mz(msidata)), digits=2)
311 ## Number of spectra (pixels) 334 ## Number of spectra (pixels)
312 pixelcount2 = length(pixels(msidata)) 335 pixelcount2 = ncol(msidata)
313 ## Range x coordinates 336 ## Range x coordinates
314 minimumx2 = min(coord(msidata)[,1]) 337 minimumx2 = min(coord(msidata)\$x)
315 maximumx2 = max(coord(msidata)[,1]) 338 maximumx2 = max(coord(msidata)\$x)
316 ## Range y coordinates 339 ## Range y coordinates
317 minimumy2 = min(coord(msidata)[,2]) 340 minimumy2 = min(coord(msidata)\$y)
318 maximumy2 = max(coord(msidata)[,2]) 341 maximumy2 = max(coord(msidata)\$y)
319 342
320 properties = c("Number of m/z features", 343 properties = c("Number of m/z features",
321 "Range of m/z values", 344 "Range of m/z values",
322 "Number of pixels", 345 "Number of pixels",
323 "Range of x coordinates", 346 "Range of x coordinates",
345 368
346 ########################### PDF QC and MSI output ########################### 369 ########################### PDF QC and MSI output ###########################
347 370
348 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12) 371 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
349 plot(0,type='n',axes=FALSE,ann=FALSE) 372 plot(0,type='n',axes=FALSE,ann=FALSE)
350 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name")) 373 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.element_identifier"))
351 grid.table(property_df, rows= NULL) 374 grid.table(property_df, rows= NULL)
352 375
353 ## QC report only when pixels/features are left 376 ## QC report only when pixels/features are left
354 if (ncol(msidata)>0 & nrow(msidata) >0) 377 if (ncol(msidata)>0 & nrow(msidata) >0)
355 { 378 {
360 geom_tile(height = 1, width=1)+ 383 geom_tile(height = 1, width=1)+
361 coord_fixed()+ 384 coord_fixed()+
362 ggtitle("Spatial orientation of filtered pixels")+ 385 ggtitle("Spatial orientation of filtered pixels")+
363 theme_bw()+ 386 theme_bw()+
364 theme(plot.title = element_text(hjust = 0.5))+ 387 theme(plot.title = element_text(hjust = 0.5))+
365 theme(legend.position="bottom",legend.direction="vertical") 388 theme(legend.position="bottom",legend.direction="vertical")+
389 guides(fill=guide_legend(ncol=5,byrow=TRUE))
366 print(pixel_image) 390 print(pixel_image)
367 391
368 ### plot features which are removed 392
369 hist(mz(msidata), xlab="m/z", main="Kept m/z values") 393 ### visual mz feature control
370 #if str($features_cond.features_filtering) == "none": 394
371 print("no difference histogram as no m/z filtering took place") 395 kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata)))
372 #else: 396 colnames(kept_df) = c("mz", "legend")
373 if (isTRUE(all.equal(featuresinfile, mz(msidata)))){ 397
374 print("No difference in m/z values before and after filtering, no histogram drawn") 398 mz_removed = setdiff(featuresinfile, mz(msidata))
375 }else{ 399 removed_df = data.frame(mz_removed, rep("removed m/z", length(mz_removed)))
376 hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")} 400 colnames(removed_df) = c("mz", "legend")
377 #end if 401 histogram_df = rbind(removed_df,kept_df)
402
403 histogram_mz= ggplot(histogram_df, aes(x=mz, fill=legend)) +
404 geom_histogram()+ theme_bw()+
405 theme(plot.title = element_text(hjust = 0.5))+
406 theme(legend.position="bottom",legend.direction="vertical")+
407 labs(title="Overview of filtered m/z", x="m/z", y = "count") +
408 guides(fill=guide_legend(ncol=5,byrow=TRUE))
409 print(histogram_mz)
410
378 411
379 dev.off() 412 dev.off()
380 413
381 ## save msidata as imzML file, will only work if there is at least 1 m/z left 414 ## save msidata as imzML file, will only work if there is at least 1 m/z left
382 415
383 #if str($imzml_output) == "imzml_format":
384 if (maxfeatures2 > 0){ 416 if (maxfeatures2 > 0){
385 ## make sure that coordinates are integers 417 ## make sure that coordinates are integers
386 coord(msidata)\$y = as.integer(coord(msidata)\$y) 418 coord(msidata)\$y = as.integer(coord(msidata)\$y)
387 coord(msidata)\$x = as.integer(coord(msidata)\$x) 419 coord(msidata)\$x = as.integer(coord(msidata)\$x)
388 writeImzML(msidata, "out")} 420 writeImzML(msidata, "out")}
389 #elif str($imzml_output) == "rdata_format":
390 ## save msidata as Rfile
391 iData(msidata) = iData(msidata)[]
392 save(msidata, file="$outfile_rdata")
393 #end if
394 421
395 422
396 }else{ 423 }else{
397 print("Inputfile or filtered file has no intensities > 0") 424 print("Inputfile or filtered file has no intensities > 0")
398 dev.off() 425 dev.off()
446 <option value="ppm" selected="True">ppm</option> 473 <option value="ppm" selected="True">ppm</option>
447 <option value="Da">Da</option> 474 <option value="Da">Da</option>
448 </param> 475 </param>
449 </when> 476 </when>
450 </conditional> 477 </conditional>
451 <param name="imzml_output" type="select" display = "radio" optional = "False"
452 label="Output format" help= "Choose the output format">
453 <option value="imzml_format" >imzML</option>
454 <option value="rdata_format" selected="True" >RData</option>
455 </param>
456 </inputs> 478 </inputs>
457 479
458 <outputs> 480 <outputs>
459 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"> 481 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
460 <filter>imzml_output =='imzml_format'</filter>
461 </data>
462 <data format="rdata" name="outfile_rdata" label="${tool.name} on ${on_string}: RData">
463 <filter>imzml_output == 'rdata_format'</filter>
464 </data>
465 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/> 482 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/>
466 </outputs> 483 </outputs>
467 <tests> 484 <tests>
468 <test> 485 <test>
469 <expand macro="infile_imzml"/> 486 <expand macro="infile_imzml"/>
473 <param name="min_y_range" value="2"/> 490 <param name="min_y_range" value="2"/>
474 <param name="max_y_range" value="2"/> 491 <param name="max_y_range" value="2"/>
475 <param name="features_filtering" value="features_range"/> 492 <param name="features_filtering" value="features_range"/>
476 <param name="min_mz" value="350"/> 493 <param name="min_mz" value="350"/>
477 <param name="max_mz" value="500"/> 494 <param name="max_mz" value="500"/>
478 <param name="imzml_output" value="imzml_format"/>
479 <output name="QC_overview" file="imzml_filtered3.pdf" compare="sim_size"/> 495 <output name="QC_overview" file="imzml_filtered3.pdf" compare="sim_size"/>
480 <output name="outfile_imzml" ftype="imzml" file="out3.imzml.txt" compare="sim_size"> 496 <output name="outfile_imzml" ftype="imzml" file="out3.imzml.txt" compare="sim_size">
481 <extra_files type="file" file="out3.imzml" name="imzml" lines_diff="4"/> 497 <extra_files type="file" file="out3.imzml" name="imzml" lines_diff="6"/>
482 <extra_files type="file" file="out3.ibd" name="ibd" compare="sim_size"/> 498 <extra_files type="file" file="out3.ibd" name="ibd" compare="sim_size"/>
483 </output> 499 </output>
484 </test> 500 </test>
485 <test> 501 <test>
486 <expand macro="infile_imzml"/> 502 <expand macro="infile_imzml"/>
487 <param name="pixel_filtering" value="two_columns"/> 503 <param name="pixel_filtering" value="two_columns"/>
488 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/> 504 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
489 <param name="column_x" value="1"/> 505 <param name="column_x" value="1"/>
490 <param name="column_y" value="3"/> 506 <param name="column_y" value="3"/>
491 <param name="imzml_output" value="imzml_format"/>
492 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/> 507 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/>
493 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size"> 508 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size">
494 <extra_files type="file" file="out4.imzml" name="imzml" lines_diff="4"/> 509 <extra_files type="file" file="out4.imzml" name="imzml" lines_diff="6"/>
495 <extra_files type="file" file="out4.ibd" name="ibd" compare="sim_size"/> 510 <extra_files type="file" file="out4.ibd" name="ibd" compare="sim_size"/>
496 </output> 511 </output>
497 </test> 512 </test>
498 <test> 513 <test>
499 <expand macro="infile_imzml"/> 514 <expand macro="infile_imzml"/>
504 <param name="max_y_range" value="20"/> 519 <param name="max_y_range" value="20"/>
505 <param name="features_filtering" value="features_list"/> 520 <param name="features_filtering" value="features_list"/>
506 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/> 521 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
507 <param name="feature_column" value="1"/> 522 <param name="feature_column" value="1"/>
508 <param name="feature_header" value="0"/> 523 <param name="feature_header" value="0"/>
509 <param name="imzml_output" value="imzml_format"/>
510 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/> 524 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/>
511 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size"> 525 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size">
512 <extra_files type="file" file="out5.imzml" name="imzml" lines_diff="4"/> 526 <extra_files type="file" file="out5.imzml" name="imzml" lines_diff="6"/>
513 <extra_files type="file" file="out5.ibd" name="ibd" compare="sim_size"/> 527 <extra_files type="file" file="out5.ibd" name="ibd" compare="sim_size"/>
514 </output> 528 </output>
515 </test> 529 </test>
516 <test> 530 <test>
517 <expand macro="infile_analyze75"/> 531 <expand macro="infile_analyze75"/>
518 <param name="imzml_output" value="imzml_format"/>
519 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/> 532 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/>
520 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size"> 533 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size">
521 <extra_files type="file" file="out6.imzml" name="imzml" lines_diff="4"/> 534 <extra_files type="file" file="out6.imzml" name="imzml" lines_diff="6"/>
522 <extra_files type="file" file="out6.ibd" name="ibd" compare="sim_size"/> 535 <extra_files type="file" file="out6.ibd" name="ibd" compare="sim_size"/>
523 </output> 536 </output>
524 </test> 537 </test>
525 <test> 538 <test>
526 <param name="infile" value="preprocessed.RData" ftype="rdata"/> 539 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
527 <conditional name="outputs">
528 <param name="outputs_select" value="no_quality_control"/>
529 </conditional>
530 <param name="imzml_output" value="imzml_format"/>
531 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" /> 540 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" />
532 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size"> 541 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size">
533 <extra_files type="file" file="out7.imzml" name="imzml" lines_diff="4"/> 542 <extra_files type="file" file="out7.imzml" name="imzml" lines_diff="6"/>
534 <extra_files type="file" file="out7.ibd" name="ibd" compare="sim_size"/> 543 <extra_files type="file" file="out7.ibd" name="ibd" compare="sim_size"/>
544 </output>
545 </test>
546 <test>
547 <expand macro="processed_infile_imzml"/>
548 <conditional name="processed_cond">
549 <param name="processed_file" value="processed"/>
550 <param name="accuracy" value="100"/>
551 <param name="units" value="ppm"/>
552 </conditional>
553 <param name="pixel_filtering" value="two_columns"/>
554 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
555 <param name="column_x" value="1"/>
556 <param name="column_y" value="3"/>
557 <param name="features_filtering" value="remove_features"/>
558 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
559 <param name="feature_column" value="1"/>
560 <param name="feature_header" value="0"/>
561 <param name="removal_plusminus" value="100"/>
562 <param name="units_removal" value="ppm"/>
563 <output name="QC_overview" file="imzml_filtered8.pdf" compare="sim_size"/>
564 <output name="outfile_imzml" ftype="imzml" file="out8.imzml.txt" compare="sim_size">
565 <extra_files type="file" file="out8.imzml" name="imzml" lines_diff="6"/>
566 <extra_files type="file" file="out8.ibd" name="ibd" compare="sim_size"/>
535 </output> 567 </output>
536 </test> 568 </test>
537 </tests> 569 </tests>
538 <help> 570 <help>
539 <![CDATA[ 571 <![CDATA[
579 - An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset 611 - An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset
580 612
581 613
582 - m/z feature removing: 614 - m/z feature removing:
583 615
584 - Perturbing m/z features such as matrix contaminants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed 616 - Perturbing m/z features such as matrix contaminants, tryptic peptides and internal calibrants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed
585 617
586 618
587 **Tips** 619 **Tips**
588 620
589 - m/z feautre filtering with a tabular file: 621 - m/z feautre filtering with a tabular file:
596 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from 'tabular' - datatype can be changed by pressing the pen button of the dataset (edit attributes) 628 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from 'tabular' - datatype can be changed by pressing the pen button of the dataset (edit attributes)
597 629
598 630
599 **Output** 631 **Output**
600 632
601 - MSI data as imzML file or .RData (can be read with the Cardinal package in R) 633 - MSI data as (continuous) imzML file
602 - pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z 634 - pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z
603 635
604 636
605 ]]> 637 ]]>
606 </help> 638 </help>