Mercurial > repos > galaxyp > maldi_quant_preprocessing
annotate maldi_quant_preprocessing.xml @ 3:71411ac28268 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
author | galaxyp |
---|---|
date | Fri, 15 Feb 2019 10:26:00 -0500 (2019-02-15) |
parents | e754c2b545a9 |
children | 60ee8c592b13 |
rev | line source |
---|---|
3
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.3"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
2 <description> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
3 Preprocessing of mass-spectrometry imaging data |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
4 </description> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
5 <macros> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
6 <import>maldi_macros.xml</import> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
7 </macros> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
8 <expand macro="requirements"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
9 <command detect_errors="exit_code"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
10 <![CDATA[ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
11 cat '${maldi_quant_preprocessing}' && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
12 #if $infile.ext == 'imzml' |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
13 cp '${infile.extra_files_path}/imzml' infile.imzML && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
14 cp '${infile.extra_files_path}/ibd' infile.ibd && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
15 #elif $infile.ext == 'analyze75' |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
16 cp '${infile.extra_files_path}/hdr' infile.hdr && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
17 cp '${infile.extra_files_path}/img' infile.img && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
18 cp '${infile.extra_files_path}/t2m' infile.t2m && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
19 du infile.hdr && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
20 du infile.img && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
21 du -s -B1 infile.hdr && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
22 #else |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
23 ln -s $infile infile.RData && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
24 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
25 Rscript "${maldi_quant_preprocessing}" && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
26 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
27 mkdir $outfile_imzml.files_path && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
28 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
29 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
30 echo "imzML file:" > $outfile_imzml && |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
31 ls -l "$outfile_imzml.files_path" >> $outfile_imzml |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
32 ]]> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
33 </command> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
34 <configfiles> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
35 <configfile name="maldi_quant_preprocessing"><![CDATA[ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
36 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
37 @R_IMPORTS@ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
38 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
39 #if $restriction_conditional.restriction == 'restrict': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
40 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
41 print('Reading mask region') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
42 ## Import imzML file |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
43 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
44 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2] |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
45 coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)] |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
46 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
47 maldi_data = importImzMl('infile.imzML', |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
48 coordinates = coordinate_matrix) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
49 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2]) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
50 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
51 #else: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
52 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
53 print('Reading entire file') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
54 #if $infile.ext == 'imzml' |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
55 ## Import imzML file |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
56 maldi_data = import( 'infile.imzML', type="imzML" ) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
57 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
58 #elif $infile.ext == 'analyze75' |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
59 ## Import analyze7.5 file |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
60 maldi_data = importAnalyze( 'infile.hdr' ) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
61 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
62 #else |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
63 loadRData <- function(fileName){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
64 ##loads an RData file, and returns it |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
65 load(fileName) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
66 get(ls()[ls() != "fileName"]) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
67 } |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
68 msidata = loadRData('infile.RData') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
69 ## save coordinates |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
70 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2]) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
71 ## save mz values |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
72 cardinal_mzs = Cardinal::mz(msidata) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
73 ## create MALDIquant MassSpectrum object, order of pixels in iData is same as in coord(msidata): |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
74 maldi_data = list() |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
75 for(number_spectra in 1:ncol(msidata)){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
76 maldi_data[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra]) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
77 } |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
78 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
79 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
80 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
81 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
82 ## Quality control plots during preprocessing |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
83 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
84 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
85 plot(0,type='n',axes=FALSE,ann=FALSE) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
86 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
87 ## if no filename is given, name of file in Galaxy history is used |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
88 #set $filename = $infile.display_name |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
89 title(main=paste("$filename")) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
90 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
91 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
92 #################### Preprocessing methods ##################################### |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
93 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
94 ## QC plot on input file |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
95 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
96 plot(avgSpectra, main="Average spectrum for input file") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
97 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
98 pixel_number = length(maldi_data) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
99 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
100 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
101 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
102 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
103 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
104 inputdata = c(minmz, maxmz,number_features,mean_features,medint, pixel_number) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
105 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint, pixel_number)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
106 vectorofactions = "inputdata" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
107 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
108 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
109 #for $method in $methods: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
110 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
111 #if str( $method.methods_conditional.method ) == 'Transformation': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
112 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
113 print('transforming') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
114 ##transformation |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
115 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
116 ## QC plot and numbers |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
117 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
118 plot(avgSpectra, main="Average spectrum after transformation") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
119 pixel_number = length(maldi_data) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
120 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
121 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
122 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
123 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
124 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
125 transformed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
126 QC_numbers= cbind(QC_numbers, transformed) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
127 vectorofactions = append(vectorofactions, "transformed") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
128 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
129 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
130 #elif str( $method.methods_conditional.method ) == 'Smoothing': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
131 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
132 print('smoothing') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
133 ##smoothing |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
134 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
135 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
136 print('SavitzkyGolay') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
137 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
138 maldi_data = smoothIntensity(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
139 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
140 halfWindowSize=$method.methods_conditional.halfWindowSize) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
141 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
142 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
143 print('MovingAverage') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
144 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
145 maldi_data = smoothIntensity(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
146 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
147 halfWindowSize=$method.methods_conditional.halfWindowSize) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
148 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
149 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
150 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
151 ## QC plot and numbers |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
152 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
153 plot(avgSpectra, main="Average spectrum after smoothing", sub="") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
154 pixel_number = length(maldi_data) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
155 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
156 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
157 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
158 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
159 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
160 smoothed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
161 QC_numbers= cbind(QC_numbers, smoothed) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
162 vectorofactions = append(vectorofactions, "smoothed") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
163 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
164 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
165 #elif str( $method.methods_conditional.method ) == 'Baseline': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
166 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
167 print('baseline removing') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
168 ## Remove baseline |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
169 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
170 ## Choose random spectra for QC plots |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
171 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
172 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
173 #if str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'SNIP': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
174 print('SNIP') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
175 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
176 par(mfrow = c(2,2)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
177 for (random_sample in random_spectra){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
178 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]], |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
179 method="SNIP", iterations=$method.methods_conditional.methods_for_baseline.iterations) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
180 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
181 lines(maldi_data_baseline, col="blue", lwd=2)} |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
182 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
183 maldi_data = removeBaseline(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
184 method="SNIP", |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
185 iterations=$method.methods_conditional.methods_for_baseline.iterations) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
186 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
187 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
188 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'TopHat': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
189 print('TopHat') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
190 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
191 par(mfrow = c(2,2)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
192 for (random_sample in random_spectra){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
193 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]], |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
194 method="TopHat", halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
195 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
196 lines(maldi_data_baseline, col="blue", lwd=2)} |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
197 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
198 maldi_data = removeBaseline(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
199 method="TopHat", |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
200 halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
201 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
202 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
203 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'ConvexHull': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
204 print('ConvexHull') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
205 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
206 par(mfrow = c(2,2)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
207 for (random_sample in random_spectra){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
208 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]], |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
209 method="ConvexHull") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
210 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
211 lines(maldi_data_baseline, col="blue", lwd=2)} |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
212 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
213 maldi_data = removeBaseline(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
214 method="ConvexHull") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
215 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
216 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
217 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'median': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
218 print('median') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
219 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
220 par(mfrow = c(2,2)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
221 for (random_sample in random_spectra){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
222 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]], |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
223 method="median", halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
224 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
225 lines(maldi_data_baseline, col="blue", lwd=2)} |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
226 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
227 maldi_data = removeBaseline(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
228 method="median", |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
229 halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
230 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
231 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
232 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
233 ## QC plot and numbers |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
234 par(mfrow = c(1,1)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
235 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
236 plot(avgSpectra, main="Average spectrum after baseline removal") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
237 pixel_number = length(maldi_data) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
238 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
239 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
240 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
241 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
242 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
243 baseline_removed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
244 QC_numbers= cbind(QC_numbers, baseline_removed) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
245 vectorofactions = append(vectorofactions, "bl_removed") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
246 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
247 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
248 #elif str( $method.methods_conditional.method ) == 'Calibrate': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
249 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
250 print('calibrate') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
251 ##calibrate |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
252 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
253 #if str($method.methods_conditional.cond_calibration_range) == "yes": |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
254 ## calibrate only given m/z range |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
255 maldi_data = calibrateIntensity(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
256 method="$method.methods_conditional.calibrate_method", |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
257 range=c($method.methods_conditional.cond_calibration_range.mass_start, $method.methods_conditional.cond_calibration_range.mass_end)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
258 #else: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
259 maldi_data = calibrateIntensity(maldi_data, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
260 method="$method.methods_conditional.calibrate_method") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
261 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
262 ## QC plot and numbers |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
263 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
264 plot(avgSpectra, main="Average spectrum after normalization") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
265 pixel_number = length(maldi_data) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
266 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
267 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
268 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
269 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
270 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
271 intensity_calibrated = c(minmz, maxmz,number_features,mean_features,medint,pixel_number) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
272 QC_numbers= cbind(QC_numbers, intensity_calibrated) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
273 vectorofactions = append(vectorofactions, "calibrated") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
274 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
275 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
276 #elif str( $method.methods_conditional.method ) == 'Align': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
277 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
278 print('align') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
279 ##align spectra with 3 separate functions |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
280 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
281 ## create reference if needed |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
282 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
283 ## 1) detect peaks: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
284 peaks <- detectPeaks(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
285 method="$method.methods_conditional.peak_method", SNR=$method.methods_conditional.snr) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
286 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
287 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
288 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
289 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
290 ## 2) calculate warping: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
291 warping_function <- determineWarpingFunctions(peaks, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
292 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method", |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
293 allowNoMatches=$method.methods_conditional.allow_nomatch, minFrequency = $method.methods_conditional.reference_for_alignment.min_frequency) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
294 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
295 ## 3) warp spectra: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
296 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
297 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
298 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
299 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
300 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
301 ## create reference mass_vector from tabular file |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
302 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = $method.methods_conditional.reference_for_alignment.reference_header, stringsAsFactors = FALSE)[,$method.methods_conditional.reference_for_alignment.mz_column] |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
303 int_vector = rep(1,length(mass_vector)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
304 mass_list = createMassPeaks(mass_vector, int_vector) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
305 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
306 #if str($method.methods_conditional.reference_for_alignment.separate_alignment) == "FALSE" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
307 print('default alignment') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
308 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
309 ## 2) calculate warping: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
310 warping_function <- determineWarpingFunctions(peaks, |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
311 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method", |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
312 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
313 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
314 ## 3) warp spectra: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
315 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
316 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
317 #elif str($method.methods_conditional.reference_for_alignment.separate_alignment) == "TRUE" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
318 print('spectra wise alignment') |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
319 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
320 maldi_data_new_list =list() |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
321 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
322 for (pixelnb in 1:length(peaks)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
323 { |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
324 ## 2) calculate warping: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
325 warping_function <- determineWarpingFunctions(peaks[[pixelnb]], |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
326 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method", |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
327 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
328 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
329 ## 3) warp spectra: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
330 maldi_data_new = warpMassSpectra(list(maldi_data[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
331 maldi_data_new_list = c(maldi_data_new_list, maldi_data_new) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
332 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
333 } |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
334 maldi_data = maldi_data_new_list |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
335 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
336 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
337 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
338 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
339 #if $method.methods_conditional.remove_empty: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
340 print(paste(length(findEmptyMassObjects(maldi_data)), " empty spectra were removed", sep=" ")) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
341 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
342 ## only if there are empty spectra to remove |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
343 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
344 if (length(findEmptyMassObjects(maldi_data))>0) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
345 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
346 { |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
347 #if $infile.ext == 'rdata' |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
348 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
349 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
350 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
351 maldi_data = removeEmptyMassObjects(maldi_data) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
352 } |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
353 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
354 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
355 ## QC plot |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
356 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
357 if (length(maldi_data)>0){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
358 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
359 plot(avgSpectra, main="Average spectrum after alignment") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
360 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
361 }else{print("All spectra are empty")} |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
362 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
363 pixel_number = length(maldi_data) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
364 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
365 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
366 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
367 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
368 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
369 spectra_aligned = c(minmz, maxmz,number_features,mean_features, medint,pixel_number) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
370 QC_numbers= cbind(QC_numbers, spectra_aligned) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
371 vectorofactions = append(vectorofactions, "aligned") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
372 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
373 #elif str( $method.methods_conditional.method ) == 'skip_preprocessing': |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
374 ##for now as option to filter large files |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
375 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
376 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
377 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
378 #end for |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
379 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
380 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# peaks (int.>0)", "median\nintensity", "pixel\nnumber") |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
381 colnames(QC_numbers) = vectorofactions |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
382 plot(0,type='n',axes=FALSE,ann=FALSE) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
383 grid.table(t(QC_numbers)) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
384 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
385 dev.off() |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
386 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
387 ## export imzML file |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
388 if (length(maldi_data)>0){ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
389 #if $infile.ext == 'rdata' |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
390 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
391 #else |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
392 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
393 #end if |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
394 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
395 }else{"All spectra are empty, outputfiles will be empty,too."} |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
396 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
397 ]]> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
398 </configfile> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
399 </configfiles> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
400 <inputs> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
401 <param name="infile" type="data" format="imzml,rdata,analyze75" label="MSI data" help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload). The file must be in profile mode, not centroided."/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
402 <conditional name="restriction_conditional"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
403 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
404 <option value="no_restriction" selected="True">No, calculate on entire file</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
405 <option value="restrict">Yes, restrict to spectra of interest</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
406 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
407 <when value="restrict"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
408 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
409 <param name="column_x" data_ref="coordinates_file" label="Column with x values" type="data_column"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
410 <param name="column_y" data_ref="coordinates_file" label="Column with y values" type="data_column"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
411 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
412 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
413 <when value="no_restriction"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
414 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
415 <repeat name="methods" title="Method" min="1"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
416 <conditional name="methods_conditional"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
417 <param name="method" type="select" label="Select a method"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
418 <option value="Transformation" selected="True">Transformation</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
419 <option value="Smoothing">Smoothing</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
420 <option value="Baseline">Baseline removal</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
421 <option value="Calibrate">Intensity calibration (normalization)</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
422 <option value="Align">Align spectra (warping/phase correction)</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
423 <option value="skip_preprocessing">Skip preprocessing</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
424 <validator type="empty_field" /> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
425 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
426 <when value="Transformation"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
427 <param name="transform_method" type="select" label="Transformation method"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
428 <option value="sqrt" selected="True">sqrt</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
429 <option value="log">log</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
430 <option value="log2">log2</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
431 <option value="log10">log10</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
432 <validator type="empty_field" /> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
433 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
434 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
435 <when value="Smoothing"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
436 <conditional name="methods_for_smoothing"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
437 <param name="smooth_method" type="select" label="Smoothing method" help="This method smoothes the intensity values of a MassSpectrum object."> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
438 <option value="SavitzkyGolay" selected="True">SavitzkyGolay</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
439 <option value="MovingAverage">MovingAverage</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
440 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
441 <when value="SavitzkyGolay"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
442 <param name="polynomial" value="3" type="text" label="Polynomial order" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
443 help="Controls the order of the filter, should be smaller than the resulting window."/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
444 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
445 <when value="MovingAverage"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
446 <param name="weighted" type="boolean" label="Weighted average" help = "Indicates if the average should be equal weight or if it should have weights depending on the distance from the center as calculated as 1/2^abs(-halfWindowSize:halfWindowSize) with the sum of all weigths normalized to 1" truevalue="TRUE" falsevalue="FALSE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
447 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
448 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
449 <param name="halfWindowSize" type="integer" value="10" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
450 label="Half window size" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
451 help="Number of data points, the resulting window reaches from |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
452 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize] |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
453 (window size is 2*halfWindowSize+1)."/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
454 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
455 <when value="Baseline"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
456 <conditional name="methods_for_baseline"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
457 <param name="baseline_method" type="select" label="Baseline removal method"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
458 <option value="SNIP" selected="True">SNIP</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
459 <option value="TopHat">TopHat</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
460 <option value="ConvexHull">ConvexHull</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
461 <option value="median">median</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
462 <validator type="empty_field" /> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
463 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
464 <when value="SNIP"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
465 <param name="iterations" type="integer" value="100" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
466 label="Number of iterations" help="Corresponds to half window size: The resulting window reaches from mass[cur_index-iterations] to mass[cur_index+iterations]"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
467 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
468 <when value="TopHat"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
469 <param name="tophat_halfWindowSize" type="integer" value="10" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
470 label="Half window size" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
471 help="Number of data points, the resulting window reaches from |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
472 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
473 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
474 <when value="ConvexHull"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
475 <when value="median"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
476 <param name="median_halfWindowSize" type="integer" value="10" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
477 label="Half window size" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
478 help="Number of data points, the resulting window reaches from |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
479 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
480 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
481 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
482 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
483 <when value="Calibrate"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
484 <param name="calibrate_method" type="select" label="Intensity calibration method" help="Intensity normalization"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
485 <option value="TIC" selected="True">TIC</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
486 <option value="PQN">PQN</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
487 <option value="median">median</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
488 <validator type="empty_field" /> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
489 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
490 <conditional name="cond_calibration_range"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
491 <param name="calibration_range" type="select" label="m/z range" help="Instead of the whole m/z range, a specified m/z range can be used to calculate the scaling factor."> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
492 <option value="no" selected="True">complete m/z range</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
493 <option value="yes">specify a m/z range</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
494 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
495 <when value="no"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
496 <when value="yes"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
497 <param name="mass_start" type="integer" value="800" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
498 label="Start of m/z range, has to be inside m/z range" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
499 help="Scaling factor is calculated on the mass range and applied to the whole spectrum."/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
500 <param name="mass_end" type="integer" value="3000" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
501 label="End of m/z range, has to be inside m/z range"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
502 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
503 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
504 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
505 <when value="Align"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
506 <param name="warping_method" type="select" label="Alignment method"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
507 <option value="lowess" selected="True">Lowess</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
508 <option value="linear">Linear</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
509 <option value="quadratic">Quadratic</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
510 <option value="cubic">Cubic</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
511 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
512 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
513 <param name="tolerance" type="float" value="0.00005" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
514 label="Tolerance" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
515 help="abs(mz1 - mz2)/mz2, maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 5e-5" /> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
516 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
517 <param name="halfWindowSize" type="integer" value="20" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
518 label="Half window size" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
519 help="Number of data points, the resulting window reaches from |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
520 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize] |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
521 (window size is 2*halfWindowSize+1). |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
522 The best size differs depending on the selected smoothing method."/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
523 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
524 <param name="peak_method" type="select" label="Noise estimation function"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
525 <option value="MAD" selected="True">MAD</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
526 <option value="SuperSmoother">SuperSmoother</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
527 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
528 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
529 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
530 <param name="allow_nomatch" type="boolean" label="Allow no matches" help="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
531 <param name="empty_nomatch" type="boolean" label="Empty no matches" help="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
532 <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
533 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
534 <conditional name="reference_for_alignment"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
535 <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
536 <option value="no_reference" selected="True">no reference</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
537 <option value="yes_reference">reference from tabular file</option> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
538 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
539 <when value="no_reference"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
540 <param name="min_frequency" type="float" value="0.9" label = "minFrequency" help="Removal of all peaks which occur in less than minFrequency spectra to generate the reference m/z"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
541 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
542 <when value="yes_reference"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
543 <param name="reference_file" type="data" format="tabular" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
544 label="Reference m/z values" |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
545 help="Tabular file"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
546 <param name="mz_column" data_ref="reference_file" label="Column with m/z values" type="data_column"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
547 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
548 <param name="separate_alignment" type="boolean" label="Spectrum wise alignment" help="Internal binning is omitted to avoid interaction between spectra" truevalue="TRUE" falsevalue="FALSE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
549 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
550 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
551 </when> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
552 <when value="skip_preprocessing"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
553 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
554 </repeat> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
555 <param name="export_processed" type="boolean" label="Export processed imzML" help="otherwise continuous imzML will be exported" truevalue="TRUE" falsevalue="FALSE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
556 </inputs> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
557 <outputs> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
558 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}" /> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
559 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="${tool.name} on ${on_string}: QC"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
560 </outputs> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
561 <tests> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
562 <test> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
563 <param name="infile" value="" ftype="imzml"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
564 <composite_data value="Example_Continuous.imzML"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
565 <composite_data value="Example_Continuous.ibd"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
566 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
567 <conditional name="restriction_conditional"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
568 <param name="restriction" value="restrict"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
569 <param name="coordinates_file" value="restricted_pixels.tabular"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
570 <param name="column_x" value="1"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
571 <param name="column_y" value="2"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
572 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
573 <conditional name="methods_conditional"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
574 <param name="method" value="Transformation"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
575 <param name="transform_method" value="log2"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
576 <param name="method" value="Smoothing"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
577 <param name="smooth_method" value="SavitzkyGolay"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
578 <param name="method" value="Basline"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
579 <param name="baseline_method" value ="TopHat"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
580 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
581 <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
582 <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="6"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
583 <extra_files type="file" file="outfile1.ibd" name="ibd" compare="sim_size"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
584 </output> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
585 <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
586 </test> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
587 <test> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
588 <param name="infile" value="msidata_1.RData" ftype="rdata"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
589 <conditional name="methods_conditional"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
590 <param name="method" value="Align"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
591 <param name="warping_method" value="lowess"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
592 <param name="halfWindowSize" value="5"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
593 <param name="tolerance" value="0.001"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
594 <param name="allow_nomatch" value="TRUE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
595 <param name="remove_empty" value="TRUE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
596 <param name="empty_nomatch" value="TRUE"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
597 <conditional name="reference_for_alignment"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
598 <param name="align_ref" value="yes_reference"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
599 <param name="reference_file" value="inputpeptides.tabular" ftype="tabular"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
600 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
601 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
602 <output name="outfile_imzml" ftype="imzml" file="preprocessing2.imzml.txt" lines_diff="4"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
603 <extra_files type="file" file="outfile2.imzml" name="imzml" lines_diff="6"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
604 <extra_files type="file" file="outfile2.ibd" name="ibd" compare="sim_size"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
605 </output> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
606 <output name="plots" file="Preprocessing2_QC.pdf" compare="sim_size"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
607 </test> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
608 <test> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
609 <param name="infile" value="" ftype="imzml"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
610 <composite_data value="Example_Continuous.imzML"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
611 <composite_data value="Example_Continuous.ibd"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
612 </param> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
613 <conditional name="methods_conditional"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
614 <param name="method" value="Calibrate"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
615 <param name="calibrate_method" value="median"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
616 </conditional> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
617 <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4"> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
618 <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="6"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
619 <extra_files type="file" file="outfile3.ibd" name="ibd" compare="sim_size"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
620 </output> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
621 <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
622 </test> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
623 </tests> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
624 <help><![CDATA[ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
625 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
626 @MADLI_QUANT_DESCRIPTION@ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
627 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
628 ----- |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
629 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
630 **Input data** |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
631 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
632 - MSI data: 2 types of input data can be used: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
633 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
634 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
635 - Cardinal "MSImageSet" data saved as .RData |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
636 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
637 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
638 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
639 :: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
640 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
641 x_coord y_coord |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
642 1 1 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
643 2 1 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
644 3 1 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
645 ... |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
646 ... |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
647 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
648 - Optional: Tabular file with reference m/z for the spectra align function. At least 2 m/z values of the input list must be present in every spectrum to peform the alignment. First column must contain m/z values, without empty fields or letters. Tabular files with any header name or no header at all are supported. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
649 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
650 :: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
651 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
652 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
653 m/z |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
654 100.0 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
655 100.01 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
656 100.02 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
657 ... |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
658 ... |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
659 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
660 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
661 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
662 **Options** |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
663 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
664 - Transformation: Variance stabilization through intensity transformation:'log', 'log2', 'log10' and 'squareroot' (sqrt) are available |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
665 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are 'SavitzkyGolay' and 'Moving Average' |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
666 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
667 - For all smoothing methods: The larger the 'Half window size', the stronger the smoothing. The resulting window should be smaller than the FWHM (full width at half maximum) of the typical peaks. Moving average needs smaller window size than SavitzkyGolay. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
668 - Moving average: Recommended for broader peaks/high m/z range spectra. Weighted moving average: Points in the center get larger weight factors than points away from the center. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
669 - SavitzkyGolay: Recommended for sharp peaks/low m/z range, preserves the shape of the local maxima. The PolynomialOrder should be smaller than the resulting window. Negative values will be replaced with 0. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
670 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
671 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets). |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
672 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
673 - Available methods are SNIP, TopHat,ConvexHull and median: |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
674 - SNIP is the default baseline reduction method in MALDIquant. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
675 - ConvexHull is not appropriate for MALDI-TOF baseline removal. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
676 - The moving median may generate negative intensities. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
677 - Except for the ConvexHull all methods have a parameter for the 'Half window size' (in SNIP it is called 'iterations'). The smaller the window the more baseline will be removed but also parts of the peaks. Wider windows preserve the peak height better and produce a smoother baseline, but some local background variation will remain. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
678 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
679 - Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
680 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
681 - TIC and median are local calibration methods: each spectrum is normalized on its own (each peak is divided by the TIC or median of the spectrum) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
682 - PQN is a global calibration method: In PQN all spectra are calibrated using the TIC calibration first. Subsequently, a median reference spectrum is created and the intensities in all spectra are standardized using the reference spectrum and a spectrum-specific median is calculated for each spectrum. Finally, each spectrum is rescaled by the median of the ratios of its intensity values and that of the reference spectrum |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
683 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
684 - Spectra alignment (warping): alignment for (re)calibration of m/z values. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
685 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
686 - peak detection is performed, the reference peaks will be matched to those detected peaks |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
687 - without external reference m/z: internal reference is obtained by filtering and binning the picked peaks to find landmark peaks and their average m/z |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
688 - with external reference m/z: the given m/z are used as a reference, at least 10 reference values are recommended |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
689 - non linear warping (parametric time warping plus binning) to match the reference peaks (internal or external) to the present (picked) peaks with the given tolerance. At least two m/z per spectrum are needed for the alignment. To prevent an error when this criterium is not fullfilled, "Don't throw an error when less than 2 reference m/z were found in a spectrum" should be set to yes. If the not aligned spectra should be set to zero select yes in "If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero". In order to remove such empty spectra set "Should empty spectra be removed" to yes. |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
690 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
691 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
692 **Output** |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
693 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
694 - imzML file (imzML format can be continuous or processed) |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
695 - PDF with average mass spectra after each preprocessing step |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
696 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
697 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/ |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
698 |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
699 ]]> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
700 </help> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
701 <expand macro="citation"/> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
702 </tool> |
71411ac28268
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
2
diff
changeset
|
703 |