Mercurial > repos > galaxyp > msi_filtering
annotate msi_filtering.xml @ 0:f17d3f1a065f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
author | galaxyp |
---|---|
date | Wed, 28 Feb 2018 14:02:21 -0500 |
parents | |
children | 98c101b19f3c |
rev | line source |
---|---|
0
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
1 <tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.7.0"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
2 <description>tool for filtering mass spectrometry imaging data</description> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
3 <requirements> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
4 <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
5 <requirement type="package" version="2.2.1">r-gridextra</requirement> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
6 </requirements> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
7 <command detect_errors="exit_code"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
8 <![CDATA[ |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
9 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
10 #if $infile.ext == 'imzml' |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
11 cp '${infile.extra_files_path}/imzml' infile.imzML && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
12 cp '${infile.extra_files_path}/ibd' infile.ibd && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
13 #elif $infile.ext == 'analyze75' |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
14 cp '${infile.extra_files_path}/hdr' infile.hdr && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
15 cp '${infile.extra_files_path}/img' infile.img && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
16 cp '${infile.extra_files_path}/t2m' infile.t2m && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
17 #else |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
18 ln -s $infile infile.RData && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
19 #end if |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
20 cat '${MSI_subsetting}' && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
21 echo ${MSI_subsetting} && |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
22 Rscript '${MSI_subsetting}' |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
23 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
24 ]]> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
25 </command> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
26 <configfiles> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
27 <configfile name="MSI_subsetting"><![CDATA[ |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
28 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
29 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
30 ################################# load libraries and read file ######################### |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
31 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
32 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
33 library(Cardinal) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
34 library(gridExtra) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
35 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
36 ## Read MALDI Imaging dataset |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
37 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
38 #if $infile.ext == 'imzml' |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
39 msidata = readMSIData('infile.imzML') |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
40 #elif $infile.ext == 'analyze75' |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
41 msidata = readMSIData('infile.hdr') |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
42 #else |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
43 load('infile.RData') |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
44 #end if |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
45 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
46 ###################################### inputfile properties in numbers ###################### |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
47 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
48 #if $outputs.outputs_select == "quality_control" |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
49 ## Number of features (mz) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
50 maxfeatures = length(features(msidata)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
51 ## Range mz |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
52 minmz = round(min(mz(msidata)), digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
53 maxmz = round(max(mz(msidata)), digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
54 ## Number of spectra (pixels) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
55 pixelcount = length(pixels(msidata)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
56 ## Range x coordinates |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
57 minimumx = min(coord(msidata)[,1]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
58 maximumx = max(coord(msidata)[,1]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
59 ## Range y coordinates |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
60 minimumy = min(coord(msidata)[,2]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
61 maximumy = max(coord(msidata)[,2]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
62 ## Number of intensities > 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
63 npeaks= sum(spectra(msidata)[]>0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
64 ## Spectra multiplied with mz (potential number of peaks) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
65 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
66 ## Percentage of intensities > 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
67 percpeaks = round(npeaks/numpeaks*100, digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
68 ## Number of empty TICs |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
69 TICs = colSums(spectra(msidata)[]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
70 NumemptyTIC = sum(TICs == 0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
71 ## median TIC |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
72 medint = round(median(TICs), digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
73 ## Store features for QC plot |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
74 featuresinfile = mz(msidata) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
75 #end if |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
76 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
77 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
78 ###################################### filtering of pixels ###################### |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
79 #if $inputpixels: |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
80 input_list = read.delim("$inputpixels", header = FALSE, |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
81 na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
82 validpixels = input_list[,$pixel_column] %in% names(pixels(msidata)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
83 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
84 if (validpixels != 0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
85 { |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
86 pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[validpixels,$pixel_column]] |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
87 msidata = msidata[,pixelsofinterest] |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
88 numberpixels = length(input_list[,$pixel_column]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
89 }else { |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
90 numberpixels = 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
91 } |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
92 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
93 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
94 #else |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
95 input_list = data.frame(0, 0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
96 validpixels=0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
97 numberpixels = 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
98 #end if |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
99 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
100 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
101 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
102 ###################################### filtering of features ###################### |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
103 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
104 #if $inputfeatures: |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
105 input_features = read.delim("$inputfeatures", header = FALSE, |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
106 na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
107 validfeatures = input_features[,$feature_column] %in% names(features(msidata)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
108 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
109 if (validfeatures != 0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
110 { |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
111 featuresofinterest = features(msidata)[names(features(msidata)) %in% input_features[validfeatures,$feature_column]] |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
112 msidata = msidata[featuresofinterest,] |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
113 numberfeatures = length(input_features[,$feature_column]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
114 } else { |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
115 numberfeatures = 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
116 } |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
117 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
118 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
119 #else |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
120 input_features = data.frame(0, 0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
121 validfeatures = 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
122 numberfeatures = 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
123 #end if |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
124 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
125 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
126 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
127 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
128 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
129 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
130 # save msidata as Rfile |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
131 save(msidata, file="$msidata_filtered") |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
132 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
133 ###################################### outputfile properties in numbers ###################### |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
134 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
135 #if $outputs.outputs_select == "quality_control" |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
136 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
137 ## Number of features (mz) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
138 maxfeatures2 = length(features(msidata)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
139 ## Range mz |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
140 minmz2 = round(min(mz(msidata)), digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
141 maxmz2 = round(max(mz(msidata)), digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
142 ## Number of spectra (pixels) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
143 pixelcount2 = length(pixels(msidata)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
144 ## Range x coordinates |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
145 minimumx2 = min(coord(msidata)[,1]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
146 maximumx2 = max(coord(msidata)[,1]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
147 ## Range y coordinates |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
148 minimumy2 = min(coord(msidata)[,2]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
149 maximumy2 = max(coord(msidata)[,2]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
150 ## Number of intensities > 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
151 npeaks2= sum(spectra(msidata)[]>0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
152 ## Spectra multiplied with mz (potential number of peaks) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
153 numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
154 ## Percentage of intensities > 0 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
155 percpeaks2 = round(npeaks2/numpeaks2*100, digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
156 ## Number of empty TICs |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
157 TICs2 = colSums(spectra(msidata)[]) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
158 NumemptyTIC2 = sum(TICs2 == 0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
159 ## median TIC |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
160 medint2 = round(median(TICs2), digits=2) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
161 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
162 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
163 properties = c("Number of mz features", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
164 "Range of mz values [Da]", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
165 "Number of pixels", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
166 "Range of x coordinates", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
167 "Range of y coordinates", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
168 "Intensities > 0", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
169 "Median TIC per pixel", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
170 "Number of zero TICs", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
171 paste0("# pixels in ", "$inputpixels.display_name"), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
172 paste0("# mz in ", "$inputfeatures.display_name")) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
173 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
174 before = c(paste0(maxfeatures), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
175 paste0(minmz, " - ", maxmz), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
176 paste0(pixelcount), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
177 paste0(minimumx, " - ", maximumx), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
178 paste0(minimumy, " - ", maximumy), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
179 paste0(percpeaks, " %"), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
180 paste0(medint), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
181 paste0(NumemptyTIC), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
182 paste0("input pixels: ", numberpixels), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
183 paste0("input mz: ", numberfeatures)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
184 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
185 filtered = c(paste0(maxfeatures2), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
186 paste0(minmz2, " - ", maxmz2), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
187 paste0(pixelcount2), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
188 paste0(minimumx2, " - ", maximumx2), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
189 paste0(minimumy2, " - ", maximumy2), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
190 paste0(percpeaks2, " %"), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
191 paste0(medint2), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
192 paste0(NumemptyTIC2), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
193 paste0("valid pixels: ", sum(validpixels)), |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
194 paste0("valid mz: ", sum(validfeatures))) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
195 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
196 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
197 property_df = data.frame(properties, before, filtered) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
198 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
199 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
200 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
201 ######################################## PDF QC ############################################# |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
202 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
203 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
204 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
205 plot(0,type='n',axes=FALSE,ann=FALSE) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
206 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
207 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name")) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
208 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
209 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
210 grid.table(property_df, rows= NULL) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
211 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
212 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
213 ### heatmap image as visual pixel control |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
214 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
215 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
216 image(msidata, mz=$outputs.inputmz, plusminus = $outputs.plusminus_dalton, contrast.enhance = "none", |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
217 main= paste0($outputs.inputmz," ± ", $outputs.plusminus_dalton, " Da"), ylim = c(maximumy2+0.2*maximumy2,minimumy2-0.2*minimumy2)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
218 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
219 ### control features which are left |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
220 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
221 par(mfrow = c(2,1)) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
222 plot(featuresinfile, ylab = "m/z in Dalton", xlab = "feature index") |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
223 plot(mz(msidata), ylab = "m/z in Dalton", xlab = "feature index") |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
224 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
225 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
226 dev.off() |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
227 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
228 #end if |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
229 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
230 ######################################## intensity matrix ################################## |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
231 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
232 #if $output_matrix: |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
233 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
234 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
235 { |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
236 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
237 spectramatrix = spectra(msidata) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
238 rownames(spectramatrix) = mz(msidata) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
239 newmatrix = rbind(pixels(msidata), spectramatrix) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
240 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
241 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
242 }else{ |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
243 print("file has no features or pixels left") |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
244 } |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
245 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
246 #end if |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
247 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
248 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
249 ]]></configfile> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
250 </configfiles> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
251 <inputs> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
252 <param name="infile" type="data" format="imzml, rdata, analyze75" |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
253 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
254 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
255 <param name="inputpixels" type="data" optional="true" format="tabular" label="pixels for filtering of MSI data" |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
256 help="tabular file with pixels of interest in the form x = 1, y = 1"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
257 <param name="pixel_column" data_ref="inputpixels" optional="true" label="Column with pixels" type="data_column" /> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
258 <param name="inputfeatures" type="data" optional="true" format="tabular" label="features for filtering of MSI data" |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
259 help="tabular file with masses of interest in the form mz = 800.05"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
260 <param name="feature_column" data_ref="inputfeatures" optional="true" label="Column with features" type="data_column" /> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
261 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
262 <conditional name="outputs"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
263 <param name="outputs_select" type="select" label="Quality control output"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
264 <option value="quality_control" selected="True">yes</option> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
265 <option value="no_quality_control" >no</option> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
266 </param> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
267 <when value="quality_control"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
268 <param name="inputmz" type="float" value="1296.7" label="Mass for which a heatmap image will be drawn" help="Use a mass which is still present in all pixels to control if the pixel filtering went well"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
269 <param name="plusminus_dalton" value="0.25" type="float" label="mass range for mz value" help="plusminus mass window in Dalton"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
270 </when> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
271 </conditional> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
272 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
273 </inputs> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
274 <outputs> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
275 <data format="rdata" name="msidata_filtered" label="${tool.name} on $infile.display_name"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
276 <data format="pdf" name="filtering_qc" from_work_dir="filtertool_QC.pdf" label = "QC ${tool.name} on $infile.display_name"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
277 <filter>outputs["outputs_select"] == "quality_control"</filter> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
278 </data> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
279 <data format="tabular" name="matrixasoutput" label="matrix ${tool.name} on $infile.display_name"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
280 <filter>output_matrix</filter> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
281 </data> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
282 </outputs> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
283 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
284 <tests> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
285 <test expect_num_outputs="2"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
286 <param name="infile" value="" ftype="imzml"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
287 <composite_data value="Example_Continuous.imzML"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
288 <composite_data value="Example_Continuous.ibd"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
289 </param> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
290 <param name="inputpixels" ftype="tabular" value = "inputpixels.tabular"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
291 <param name="pixel_column" value="1"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
292 <param name="inputfeatures" ftype="tabular" value = "inputfeatures.tabular"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
293 <param name="feature_column" value="2"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
294 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
295 <conditional name="outputs"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
296 <param name="outputs_select" value="quality_control"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
297 <param name="inputmz" value="328.9"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
298 <param name="plusminus_dalton" value="0.25"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
299 </conditional> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
300 <output name="filtering_qc" file="imzml_filtered.pdf" compare="sim_size" delta="20000"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
301 <output name="msidata_filtered" file="imzml_filtered.RData" compare="sim_size" /> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
302 </test> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
303 <test expect_num_outputs="3"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
304 <param name="infile" value="" ftype="analyze75"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
305 <composite_data value="Analyze75.hdr"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
306 <composite_data value="Analyze75.img"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
307 <composite_data value="Analyze75.t2m"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
308 </param> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
309 <param name="inputpixels" ftype="tabular" value = "inputpixels2.tabular"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
310 <param name="pixel_column" value="1"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
311 <param name="inputfeatures" ftype="tabular" value = "featuresofinterest2.tabular"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
312 <param name="feature_column" value="1"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
313 <conditional name="outputs"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
314 <param name="outputs_select" value="quality_control"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
315 <param name="inputmz" value="702"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
316 <param name="plusminus_dalton" value="0.25"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
317 </conditional> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
318 <param name="output_matrix" value="True"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
319 <output name="filtering_qc" file="analyze_filtered.pdf" compare="sim_size" delta="20000"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
320 <output name="msidata_filtered" file="analyze_filtered.RData" compare="sim_size" /> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
321 <output name="matrixasoutput" file="analyze_matrix.tabular"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
322 </test> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
323 <test expect_num_outputs="1"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
324 <param name="infile" value="" ftype="analyze75"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
325 <composite_data value="Analyze75.hdr"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
326 <composite_data value="Analyze75.img"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
327 <composite_data value="Analyze75.t2m"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
328 </param> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
329 <conditional name="outputs"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
330 <param name="outputs_select" value="no_quality_control"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
331 </conditional> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
332 <output name="msidata_filtered" file="analyze_originaloutput.RData" compare="sim_size" /> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
333 </test> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
334 <test expect_num_outputs="2"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
335 <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
336 <conditional name="outputs"> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
337 <param name="outputs_select" value="no_quality_control"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
338 </conditional> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
339 <param name="output_matrix" value="True"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
340 <output name="matrixasoutput" file="rdata_matrix.tabular"/> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
341 </test> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
342 </tests> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
343 <help> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
344 <![CDATA[ |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
345 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
346 This tool can filter three types of mass-spectrometry imaging files (see below) for pixels and features of interest. This can be used to keep only pixels in a regions of interest. |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
347 For filtering at least one valid pixel/feature is needed otherwise no filtering will be performed. |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
348 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
349 Input data: 3 types of input data can be used: |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
350 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
351 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_ |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
352 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
353 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData) |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
354 |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
355 The output of this tool is a subsetted Cardinal "MSImageSet" with the variable name "msidata" saved as .RData. |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
356 ]]> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
357 </help> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
358 <citations> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
359 <citation type="doi">10.1093/bioinformatics/btv146</citation> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
360 </citations> |
f17d3f1a065f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff
changeset
|
361 </tool> |