Mercurial > repos > galaxyp > msi_spectra_plot

annotate msi_spectra_plots.xml @ 9:ebca696cb024 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
author galaxyp
date Tue, 04 Sep 2018 13:42:04 -0400
parents d0e13a160a6c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.7">
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
2 <description>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
3 mass spectrometry imaging mass spectra plots
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
4 </description>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
5 <requirements>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
7 <requirement type="package" version="2.2.1">r-gridextra</requirement>
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
8 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
9 <requirement type="package" version="0.5.0">r-scales</requirement>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
10 </requirements>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
11 <command detect_errors="exit_code">
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
12 <![CDATA[
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
13 #if $infile.ext == 'imzml'
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
14 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
15 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
16 #elif $infile.ext == 'analyze75'
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
17 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
18 ln -s '${infile.extra_files_path}/img' infile.img &&
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
19 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
20 #else
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
21 ln -s $infile infile.RData &&
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
22 #end if
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
23 cat '${MSI_mzplots}' &&
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
24 Rscript '${MSI_mzplots}'
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
25 ]]>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
26 </command>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
27 <configfiles>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
28 <configfile name="MSI_mzplots"><![CDATA[
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
29
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
30 ################################# load libraries and read file #################
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
31
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
32 library(Cardinal)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
33 library(gridExtra)
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
34 library(ggplot2)
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
35 library(scales)
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
36
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
37
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
38 #if $infile.ext == 'imzml'
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
39 #if str($processed_cond.processed_file) == "processed":
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
40 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
41 #else
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
42 msidata <- readImzML('infile', attach.only=TRUE)
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
43 #end if
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
44 #elif $infile.ext == 'analyze75'
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
45 msidata = readAnalyze('infile', attach.only=TRUE)
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
46 #else
8
d0e13a160a6c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 7
diff changeset
47 loadRData <- function(fileName){
d0e13a160a6c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 7
diff changeset
48 load(fileName)
d0e13a160a6c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 7
diff changeset
49 get(ls()[ls() != "fileName"])
d0e13a160a6c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 7
diff changeset
50 }
d0e13a160a6c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 7
diff changeset
51 msidata = loadRData('infile.RData')
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
52 #end if
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
53
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
54 ###################################### file properties in numbers ##############
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
55
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
56 ## Number of features (m/z)
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
57 maxfeatures = length(features(msidata))
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
58 ## Range m/z
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
59 minmz = round(min(mz(msidata)), digits=2)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
60 maxmz = round(max(mz(msidata)), digits=2)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
61 ## Number of spectra (pixels)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
62 pixelcount = length(pixels(msidata))
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
63 ## Range x coordinates
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
64 minimumx = min(coord(msidata)[,1])
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
65 maximumx = max(coord(msidata)[,1])
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
66 ## Range y coordinates
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
67 minimumy = min(coord(msidata)[,2])
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
68 maximumy = max(coord(msidata)[,2])
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
69 ## Range of intensities
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
70 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
71 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
72 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
73 ## Number of intensities > 0
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
74 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
75 ## Spectra multiplied with m/z (potential number of peaks)
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
76 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
77 ## Percentage of intensities > 0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
78 percpeaks = round(npeaks/numpeaks*100, digits=2)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
79 ## Number of empty TICs
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
80 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
81 NumemptyTIC = sum(TICs == 0)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
82
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
83
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
84 ## Processing informations
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
85 processinginfo = processingData(msidata)
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
86 centroidedinfo = processinginfo@centroided
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
87
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
88 ## if TRUE write processinginfo if FALSE write FALSE
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
89
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
90 ## normalization
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
91 if (length(processinginfo@normalization) == 0) {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
92 normalizationinfo='FALSE'
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
93 } else {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
94 normalizationinfo=processinginfo@normalization
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
95 }
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
96 ## smoothing
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
97 if (length(processinginfo@smoothing) == 0) {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
98 smoothinginfo='FALSE'
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
99 } else {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
100 smoothinginfo=processinginfo@smoothing
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
101 }
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
102 ## baseline
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
103 if (length(processinginfo@baselineReduction) == 0) {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
104 baselinereductioninfo='FALSE'
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
105 } else {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
106 baselinereductioninfo=processinginfo@baselineReduction
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
107 }
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
108 ## peak picking
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
109 if (length(processinginfo@peakPicking) == 0) {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
110 peakpickinginfo='FALSE'
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
111 } else {
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
112 peakpickinginfo=processinginfo@peakPicking
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
113 }
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
114
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
115 properties = c("Number of m/z features",
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
116 "Range of m/z values",
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
117 "Number of pixels",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
118 "Range of x coordinates",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
119 "Range of y coordinates",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
120 "Range of intensities",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
121 "Median of intensities",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
122 "Intensities > 0",
9
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
123 "Number of empty spectra",
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
124 "Preprocessing",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
125 "Normalization",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
126 "Smoothing",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
127 "Baseline reduction",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
128 "Peak picking",
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
129 "Centroided")
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
130
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
131 values = c(paste0(maxfeatures),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
132 paste0(minmz, " - ", maxmz),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
133 paste0(pixelcount),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
134 paste0(minimumx, " - ", maximumx),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
135 paste0(minimumy, " - ", maximumy),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
136 paste0(minint, " - ", maxint),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
137 paste0(medint),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
138 paste0(percpeaks, " %"),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
139 paste0(NumemptyTIC),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
140 paste0(" "),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
141 paste0(normalizationinfo),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
142 paste0(smoothinginfo),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
143 paste0(baselinereductioninfo),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
144 paste0(peakpickinginfo),
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
145 paste0(centroidedinfo))
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
146
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
147 property_df = data.frame(properties, values)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
148
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
149 ######################################## PDF ###################################
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
150 ################################################################################
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
151 ################################################################################
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
152
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
153
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
154 pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
155 plot(0,type='n',axes=FALSE,ann=FALSE)
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
156 #if not $filename:
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
157 #set $filename = $infile.display_name
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
158 #end if
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
159 title(main=paste0("Mass spectra for file: \n\n","$filename"))
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
160
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
161
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
162 ############################# I) numbers ######################################
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
163 ###############################################################################
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
164
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
165 grid.table(property_df, rows= NULL)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
166
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
167 if (npeaks > 0){
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
168
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
169 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
170
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
171 ############################# single pixel ################################
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
172 ###########################################################################
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
173
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
174 #if str( $pixel_conditional.pixel_type) == 'single_pixel':
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
175 print("single_pixel")
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
176
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
177 #for $chosenpixel in $pixel_conditional.repeatpixel:
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
178
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
179 pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y)
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
180 pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy)
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
181 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
182
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
183 ############################# II) control image ####################
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
184
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
185 if (pixelisvalid == "TRUE"){
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
186 print(pixelisvalid)
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
187
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
188 image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
189 colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton,
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
190 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
191
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
192 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
193 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
194
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
195 ##################### III) plot full mass spectrum #################
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
196
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
197 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
198
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
199 ##################### IV) plot zoom-in mass spectrum ###############
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
200
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
201 #if $chosenpixel.zoomedplot:
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
202 iData(msidata) <- iData(msidata)[] ## getting back data on disk
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
203
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
204 #for $token in $chosenpixel.zoomedplot:
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
205
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
206 minmasspixel = features(msidata, mz=$token.xlimmin)
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
207 maxmasspixel = features(msidata, mz=$token.xlimmax)
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
208
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
209 plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
210 xlim= c($token.xlimmin,$token.xlimmax))
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
211
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
212 #end for
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
213 #end if
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
214 }else{
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
215 print("The pixel coordinates did not correspond to a real pixel")}
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
216 #end for
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
217
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
218 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
219
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
220 ############################# sample pixel ################################
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
221 ###########################################################################
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
222
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
223 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
224 print("sample pixels")
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
225
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
226 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
227
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
228 #if str($pixel_conditional.tabular_annotation.load_annotation) == 'yes_annotation':
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
229
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
230 ## read and extract x,y,annotation information
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
231 input_tabular = read.delim("$pixel_conditional.tabular_annotation.annotation_file", header = $pixel_conditional.tabular_annotation.tabular_header, stringsAsFactors = FALSE)
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
232 annotation_input = input_tabular[,c($pixel_conditional.tabular_annotation.column_x, $pixel_conditional.tabular_annotation.column_y, $pixel_conditional.tabular_annotation.column_names)]
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
233 colnames(annotation_input) = c("x", "y", "annotation")
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
234
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
235 ## merge with coordinate information of msidata
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
236 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
237 colnames(msidata_coordinates)[3] = "pixel_index"
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
238 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
239 merged_annotation[is.na(merged_annotation)] = "NA"
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
240 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
241 msidata\$annotation = as.factor(merged_annotation[,4])
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
242
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
243 #end if
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
244
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
245 ##################### I) Sample: plot full mass spectrum ##############
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
246
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
247 ## coloured plot with mean over all spectra with the same annotation, if no annotation is provided all pixels are considered as one sample
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
248
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
249 if (!is.null(levels(msidata\$annotation))){
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
250 print("annotated samples")
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
251
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
252 ## overview plot over annotated samples
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
253 number_combined = length(levels(msidata\$annotation))
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
254
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
255 ## the more annotation groups a file has the smaller will be the legend
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
256 if (number_combined<20){
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
257 legend_size = 10
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
258 }else if (number_combined>20 && number_combined<40){
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
259 legend_size = 9
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
260 }else if (number_combined>40 && number_combined<60){
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
261 legend_size = 8
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
262 }else if (number_combined>60 && number_combined<100){
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
263 legend_size = 7
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
264 }else{
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
265 legend_size = 6
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
266 }
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
267
9
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
268 position_df = cbind(coord(msidata)[,1:2], as.factor(msidata\$annotation))
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
269 colnames(position_df)[3] = "sample_name"
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
270
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
271 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
9
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
272 geom_tile(height = 1, width=1)+
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
273 coord_fixed()+
7
7d94faee0731 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 620a469e20836b921b6c0147421c8a4268b66ebd
galaxyp
parents: 6
diff changeset
274 ggtitle("Spatial orientation of pixel annotations")+
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
275 theme_bw()+
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
276 theme(plot.title = element_text(hjust = 0.5))+
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
277 theme(text=element_text(family="ArialMT", face="bold", size=12))+
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
278 theme(legend.position="bottom",legend.direction="vertical")+
9
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
279 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
280 guides(fill=guide_legend(ncol=4,byrow=TRUE))
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
281
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
282 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
283 coord_labels\$file_number = 1:length(levels(position_df\$sample_name))
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
284
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
285 for(file_count in 1:nrow(coord_labels))
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
286 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
ebca696cb024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit e87eea03505ab1ba067e192bbbcdc6197dc4b42e
galaxyp
parents: 8
diff changeset
287 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
288
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
289 print(combine_plot)
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
290
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
291 ## print legend only for less than 10 samples
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
292 if (length(levels(msidata\$annotation)) < 10){
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
293 key_legend = TRUE
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
294 }else{key_legend = FALSE}
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
295
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
296 is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
297 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE)
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
298 }else{
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
299 is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
300 plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
301
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
302 ##################### II) Sample: plot zoom-in mass spectrum ##########
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
303
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
304 #if $pixel_conditional.zoomed_sample:
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
305 iData(msidata) <- iData(msidata)[] ## getting back data on disk
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
306 #for $token in $pixel_conditional.zoomed_sample:
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
307 print("zoomed sample pixels")
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
308
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
309 minmasspixel = features(msidata, mz=$token.xlimmin)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
310 maxmasspixel = features(msidata, mz=$token.xlimmax)
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
311
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
312 ## coloured plot with mean over all spectra for annotation group, otherwise only 1 black plot
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
313 if (!is.null(levels(msidata\$annotation))){
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
314 print("annotation samples")
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
315 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
316 xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation,
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
317 key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE)
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
318 }else{
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
319 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
320
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
321 #end for
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
322 #end if
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
323
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
324 if (!is.null(levels(msidata\$annotation))){
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
325 pixeldf = data.frame(table(msidata\$annotation))
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
326 }else{
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
327 pixeldf = data.frame("$filename", ncol(msidata))}
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
328 colnames(pixeldf) = c("sample name", "number of pixels")
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
329
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
330 #end if
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
331
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
332
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
333 ############################# pixel table ######################################
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
334 ###############################################################################
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
335
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
336
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
337 ### overview table of pixels or samples:
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
338 plot(0,type='n',axes=FALSE,ann=FALSE)
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
339 title(main="Overview of chosen pixel:")
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
340
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
341 ### for more than 20 annotation groups print only 20 samples per page:
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
342 if (is.null(levels(msidata\$annotation))){
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
343 grid.table(pixeldf, rows= NULL)
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
344 }else if (length(levels(msidata\$annotation)) <= 20){
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
345 grid.table(pixeldf, rows= NULL)
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
346 }else{
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
347 grid.table(pixeldf[1:20,], rows= NULL)
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
348 mincount = 21
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
349 maxcount = 40
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
350 for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
351 plot(0,type='n',axes=FALSE,ann=FALSE)
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
352 if (maxcount <= nrow(pixeldf)){
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
353 grid.table(pixeldf[mincount:maxcount,], rows= NULL)
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
354 mincount = mincount+20
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
355 maxcount = maxcount+20
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
356 }else{### stop last page with last sample otherwise NA in table
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
357 grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)}
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
358 }
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
359 }
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
360
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
361 dev.off()
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
362
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
363 }else{
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
364 print("Inputfile has no intensities > 0")
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
365 dev.off()
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
366 }
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
367 ]]></configfile>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
368 </configfiles>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
369 <inputs>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
370 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
371 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
372 <conditional name="processed_cond">
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
373 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
374 <option value="no_processed" selected="True">not a processed imzML</option>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
375 <option value="processed">processed imzML</option>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
376 </param>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
377 <when value="no_processed"/>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
378 <when value="processed">
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
379 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
380 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
381 <option value="mz" >mz</option>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
382 <option value="ppm" selected="True" >ppm</option>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
383 </param>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
384 </when>
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
385 </conditional>
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
386 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
387 <conditional name="pixel_conditional">
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
388 <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or the average spectrum of all pixels of a sample">
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
389 <option value="single_pixel" selected="True">Single pixel</option>
5
4f13aec6d8ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
390 <option value="sample_pixel">Average spectrum for each sample</option>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
391 </param>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
392 <when value="single_pixel">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
393 <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
394 <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
395 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
396 <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, define m/z here" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
397 <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window "/>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
398 <param name="inputcolour" type="select" label="select the colour for the lines at x and y position">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
399 <option value="white" selected="True">white</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
400 <option value="black">black</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
401 <option value="grey">grey</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
402 <option value="blue">blue</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
403 <option value="red">red</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
404 <option value="green">green</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
405 </param>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
406 <param name="inputtype" type="select" label="select the line type for the lines at x and y position">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
407 <option value="solid" selected="True">solid</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
408 <option value="dashed">dashed</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
409 <option value="dotted">dotted</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
410 <option value="longdash">longdash</option>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
411 </param>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
412 <param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/>
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
413 <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
414 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
415 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
416 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
417 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
418 </when>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
419 <when value="sample_pixel">
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
420 <conditional name="tabular_annotation">
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
421 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for spectra plots">
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
422 <option value="no_annotation" selected="True">pixels belong into one group only</option>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
423 <option value="yes_annotation">group pixels according to annotations</option>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
424 </param>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
425 <when value="yes_annotation">
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
426 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
427 help="Tabular file with three columns: x values, y values and pixel annotations"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
428 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
429 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
430 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
431 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
432 </when>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
433 <when value="no_annotation"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
434 </conditional>
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
435 <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
436 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
437 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
438 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
439 </when>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
440 </conditional>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
441 </inputs>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
442 <outputs>
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
443 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label = "$infile.display_name mass_spectra"/>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
444 </outputs>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
445 <tests>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
446 <test>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
447 <param name="infile" value="" ftype="imzml">
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
448 <composite_data value="Example_Continuous.imzML"/>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
449 <composite_data value="Example_Continuous.ibd"/>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
450 </param>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
451 <conditional name="pixel_conditional">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
452 <param name="pixel_type" value="single_pixel"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
453 <repeat name="repeatpixel">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
454 <param name="plusminusinDalton" value="0.25"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
455 <param name="inputx" value="3"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
456 <param name="inputy" value="3"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
457 <repeat name="zoomedplot">
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
458 <param name="xlimmin" value="310"/>
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
459 <param name="xlimmax" value="320"/>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
460 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
461 <repeat name="zoomedplot">
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
462 <param name="xlimmin" value="350"/>
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
463 <param name="xlimmax" value="400"/>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
464 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
465 <repeat name="zoomedplot">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
466 <param name="xlimmin" value="400"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
467 <param name="xlimmax" value="420"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
468 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
469 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
470 <repeat name="repeatpixel">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
471 <param name="plusminusinDalton" value="0.25"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
472 <param name="inputx" value="2"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
473 <param name="inputy" value="2"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
474 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
475 <repeat name="repeatpixel">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
476 <param name="plusminusinDalton" value="0.25"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
477 <param name="inputx" value="1"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
478 <param name="inputy" value="1"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
479 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
480 </conditional>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
481 <output name="plots" file="Plot_imzml.pdf" compare="sim_size" delta="20000"/>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
482 </test>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
483 <test>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
484 <param name="infile" value="" ftype="analyze75">
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
485 <composite_data value="Analyze75.hdr"/>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
486 <composite_data value="Analyze75.img"/>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
487 <composite_data value="Analyze75.t2m"/>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
488 </param>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
489 <conditional name="pixel_conditional">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
490 <param name="pixel_type" value="single_pixel"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
491 <repeat name="repeatpixel">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
492 <param name="plusminusinDalton" value="0.25"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
493 <param name="inputx" value="5"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
494 <param name="inputy" value="2"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
495 <repeat name="zoomedplot">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
496 <param name="xlimmin" value="840"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
497 <param name="xlimmax" value="850"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
498 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
499 </repeat>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
500 <repeat name="repeatpixel">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
501 <param name="plusminusinDalton" value="0.25"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
502 <param name="inputx" value="2"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
503 <param name="inputy" value="2"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
504 </repeat>
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
505 </conditional>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
506 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size" delta="20000"/>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
507 </test>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
508 <test>
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
509 <param name="infile" value="" ftype="analyze75">
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
510 <composite_data value="Analyze75.hdr"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
511 <composite_data value="Analyze75.img"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
512 <composite_data value="Analyze75.t2m"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
513 </param>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
514 <conditional name="pixel_conditional">
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
515 <param name="pixel_type" value="sample_pixel"/>
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
516 <conditional name="tabular_annotation">
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
517 <param name="load_annotation" value="yes_annotation"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
518 <param name="annotation_file" value="annotations.tabular" ftype="tabular"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
519 <param name="column_x" value="1"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
520 <param name="column_y" value="2"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
521 <param name="column_names" value="4"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
522 <param name="tabular_header" value="TRUE"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
523 </conditional>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
524 <repeat name="zoomed_sample">
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
525 <param name="xlimmin" value="1250"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
526 <param name="xlimmax" value="1270"/>
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
527 </repeat>
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
528 </conditional>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
529 <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size" delta="20000"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
530 </test>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
531 <test>
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
532 <param name="infile" value="123_combined.RData" ftype="rdata"/>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
533 <conditional name="pixel_conditional">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
534 <param name="pixel_type" value="sample_pixel"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
535 <repeat name="zoomed_sample">
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
536 <param name="xlimmin" value="350"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
537 <param name="xlimmax" value="360"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
538 </repeat>
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
539 </conditional>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
540 <output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
541 </test>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
542 <test>
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
543 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
4
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
544 <conditional name="pixel_conditional">
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
545 <param name="pixel_type" value="single_pixel"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
546 <repeat name="repeatpixel">
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
547 <param name="plusminusinDalton" value="0.1"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
548 <param name="inputx" value="1"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
549 <param name="inputy" value="1"/>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
550 </repeat>
9eef2792afa4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
551 </conditional>
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
552 <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size" delta="20000"/>
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
553 </test>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
554 </tests>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
555 <help><![CDATA[
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
556
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
557 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
558
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
559 This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
560
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
561 Input data: 3 types of input data can be used:
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
562
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
563 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
564 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
565 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
566
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
567 Options:
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
568
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
569 - "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
570
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
571 - Enter the x and y coordinates of your pixel of interest
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
572 - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type.
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
573 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
6
2e0368a6bfe8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
574 - "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
575 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
576
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
577 Output:
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
578
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
579 - Pdf with the selected mass spectra plots and additional control plots
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
580
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
581 Tip:
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
582
3
fe28ca73548a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
583 - Corresponding mass spectra with m/z intensity pairs as tabular output can be obtained with the filtering tool option "ranges for x and y"
2
ea4f1c516368 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
584
0
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
585
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
586 ]]>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
587 </help>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
588 <citations>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
589 <citation type="doi">10.1093/bioinformatics/btv146</citation>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
590 </citations>
c93ae3463b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
591 </tool>