mass_spectrometry_imaging_segmentations: segmentation

annotate segmentation_tool.xml @ 6:80b6b96a175c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5

author	galaxyp
date	Tue, 19 Jun 2018 18:08:36 -0400
parents	cee9cf693709
children	adfef12c7e31

rev	line source
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	1 <tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.10.0.2">
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	2 <description>mass spectrometry imaging spatial clustering</description>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	3 <requirements>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	4 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	5 <requirement type="package" version="2.2.1">r-gridextra</requirement>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	6 <requirement type="package" version="0.20-35">r-lattice</requirement>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	7 </requirements>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	8 <command detect_errors="exit_code">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	9 <![CDATA[
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	10
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	11 #if $infile.ext == 'imzml'
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	12 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	13 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	14 #elif $infile.ext == 'analyze75'
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	15 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	16 ln -s '${infile.extra_files_path}/img' infile.img &&
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	17 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	18 #else
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	19 ln -s $infile infile.RData &&
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	20 #end if
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	21 cat '${MSI_segmentation}' &&
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	22 echo ${MSI_segmentation} &&
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	23 Rscript '${MSI_segmentation}'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	24
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	25 ]]>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	26 </command>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	27 <configfiles>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	28 <configfile name="MSI_segmentation"><![CDATA[
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	29
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	30
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	31 ################################# load libraries and read file #################
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	32
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	33 library(Cardinal)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	34 library(gridExtra)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	35 library(lattice)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	36
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	37 ## Read MALDI Imaging dataset
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	38
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	39 #if $infile.ext == 'imzml'
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	40 msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units")
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	41 #elif $infile.ext == 'analyze75'
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	42 msidata = readAnalyze('infile')
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	43 #else
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	44 load('infile.RData')
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	45 #end if
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	46
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	47 ## create full matrix to make processed imzML files compatible with segmentation
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	48 iData(msidata) <- iData(msidata)[]
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	49 ###################################### file properties in numbers ##############
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	50
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	51 ## Number of features (m/z)
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	52 maxfeatures = length(features(msidata))
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	53 ## Range m/z
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	54 minmz = round(min(mz(msidata)), digits=2)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	55 maxmz = round(max(mz(msidata)), digits=2)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	56 ## Number of spectra (pixels)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	57 pixelcount = length(pixels(msidata))
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	58 ## Range x coordinates
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	59 minimumx = min(coord(msidata)[,1])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	60 maximumx = max(coord(msidata)[,1])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	61 ## Range y coordinates
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	62 minimumy = min(coord(msidata)[,2])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	63 maximumy = max(coord(msidata)[,2])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	64 ## Range of intensities
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	65 minint = round(min(spectra(msidata)[]), digits=2)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	66 maxint = round(max(spectra(msidata)[]), digits=2)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	67 medint = round(median(spectra(msidata)[]), digits=2)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	68 ## Number of intensities > 0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	69 npeaks= sum(spectra(msidata)[]>0)
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	70 ## Spectra multiplied with m/z (potential number of peaks)
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	71 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	72 ## Percentage of intensities > 0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	73 percpeaks = round(npeaks/numpeaks*100, digits=2)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	74 ## Number of empty TICs
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	75 TICs = colSums(spectra(msidata)[])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	76 NumemptyTIC = sum(TICs == 0)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	77
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	78 ## Processing informations
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	79 processinginfo = processingData(msidata)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	80 centroidedinfo = processinginfo@centroided # TRUE or FALSE
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	81
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	82 ## if TRUE write processinginfo if FALSE write FALSE
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	83
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	84 ## normalization
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	85 if (length(processinginfo@normalization) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	86 normalizationinfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	87 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	88 normalizationinfo=processinginfo@normalization
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	89 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	90 ## smoothing
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	91 if (length(processinginfo@smoothing) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	92 smoothinginfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	93 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	94 smoothinginfo=processinginfo@smoothing
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	95 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	96 ## baseline
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	97 if (length(processinginfo@baselineReduction) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	98 baselinereductioninfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	99 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	100 baselinereductioninfo=processinginfo@baselineReduction
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	101 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	102 ## peak picking
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	103 if (length(processinginfo@peakPicking) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	104 peakpickinginfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	105 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	106 peakpickinginfo=processinginfo@peakPicking
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	107 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	108
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	109 properties = c("Number of m/z features",
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	110 "Range of m/z values",
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	111 "Number of pixels",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	112 "Range of x coordinates",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	113 "Range of y coordinates",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	114 "Range of intensities",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	115 "Median of intensities",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	116 "Intensities > 0",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	117 "Number of zero TICs",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	118 "Preprocessing",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	119 "Normalization",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	120 "Smoothing",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	121 "Baseline reduction",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	122 "Peak picking",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	123 "Centroided")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	124
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	125 values = c(paste0(maxfeatures),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	126 paste0(minmz, " - ", maxmz),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	127 paste0(pixelcount),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	128 paste0(minimumx, " - ", maximumx),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	129 paste0(minimumy, " - ", maximumy),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	130 paste0(minint, " - ", maxint),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	131 paste0(medint),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	132 paste0(percpeaks, " %"),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	133 paste0(NumemptyTIC),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	134 paste0(" "),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	135 paste0(normalizationinfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	136 paste0(smoothinginfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	137 paste0(baselinereductioninfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	138 paste0(peakpickinginfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	139 paste0(centroidedinfo))
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	140
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	141 property_df = data.frame(properties, values)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	142
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	143
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	144 ######################################## PDF ###################################
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	145 ################################################################################
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	146 ################################################################################
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	147
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	148
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	149 pdf("segmentationpdf.pdf", fonts = "Times", pointsize = 12)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	150 plot(0,type='n',axes=FALSE,ann=FALSE)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	151
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	152 title(main=paste0("Spatial segmentation for file: \n\n", "$infile.display_name"))
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	153
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	154
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	155 ############################# I) numbers ####################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	156 #############################################################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	157 grid.table(property_df, rows= NULL)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	158
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	159 if (npeaks > 0)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	160 {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	161
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	162 ######################## II) segmentation tools #############################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	163 #############################################################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	164 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $colours])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	165 colourvector = c($color_string)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	166
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	167 ### preparation for images and plots:
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	168 #if str($image_cond.image_type) == "standard_image":
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	169 print("standard image")
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	170
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	171 strip_input = TRUE
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	172 lattice_input = FALSE
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	173
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	174 #elif str($image_cond.image_type) == "lattice_image":
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	175 print("lattice image")
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	176
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	177 strip_input = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	178 lattice_input = TRUE
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	179
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	180 #end if
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	181
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	182
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	183 #if str( $segm_cond.segmentationtool ) == 'pca':
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	184 print('pca')
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	185 ##pca
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	186
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	187 component_vector = character()
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	188 for (numberofcomponents in 1:$segm_cond.pca_ncomp)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	189 {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	190 pca_result = PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE,
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	191 method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1))
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	192
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	193 ### images in pdf file
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	194 print(image(pca_result, main="PCA image", lattice=lattice_input, strip = strip_input, col=colourvector))
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	195 for (PCs in 1:$segm_cond.pca_ncomp){
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	196 print(image(pca_result, column = c(paste0("PC",PCs)), superpose = FALSE, col.regions = risk.colors(100)))}
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	197 ### plots in pdf file
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	198 print(plot(pca_result, main="PCA plot", lattice=lattice_input, col= colourvector, strip = strip_input))
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	199 for (PCs in 1:$segm_cond.pca_ncomp){
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	200 print(plot(pca_result, column = c(paste0("PC",PCs)), superpose = FALSE))}
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	201
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	202
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	203 ### values in tabular files
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	204 pcaloadings = (pca_result@resultData\$ncomp\$loadings) ### loading for each m/z value
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	205 pcascores = (pca_result@resultData\$ncomp\$scores) ### scores for each pixel
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	206
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	207 write.table(pcaloadings, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	208 write.table(pcascores, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	209
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	210 ## optional output as .RData
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	211 #if $output_rdata:
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	212 ## save as (.RData)
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	213 save(pca, file="$segmentation_rdata")
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	214
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	215 #end if
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	216
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	217 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	218 print('kmeans')
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	219 ##k-means
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	220
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	221 skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="$segm_cond.kmeans_method")
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	222 print(image(skm, key=TRUE, main="K-means clustering", lattice=lattice_input, strip=strip_input, col= colourvector, layout=c(1,1)))
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	223
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	224 print(plot(skm, main="K-means plot", lattice=lattice_input, col= colourvector, strip=strip_input, layout=c($segm_cond.kmeans_layout)))
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	225
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	226 skm_clusters = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	227 for (iteration in 1:length(skm@resultData)){
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	228 skm_cluster = ((skm@resultData)[[iteration]]\$cluster)
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	229 skm_clusters = cbind(skm_clusters, skm_cluster) }
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	230 colnames(skm_clusters) = names((skm@resultData))
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	231
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	232 skm_toplabels = topLabels(skm, n=$segm_cond.kmeans_toplabels)
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	233
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	234 write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	235 write.table(skm_clusters, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	236
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	237 ## optional output as .RData
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	238 #if $output_rdata:
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	239
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	240 ## save as (.RData)
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	241 save(skm, file="$segmentation_rdata")
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	242
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	243 #end if
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	244
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	245 #elif str( $segm_cond.segmentationtool ) == 'centroids':
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	246 print('centroids')
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	247 ##centroids
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	248
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	249 ssc = spatialShrunkenCentroids(msidata, r=c($segm_cond.centroids_r), k=c($segm_cond.centroids_k), s=c($segm_cond.centroids_s), method="$segm_cond.centroids_method")
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	250 print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=lattice_input, strip = strip_input, col= colourvector,layout=c(1,1)))
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	251 print(plot(ssc, main="Spatial shrunken centroids plot", lattice=lattice_input, col= colourvector, strip = strip_input,layout=c($segm_cond.centroids_layout)))
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	252 print(plot(ssc, mode = "tstatistics",key = TRUE, lattice=lattice_input, layout = c($segm_cond.centroids_layout), main="t-statistics", col=colourvector))
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	253 print(plot(summary(ssc), main = "Number of segments",lattice=lattice_input))
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	254
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	255 ssc_classes = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	256 for (iteration in 1:length(ssc@resultData)){
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	257 ssc_class = ((ssc@resultData)[[iteration]]\$classes)
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	258 ssc_classes = cbind(ssc_classes, ssc_class) }
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	259 colnames(ssc_classes) = names((ssc@resultData))
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	260
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	261 ssc_toplabels = topLabels(ssc, n=$segm_cond.centroids_toplabels)
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	262
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	263 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	264 write.table(ssc_classes, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	265
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	266 ## optional output as .RData
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	267 #if $output_rdata:
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	268
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	269 ## save as (.RData)
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	270 save(ssc, file="$segmentation_rdata")
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	271
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	272 #end if
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	273
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	274 #end if
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	275
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	276 dev.off()
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	277
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	278 }else{
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	279 print("Inputfile has no intensities > 0")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	280 dev.off()
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	281 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	282
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	283 ]]></configfile>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	284 </configfiles>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	285 <inputs>
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	286 <param name="infile" type="data" format="imzml,rdata,analyze75"
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	287 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	288 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	289 <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter 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"/>
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	290 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm">
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	291 <option value="mz" >mz</option>
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	292 <option value="ppm" selected="True" >ppm</option>
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	293 </param>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	294 <conditional name="segm_cond">
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	295 <param name="segmentationtool" type="select" label="Select the tool for spatial clustering">
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	296 <option value="pca" selected="True">pca</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	297 <option value="kmeans">k-means</option>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	298 <option value="centroids">spatial shrunken centroids</option>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	299 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	300 <when value="pca">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	301 <param name="pca_ncomp" type="integer" value="2"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	302 label="The number of principal components to calculate"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	303 <param name="pca_method" type="select"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	304 label="The function used to calculate the singular value decomposition">
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	305 <option value="irlba" selected="True">irlba</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	306 <option value="svd">svd</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	307 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	308 <param name="pca_scale" type="select" display="radio" optional="False"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	309 label="Scaling of data before analysis">
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	310 <option value="TRUE">yes</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	311 <option value="FALSE" selected="True">no</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	312 </param>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	313 </when>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	314
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	315 <when value="kmeans">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	316 <param name="kmeans_r" type="text" value="2"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	317 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	318 <param name="kmeans_k" type="text" value="3"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	319 label="The number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	320 <param name="kmeans_method" type="select" display="radio"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	321 label="The method to use to calculate the spatial smoothing kernels for the embedding. The 'gaussian' method refers to spatially-aware (SA) clustering, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) clustering">
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	322 <option value="gaussian">gaussian</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	323 <option value="adaptive" selected="True">adaptive</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	324 </param>
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	325 <param name="kmeans_toplabels" type="integer" value="500"
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	326 label="Number of toplabels (m/z) which should be written in tabular output"/>
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	327 <param name="kmeans_layout" type="text" value="1,1"
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	328 label="Number of rows and columns to plot pictures in pdf output" help="e.g. 1,1 means 1 plot per page; 2,3 means 2 rows with 3 plots each = 6 plots per page"/>
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	329 </when>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	330
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	331 <when value="centroids">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	332 <param name="centroids_r" type="text" value="2"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	333 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	334 <param name="centroids_k" type="text" value="5"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	335 label="The initial number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	336 <param name="centroids_s" type="text" value="2"
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	337 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)"
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	338 help="As s increases, fewer m/z features (m/z values) will be used in the spatial segmentation, and only the informative m/z features will be retained. Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	339 <param name="centroids_method" type="select" display="radio" label = "The method to use to calculate the spatial smoothing kernels for the embedding. The 'gaussian' method refers to spatially-aware (SA) weights, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) weights">
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	340 <option value="gaussian">gaussian</option>
80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	341 <option value="adaptive" selected="True">adaptive</option>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	342 </param>
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	343 <param name="centroids_toplabels" type="integer" value="500"
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	344 label="Number of toplabels (m/z) which should be written in tabular output"/>
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	345 <param name="centroids_layout" type="text" value="1,1"
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	346 label="Number of rows and columns to plot pictures in pdf output" help="e.g. 1,1 means 1 plot per page; 2,3 means 2 rows with 3 plots each = 6 plots per page"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	347 </when>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	348 </conditional>
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	349 <conditional name="image_cond">
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	350 <param name="image_type" type="select" label="Select the image type">
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	351 <option value="standard_image" selected="True">standard</option>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	352 <option value="lattice_image">lattice</option>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	353 </param>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	354 <when value="standard_image"/>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	355 <when value="lattice_image"/>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	356 </conditional>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	357 <repeat name="colours" title="Colours for the plots" min="1" max="50">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	358 <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of columns should be the same as number of components">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	359 <sanitizer>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	360 <valid initial="string.letters,string.digits">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	361 <add value="#" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	362 </valid>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	363 </sanitizer>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	364 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	365 </repeat>
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	366 <param name="output_rdata" type="boolean" display="radio" label="Results as .RData output"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	367 </inputs>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	368 <outputs>
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	369 <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "$infile.display_name segmentation"/>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	370 <data format="tabular" name="mzfeatures" label="$infile.display_name m/z features"/>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	371 <data format="tabular" name="pixeloutput" label="$infile.display_name pixels"/>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	372 <data format="rdata" name="segmentation_rdata" label="$infile.display_name segmentation">
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	373 <filter>output_rdata</filter>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	374 </data>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	375 </outputs>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	376 <tests>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	377 <test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	378 <param name="infile" value="" ftype="imzml">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	379 <composite_data value="Example_Continuous.imzML"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	380 <composite_data value="Example_Continuous.ibd"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	381 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	382 <param name="segmentationtool" value="pca"/>
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	383 <param name="image_type" value="lattice_image"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	384 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	385 <param name="feature_color" value="#ff00ff"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	386 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	387 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	388 <param name="feature_color" value="#0000FF"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	389 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	390 <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size" delta="20000"/>
1 d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a galaxyp parents: 0 diff changeset	391 <output name="mzfeatures" file="loadings_pca.tabular" compare="sim_size"/>
d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a galaxyp parents: 0 diff changeset	392 <output name="pixeloutput" file="scores_pca.tabular" compare="sim_size"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	393 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	394 <test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	395 <param name="infile" value="" ftype="analyze75">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	396 <composite_data value="Analyze75.hdr" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	397 <composite_data value="Analyze75.img" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	398 <composite_data value="Analyze75.t2m" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	399 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	400 <param name="segmentationtool" value="kmeans"/>
2 f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	401 <param name="kmeans_r" value="1:3"/>
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646 galaxyp parents: 1 diff changeset	402 <param name="kmeans_k" value="2,3"/>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	403 <param name="kmeans_toplabels" value="20"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	404 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	405 <param name="feature_color" value="#ff00ff"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	406 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	407 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	408 <param name="feature_color" value="#0000FF"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	409 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	410 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	411 <param name="feature_color" value="#00C957"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	412 </repeat>
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	413 <param name="output_rdata" value="True"/>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	414 <output name="segmentationimages" file="kmeans_analyze.pdf" compare="sim_size" delta="20000"/>
1 d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a galaxyp parents: 0 diff changeset	415 <output name="mzfeatures" file="toplabels_skm.tabular" compare="sim_size"/>
d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a galaxyp parents: 0 diff changeset	416 <output name="pixeloutput" file="cluster_skm.tabular" compare="sim_size"/>
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	417 <output name="pixeloutput" file="cluster_skm.tabular" compare="sim_size"/>
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	418 <output name="segmentation_rdata" file="cluster_skm.RData" compare="sim_size"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	419 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	420 <test>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	421 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	422 <param name="segmentationtool" value="centroids"/>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	423 <param name="centroids_r" value="1,2"/>
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	424 <param name="centroids_k" value="3"/>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	425 <param name="centroids_toplabels" value="50"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	426 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	427 <param name="feature_color" value="#0000FF"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	428 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	429 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	430 <param name="feature_color" value="#00C957"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	431 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	432 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	433 <param name="feature_color" value="#B0171F"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	434 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	435 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	436 <param name="feature_color" value="#FFD700"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	437 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	438 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	439 <param name="feature_color" value="#848484"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	440 </repeat>
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	441 <output name="segmentationimages" file="centroids_rdata.pdf" compare="sim_size" delta="20000"/>
1 d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a galaxyp parents: 0 diff changeset	442 <output name="mzfeatures" file="toplabels_ssc.tabular" compare="sim_size"/>
d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a galaxyp parents: 0 diff changeset	443 <output name="pixeloutput" file="classes_ssc.tabular" compare="sim_size"/>
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	444 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	445 </tests>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	446 <help>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	447 <![CDATA[
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	448
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	449 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	450
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	451 This tool provides three different Cardinal functions for unsupervised clustering/spatial segmentation of mass spectrometry imaging data.
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	452
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	453 Input data: 3 types of input data can be used:
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	454
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	455 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	456 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	457 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	458
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	459 Options:
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	460
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	461 - PCA: principal component analysis
6 80b6b96a175c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5 galaxyp parents: 5 diff changeset	462 - k-means: spatially-aware k-means clustering
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	463 - spatial shrunken centroids: Allows the number of segments to decrease according to the data. This allows automatic selection of the number of clusters
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	464
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	465 Output:
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	466
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	467 - Pdf with the heatmaps and plots for the segmentation
5 cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	468 - Tabular file with information on m/z and pixels: loadings/scores (PCA), toplabels/clusters (k-means), toplabels/classes (spatial shrunken centroids)
cee9cf693709 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7 galaxyp parents: 4 diff changeset	469 - Optional .RData file which contains the segmentation results and can be used for further exploration in R
4 aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 galaxyp parents: 3 diff changeset	470
0 0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	471 ]]>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	472 </help>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	473 <citations>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	474 <citation type="doi">10.1093/bioinformatics/btv146</citation>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	475 </citations>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b galaxyp parents: diff changeset	476 </tool>

Mercurial > repos > galaxyp > mass_spectrometry_imaging_segmentations

annotate segmentation_tool.xml @ 6:80b6b96a175c draft