msi_preprocessing: msi_preprocessing.xml annotate

annotate msi_preprocessing.xml @ 0:133a921f4ef5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55

author	galaxyp
date	Tue, 31 Oct 2017 15:04:41 -0400
parents
children	641316f29395

rev	line source
0 133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.7.0">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	2 <description>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	3 mass spectrometry imaging preprocessing
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	4 </description>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	5 <requirements>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	6 <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	7 </requirements>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	8 <command detect_errors="exit_code">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	9 <![CDATA[
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	10
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	11 #if $infile.ext == 'imzml'
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	12 cp '${infile.extra_files_path}/imzml' infile.imzML &&
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	13 cp '${infile.extra_files_path}/ibd' infile.ibd &&
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	14 #elif $infile.ext == 'analyze75'
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	15 cp '${infile.extra_files_path}/hdr' infile.hdr &&
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	16 cp '${infile.extra_files_path}/img' infile.img &&
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	17 cp '${infile.extra_files_path}/t2m' infile.t2m &&
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	18 #else
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	19 ln -s '$infile' infile.RData &&
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	20 #end if
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	21 cat '${cardinal_preprocessing}' &&
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	22 Rscript '${cardinal_preprocessing}'
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	23
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	24 ]]>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	25 </command>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	26 <configfiles>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	27 <configfile name="cardinal_preprocessing"><![CDATA[
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	28 library(Cardinal)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	29
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	30 #if $infile.ext == 'imzml'
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	31 msidata <- readMSIData('infile.imzML')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	32 #elif $infile.ext == 'analyze75'
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	33 msidata <- readMSIData('infile.hdr')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	34 #else
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	35 load('infile.RData')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	36 #end if
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	37
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	38 maxpixel = length(pixels(msidata))
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	39 pixelnumber = c(1:maxpixel)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	40
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	41 #for $method in $methods:
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	42 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	43 print('Normalization')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	44 ##normalization
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	45 msidata <- normalize(msidata, pixel=pixelnumber, method="tic")
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	46
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	47 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	48 print('Baseline_reduction')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	49 ##baseline reduction
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	50 msidata = reduceBaseline(msidata, pixel=pixelnumber, method="median", blocks=$method.methods_conditional.blocks_baseline)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	51
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	52 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	53 print('Smoothing')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	54 ## Smoothing
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	55
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	56 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	57 print('gaussian smoothing')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	58 msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	59 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	60 print('sgolay smoothing')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	61 msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	62 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	63 print('sgolay smoothing')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	64 msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	65 #end if
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	66
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	67 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	68 print('Peak_picking')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	69 ## Peakpicking
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	70
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	71 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	72 print('adaptive peakpicking')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	73 msidata = peakPick(msidata, pixel=pixelnumber, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, spar=$method.methods_conditional.methods_for_picking.spar_picking)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	74
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	75 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'limpic':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	76 print('limpic peakpicking')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	77 msidata = peakPick(msidata, pixel=pixelnumber, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, thresh=$method.methods_conditional.methods_for_picking.tresh_picking)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	78
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	79 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	80 print('simple peakpicking')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	81 msidata = peakPick(msidata, pixel=pixelnumber, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	82 #end if
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	83
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	84 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	85 print('Peak_alignment')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	86 ## Peakalignment
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	87
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	88 #if str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'diff':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	89 print('diff peaklignment')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	90 msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',diff.max =$method.methods_conditional.methods_for_alignment.value_diffalignment, units = "$method.methods_conditional.methods_for_alignment.units_diffalignment")
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	91
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	92 #elif str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'DP':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	93 print('DPpeaklignment')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	94 msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',gap = $method.methods_conditional.methods_for_alignment.gap_DPalignment )
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	95 #end if
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	96
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	97 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	98 print('Peak_filtering')
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	99 msidata = peakFilter(msidata, method='freq', freq.min = $method.methods_conditional.frequ_filtering)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	100 #end if
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	101 #end for
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	102
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	103 ## save as as (.RData)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	104 save(msidata, file="$msidata_preprocessed")
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	105
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	106 ## save as intensity matrix (.csv)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	107 csvmatrix = spectra(msidata)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	108 rownames(csvmatrix) = mz(msidata)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	109 newmatrix = rbind(pixels(msidata), csvmatrix)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	110 write.csv(newmatrix[2:nrow(newmatrix),], file="$preprocessed_intensity_matrix")
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	111
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	112 ]]></configfile>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	113 </configfiles>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	114 <inputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	115 <param name="infile" type="data" format="imzml,rdata,analyze75"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	116 label="MSI rawdata as imzml or Cardinal MSImageSet saved as RData"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	117 help="load imzml and ibd file by uploading composite datatype imzml"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	118
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	119 <repeat name="methods" title="Preprocessing" min="1" max="50">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	120 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	121 <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	122 <option value="Normalization" selected="True">Normalization to TIC</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	123 <option value="Baseline_reduction">Baseline Reduction</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	124 <option value="Smoothing">Peak smoothing</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	125 <option value="Peak_picking">Peak picking</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	126 <option value="Peak_alignment">Peak alignment</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	127 <option value="Peak_filtering">Peak filtering</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	128 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	129 <when value="Normalization"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	130 <when value="Baseline_reduction">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	131 <param name="blocks_baseline" type="integer" value="50"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	132 label="blocks"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	133 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	134 <when value="Smoothing">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	135 <conditional name="methods_for_smoothing">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	136 <param name="smoothing_method" type="select" label="Smoothing method">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	137 <option value="gaussian" selected="True">gaussian</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	138 <option value="sgolay">Savitsky-Golay</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	139 <option value="ma">moving average</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	140 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	141 <when value="gaussian">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	142 <param name="sd_gaussian" type="float" value="4"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	143 label="The standard deviation for the Gaussian kernel (window/sd)"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	144 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	145 <when value="sgolay">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	146 <param name="order_of_filters" type="integer" value="3"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	147 label="The order of the smoothing filter"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	148 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	149 <when value="ma">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	150 <param name="coefficients_ma_filter" type="integer" value="1"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	151 label="The coefficients for the moving average filter"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	152 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	153 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	154 <param name="window_smoothing" type="integer" value="9"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	155 label="Window size"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	156 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	157 <when value="Peak_picking">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	158 <param name="SNR_picking_method" type="integer" value="3"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	159 label="Signal to noise ratio"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	160 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	161 <param name="blocks_picking" type="integer" value="100" label = "number of blocks"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	162 help="Number of blocks in which to divide mass spectrum to calculate noise"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	163 <param name="window_picking" type="integer" value="5" label= "window size" help="Window width for seeking local maxima"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	164 <conditional name="methods_for_picking">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	165 <param name="picking_method" type="select" label="Peak picking method" help = "only simple works for processed imzML files">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	166 <option value="adaptive" selected="True">adaptive</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	167 <option value="limpic">limpic</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	168 <option value="simple">simple</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	169 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	170 <when value="adaptive">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	171 <param name="spar_picking" type="float" value="1.0"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	172 label="spar value"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	173 help = "Smoothing parameter for the spline smoothing
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	174 applied to the spectrum in order to decide the cutoffs
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	175 for throwing away false noise spikes that might occur inside peaks"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	176 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	177 <when value="limpic">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	178 <param name="tresh_picking" type="float" value="0.75"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	179 label="thresh value" help = "The thresholding quantile to use when comparing slopes in order to throw away peaks that are too flat"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	180 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	181 <when value="simple"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	182 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	183 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	184 <when value="Peak_alignment">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	185 <conditional name="methods_for_alignment">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	186 <param name="alignment_method" type="select" label="Alignment method">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	187 <option value="diff" selected="True">diff</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	188 <option value="DP">DP</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	189 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	190 <when value="diff">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	191 <param name="value_diffalignment" type="integer" value="200"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	192 label="diff.max" help="Peaks that differ less than this value will be aligned together"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	193 <param name="units_diffalignment" type="select" display = "radio" optional = "False"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	194 label="units" help= "The coefficients for the moving average filter">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	195 <option value="ppm" selected="True">ppm</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	196 <option value="Da">Da</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	197 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	198 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	199 <when value="DP">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	200 <param name="gap_DPalignment" type="integer" value="0"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	201 label="gap" help = "The gap penalty for the dynamic programming sequence alignment"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	202 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	203 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	204 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	205 <when value="Peak_filtering">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	206 <param name="frequ_filtering" type="float" value="1"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	207 label="freq.min" help = "Peaks that occur in the dataset fewer times than this will be removed"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	208 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	209 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	210 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	211 </inputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	212 <outputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	213 <data format="rdata" name="msidata_preprocessed" label="Preprocessed_output"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	214 <data format="csv" name="preprocessed_intensity_matrix" label="preprocessed intensity matrix" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	215 </outputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	216 <tests>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	217 <test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	218 <param name="infile" value="" ftype="imzml">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	219 <composite_data value="Example_Continuous.imzML" ftype="imzml"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	220 <composite_data value="Example_Continuous.ibd" ftype="ibd"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	221 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	222 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	223 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	224 <param name="preprocessing_method" value="Normalization" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	225 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	226 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	227 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	228 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	229 <param name="preprocessing_method" value="Smoothing" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	230 <conditional name="methods_for_smoothing">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	231 <param name="smoothing_method" value="sgolay" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	232 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	233 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	234 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	235 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	236 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	237 <param name="preprocessing_method" value="Peak_picking" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	238 <conditional name="methods_for_picking">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	239 <param name="picking_method" value="adaptive" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	240 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	241 <param name="blocks_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	242 <param name="window_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	243 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	244 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	245 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	246 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	247 <param name="preprocessing_method" value="Peak_alignment" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	248 <conditional name="methods_for_alignment">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	249 <param name="alignment_method" value="DP" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	250 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	251 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	252 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	253 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	254 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	255 <param name="preprocessing_method" value="Peak_filtering" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	256 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	257 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	258 <output name="msidata_preprocessed" file="preprocessing_results1.RData" compare="sim_size" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	259 <output name="preprocessed_intensity_matrix" file="preprocessing_results1.csv" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	260 </test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	261 <test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	262 <param name="infile" value="LM5_first68pixel.RData" ftype="rdata"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	263 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	264 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	265 <param name="preprocessing_method" value="Baseline_reduction" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	266 <param name="blocks_baseline" value="50" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	267 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	268 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	269 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	270 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	271 <param name="preprocessing_method" value="Peak_picking" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	272 <param name="blocks_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	273 <param name="window_picking" value="5" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	274 <param name="methods_for_picking" value="simple" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	275 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	276 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	277 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	278 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	279 <param name="preprocessing_method" value="Peak_alignment" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	280 <param name="methods_for_alignment" value="DP" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	281 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	282 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	283 <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	284 <output name="preprocessed_intensity_matrix" file="preprocessing_results2.csv" lines_diff="2"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	285 </test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	286 <test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	287 <param name="infile" value="" ftype="analyze75">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	288 <composite_data value="Analyze75.hdr" ftype="hdr"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	289 <composite_data value="Analyze75.img" ftype="img"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	290 <composite_data value="Analyze75.t2m" ftype="t2m"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	291 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	292 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	293 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	294 <param name="preprocessing_method" value="Normalization" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	295 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	296 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	297 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	298 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	299 <param name="preprocessing_method" value="Smoothing" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	300 <conditional name="methods_for_smoothing">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	301 <param name="smoothing_method" value="gaussian" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	302 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	303 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	304 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	305 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	306 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	307 <param name="preprocessing_method" value="Peak_picking" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	308 <param name="blocks_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	309 <param name="window_picking" value="5" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	310 <param name="methods_for_picking" value="limpic" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	311 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	312 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	313 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	314 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	315 <param name="preprocessing_method" value="Peak_alignment" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	316 <param name="methods_for_alignment" value="diff" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	317 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	318 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	319 <output name="msidata_preprocessed" file="preprocessing_results3.RData" compare="sim_size" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	320 <output name="preprocessed_intensity_matrix" file="preprocessing_results3.csv" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	321 </test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	322 </tests>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	323 <help>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	324 <![CDATA[
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	325 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	326
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	327 Preprocessing steps:
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	328
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	329 - Smoothening: Smoothing of the mass peaks reduces noise and improves peak detection
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	330 - Normalization: Normalization of intensities to total ion current (TIC)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	331 - Baseline reduction: Baseline reduction removes backgroundintensity generated by chemical noise (common in MALDI datasets)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	332 - Peak picking: relevant peaks are picked while noise-peaks are removed
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	333 - Peak alignment: mz inaccuracies are removed by alignment of same peaks to a common mz value
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	334 - Peak filtering: removes peaks that occur infrequently, such as those which only occur in a small proportion of pixels
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	335 ]]>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	336 </help>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	337 <citations>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	338 <citation type="doi">10.1093/bioinformatics/btv146</citation>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	339 </citations>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55 galaxyp parents: diff changeset	340 </tool>

Mercurial > repos > galaxyp > msi_preprocessing

annotate msi_preprocessing.xml @ 0:133a921f4ef5 draft