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annotate msi_qualitycontrol.xml @ 0:845073d506a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
author galaxyp
date Tue, 31 Oct 2017 06:00:03 -0400
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845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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1 <tool id="Mass_spectrometry_imaging_QC" name="MSI Qualitycontrol" version="1.7.0">
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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2 <description>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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3 mass spectrometry imaging QC
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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9 <requirement type="package" version="2.2.1"> r-gridextra</requirement>
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10 <requirement type="package" version="2.23_15">r-kernsmooth</requirement>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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11 </requirements>
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12 <command detect_errors="exit_code">
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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13 <![CDATA[
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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14
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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15 #if $infile.ext == 'imzml'
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16 cp '${infile.extra_files_path}/imzml' infile.imzML &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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17 cp '${infile.extra_files_path}/ibd' infile.ibd &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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18 #elif $infile.ext == 'analyze75'
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19 cp '${infile.extra_files_path}/hdr' infile.hdr &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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20 cp '${infile.extra_files_path}/img' infile.img &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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21 cp '${infile.extra_files_path}/t2m' infile.t2m &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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22 #else
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23 ln -s '$infile' infile.RData &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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24 #end if
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25 cat '${cardinal_qualitycontrol_script}' &&
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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26 Rscript '${cardinal_qualitycontrol_script}'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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27 ]]>
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28 </command>
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29 <configfiles>
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30 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
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31
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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32 ################################# load libraries and read file #########################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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33 library(Cardinal)
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34 library(ggplot2)
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35 library(RColorBrewer)
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36 library(gridExtra)
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37 library(KernSmooth)
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38
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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39 ## Read MALDI Imagind dataset
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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40
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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41 #if $infile.ext == 'imzml'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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42 msidata <- readMSIData('infile.imzML')
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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43 #elif $infile.ext == 'analyze75'
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44 msidata <- readMSIData('infile.hdr')
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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45
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46 #else
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47 load('infile.RData')
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48 #end if
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49
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50 #if $inputpeptidefile:
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51 ## Read tabular file with peptide masses for plots and heatmap images:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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52 input_list = read.delim("$inputpeptidefile", header = FALSE, na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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53 #else
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54 input_list = data.frame(0, 0)
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55 #end if
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56
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57 ###################################### file properties in numbers ######################
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58
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59 ## Number of features (mz)
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60 maxfeatures = length(features(msidata))
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61 ## Range mz
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62 minmz = round(min(mz(msidata)), digits=2)
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63 maxmz = round(max(mz(msidata)), digits=2)
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64 ## Number of spectra (pixels)
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65 pixelcount = length(pixels(msidata))
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66 ## Range x coordinates
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67 minimumx = min(coord(msidata)[,1])
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68 maximumx = max(coord(msidata)[,1])
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69 ## Range y coordinates
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70 minimumy = min(coord(msidata)[,2])
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71 maximumy = max(coord(msidata)[,2])
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72 ## Range of intensities
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73 minint = round(min(spectra(msidata)[]), digits=2)
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74 maxint = round(max(spectra(msidata)[]), digits=2)
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75 medint = round(median(spectra(msidata)[]), digits=2)
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76 ## Number of intensities > 0
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77 npeaks= sum(spectra(msidata)[]>0)
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78 ## Spectra multiplied with mz (potential number of peaks)
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79 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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80 ## Percentage of intensities > 0
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81 percpeaks = round(npeaks/numpeaks*100, digits=2)
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82 ## Number of empty TICs
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83 TICs = colSums(spectra(msidata)[])
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84 NumemptyTIC = sum(TICs == 0)
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85
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86 ## Processing informations
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87 processinginfo = processingData(msidata)
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88 centroidedinfo = processinginfo@centroided # TRUE or FALSE
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89
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
90 ## if TRUE write processinginfo if no write FALSE
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
91
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
92 ## normalization
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
93 if (length(processinginfo@normalization) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
94 normalizationinfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
95 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
96 normalizationinfo=processinginfo@normalization
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
97 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
98 ## smoothing
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
99 if (length(processinginfo@smoothing) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
100 smoothinginfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
101 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
102 smoothinginfo=processinginfo@smoothing
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
103 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
104 ## baseline
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
105 if (length(processinginfo@baselineReduction) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
106 baselinereductioninfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
107 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
108 baselinereductioninfo=processinginfo@baselineReduction
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
109 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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110 ## peak picking
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
111 if (length(processinginfo@peakPicking) == 0) {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
112 peakpickinginfo='FALSE'
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
113 } else {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
114 peakpickinginfo=processinginfo@peakPicking
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
115 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
116
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galaxyp
parents:
diff changeset
117
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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118 ## calculate how many input peptide masses are valid:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
119 inputpeptides = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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120 inputmasses = inputpeptides[,1]
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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121 inputnames = inputpeptides[,2]
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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122
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galaxyp
parents:
diff changeset
123 #############################################################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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124
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galaxyp
parents:
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125 properties = c("Number of mz features",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
126 "Range of mz values [Da]",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
127 "Number of pixels",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
128 "Range of x coordinates",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
129 "Range of y coordinates",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
130 "Range of intensities",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
131 "Median of intensities",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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132 "Intensities > 0",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
133 "Number of zero TICs",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
134 "Preprocessing",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
135 "Normalization",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
136 "Smoothing",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
137 "Baseline reduction",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
138 "Peak picking",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
139 "Centroided",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
140 "# valid peptidemasses")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
141
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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142 values = c(paste0(maxfeatures),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
143 paste0(minmz, " - ", maxmz),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
144 paste0(pixelcount),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
145 paste0(minimumx, " - ", maximumx),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
146 paste0(minimumy, " - ", maximumy),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
147 paste0(minint, " - ", maxint),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
148 paste0(medint),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
149 paste0(percpeaks, " %"),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
150 paste0(NumemptyTIC),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
151 paste0(" "),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
152 paste0(normalizationinfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
153 paste0(smoothinginfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
154 paste0(baselinereductioninfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
155 paste0(peakpickinginfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
156 paste0(centroidedinfo),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
157 paste0(length(inputmasses)))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
158
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galaxyp
parents:
diff changeset
159
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
160 property_df = data.frame(properties, values)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
161
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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162
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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163 ## Variables for plots
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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164 xrange = 1
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
165 yrange = 1
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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166 maxx = max(coord(msidata)[,1])+xrange
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
167 minx = min(coord(msidata)[,1])-xrange
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
168 maxy = max(coord(msidata)[,2])+yrange
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
169 miny = min(coord(msidata)[,2])-yrange
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
170
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
171
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galaxyp
parents:
diff changeset
172 ####################################### Preparation of images #########################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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173
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
174 ## Acquisitionorder
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
175
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
176 pixelnumber = 1:pixelcount
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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177 pixelxyarray=cbind(coord(msidata),pixelnumber)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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178
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galaxyp
parents:
diff changeset
179
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
180 ## Number of peaks per pixel
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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181 peaksperpixel = colSums(spectra(msidata)[]> 0)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
182 peakscoordarray=cbind(coord(msidata), peaksperpixel)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
183
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galaxyp
parents:
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184 ## Most abundant mz
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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185
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186 highestmz = apply(spectra(msidata)[],2,which.max)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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187 highestmz_matrix = cbind(coord(msidata),mz(msidata)[highestmz])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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188 colnames(highestmz_matrix)[3] = "highestmzinDa"
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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189
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galaxyp
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190 ###################################### Preparation of plots ############################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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191
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192 ## function without xaxt for plots with automatic x axis
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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193 plot_colorByDensity = function(x1,x2,
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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194 ylim=c(min(x2),max(x2)),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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195 xlim=c(min(x1),max(x1)),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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196 xlab="",ylab="",main="") {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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197
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198 df <- data.frame(x1,x2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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199 x <- densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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200 df\$dens <- col2rgb(x)[1,] + 1L
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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201 cols <- colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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202 df\$col <- cols[df\$dens]
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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203 plot(x2~x1, data=df[order(df\$dens),],
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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204 ylim=ylim,xlim=xlim,pch=20,col=col,
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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205 cex=1,xlab=xlab,ylab=ylab,las=1,
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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206 main=main)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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207 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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208
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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209 ## Number of peaks per mz - number across all pixel
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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210 peakspermz = rowSums(spectra(msidata)[] > 0 )
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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211
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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212 ## Sum of all intensities for each mz (like TIC, but for mz instead of pixel)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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213 mzTIC = rowSums(spectra(msidata)[]) # calculate intensity sum for each mz
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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214
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215
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216
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galaxyp
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217 ######################################## PDF #############################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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218 ##########################################################################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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219 ##########################################################################################
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220
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221
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222 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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223 plot(0,type='n',axes=FALSE,ann=FALSE)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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224 #if not $filename:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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225 #set $filename = $infile.display_name
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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226 #end if
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227 title(main=paste("Quality control of MSI data\n\n", "Filename:", "$filename"))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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228
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galaxyp
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229 ############################# I) numbers ####################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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230 #############################################################################
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231 grid.table(property_df, rows= NULL)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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232
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galaxyp
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233 ############################# II) ion images #################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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234 ##############################################################################
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235
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galaxyp
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236 ## 1) Acquisition image
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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237 (ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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238 +scale_y_reverse() + geom_tile() + coord_fixed()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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239 + ggtitle("1) Order of Acquisition")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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240 +theme_bw()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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241 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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242 space = "Lab", na.value = "black", name = "Acq"))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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243
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244 ## 2) Calibrant images:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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245
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246
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247
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galaxyp
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248 if (length(inputmasses) != 0)
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249 { for (mass in 1:length(inputmasses))
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250
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galaxyp
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251 {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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252 image(msidata, mz=inputmasses[mass], plusminus=$plusminusinDalton,
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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253 main= paste0("2",LETTERS[mass], ") ", inputnames[mass], " (", round(inputmasses[mass], digits = 2), " Da)"),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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254 contrast.enhance = "histogram")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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255 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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256 } else {print("The inputpeptide masses were outside the mass range")}
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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257
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258 ## 3) Number of peaks per pixel - image
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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259
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galaxyp
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260 (ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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261 +scale_y_reverse(lim=c(maxy,miny)) + geom_tile() + coord_fixed()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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262 + ggtitle("3) Number of peaks per pixel")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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263 + theme_bw()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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264 + theme(text=element_text(family="ArialMT", face="bold", size=12))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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265 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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266 ,space = "Lab", na.value = "black", name = "# peaks"))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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267
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268
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galaxyp
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269 ## 4) TIC image
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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270 TICcoordarray=cbind(coord(msidata), TICs)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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271 colo <- colorRampPalette(
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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272 c('blue', 'cyan', 'green', 'yellow','red'))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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273 (ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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274 +scale_y_reverse(lim=c(maxy,miny)) + geom_tile() + coord_fixed()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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275 + ggtitle("4) Total Ion Chromatogram")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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276 + theme_bw()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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277 + theme(text=element_text(family="ArialMT", face="bold", size=12))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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278 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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279 ,space = "Lab", na.value = "black", name = "TIC"))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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280
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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281 ## 5) Most abundant mass image
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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282
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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283 (ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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284 +scale_y_reverse(lim=c(maxy,miny)) + geom_tile() + coord_fixed()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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285 + ggtitle("5) Most abundant m/z in each pixel")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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286 + theme_bw()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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287 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z",
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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288 labels = as.character(pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)]),
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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289 breaks = pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)], limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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290 + theme(text=element_text(family="ArialMT", face="bold", size=12)))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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291
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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292 ## which mz are highest
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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293 highestmz_peptides = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[1])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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294 highestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == highestmz_peptides)[1]
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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295
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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296 secondhighestmz = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[2])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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297 secondhighestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == secondhighestmz)[1]
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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298
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299
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300
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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301 ## 6) pca image for two components
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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302 pca <- PCA(msidata, ncomp=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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303 par(mfrow = c(2,1))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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304 plot(pca, col=c("black", "darkgrey"), main="6) PCA for two components")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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305 image(pca, ylim = c(-1, maxy), col=c("black", "white"))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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306
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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307
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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308 ############################# III) properties over acquisition (spectra index)##########
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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309 ##############################################################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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310
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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311 par(mfrow = c(2,1), mar=c(5,6,4,2))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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312
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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313 ## 7a) number of peaks per spectrum - scatterplot
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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314 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="7a) Number of peaks per spectrum")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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315 title(xlab="Spectra index \n (= Acquisition time)", line=3)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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316 title(ylab="Number of peaks", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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317
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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318 ## 7b) number of peaks per spectrum - histogram
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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319 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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320 title(main="7b) Number of peaks per spectrum", line=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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321 title(ylab="Frequency = # spectra", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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322 abline(v=median(peaksperpixel), col="blue")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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323
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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324 ## 8a) TIC per spectrum - density scatterplot
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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325 zero=0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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326 par(mfrow = c(2,1), mar=c(5,6,4,2))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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327 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="8a) TIC per pixel")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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328 title(xlab="Spectra index \n (= Acquisition time)", line=3)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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329 title(ylab = "Total ion chromatogram intensity", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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330
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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331 ## 8b) TIC per spectrum - histogram
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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332 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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333 title(main= "8b) TIC per spectrum", line=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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334 title(ylab="Frequency = # spectra", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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335 abline(v=median(log(TICs[TICs>0])), col="blue")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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336
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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337
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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338 ## 9) intensity of chosen peptides over acquisition (pixel index)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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339
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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340 if (length(inputmasses) != 0)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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341 {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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342
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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343 par(mfrow = c(3, 2))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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344 intensityvector = vector()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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345 for (mass in 1:length(inputmasses))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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346 {
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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347 mznumber = features(msidata, mz = inputmasses[mass])
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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348 intensityvector = spectra(msidata)[][mznumber,]
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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349 plot(intensityvector, main=inputnames[mass], xlab="Spectra index \n (= Acquisition time)")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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350 }
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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351 } else {print("The inputpeptide masses were outside the mass range")}
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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352
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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353 ################################## IV) changes over mz ############################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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354 ###################################################################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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355
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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356 ## 10) Number of peaks per mz
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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357
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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358 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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359 ## 10a) Number of peaks per mz - scatterplot
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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parents:
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360 plot_colorByDensity(mz(msidata),peakspermz, main= "10a) Number of peaks for each mz", ylab ="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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361 title(xlab="mz in Dalton", line=2.5)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
362 title(ylab = "Number of peaks", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
363 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
364 mtext("Coverage of spectra [%]", 4, line=3, adj=1)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
365
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
366 # make plot smaller to fit axis and labels, add second y axis with %
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
367 ## 10b) Number of peaks per mz - histogram
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
368 hist(peakspermz, main="", las=1, ylab="", xlab="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
369 title(ylab = "Frequency", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
370 title(main="10b) Number of peaks per mz", xlab = "Number of peaks per mz", line=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
371 abline(v=median(peakspermz), col="blue")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
372
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
373
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
374 ## 11) Sum of intensities per mz
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
375
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
376 par(mfrow = c(2,1), mar=c(5,6,4,2))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
377 # 11a) sum of intensities per mz - scatterplot
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
378 plot_colorByDensity(mz(msidata),mzTIC, main= "11a) Sum of all peak intensities for each mz", ylab ="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
379 title(xlab="mz in Dalton", line=2.5)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
380 title(ylab="Intensity sum", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
381 # 11b) sum of intensities per mz - histogram
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
382 hist(log(mzTIC), main="", xlab = "", las=1, ylab="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
383 title(main="11b) Sum of intensities per mz", line=2, ylab="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
384 title(xlab = "log (sum of intensities per mz)")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
385 title(ylab = "Frequency", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
386 abline(v=median(log(mzTIC[mzTIC>0])), col="blue")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
387
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
388
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
389
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
390 ################################## V) general plots ############################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
391 ###################################################################################
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
392
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
393
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
394 ## 12) Intensity distribution
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
395
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
396 par(mfrow = c(2,1), mar=c(5,6,4,2))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
397
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
398 ## 12a) Intensity histogram:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
399 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
400 title(main="12a) Log2-transformed intensities", line=2)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
401 title(xlab="log2 intensities")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
402 title(ylab="Frequency", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
403 abline(v=median(log2(spectra(msidata)[(spectra(msidata)>0)])), col="blue")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
404
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
405 ## 12b) Median intensity over spectra
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
406 medianint_spectra = apply(spectra(msidata), 2, median)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
407 plot(medianint_spectra, main="12b) Median intensity per spectrum",las=1, xlab="Spectra index \n (= Acquisition time)", ylab="")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
408 title(ylab="Median spectrum intensity", line=4)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
409
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
410 ## 13) Mass spectra
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
411
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
412 par(mfrow = c(2, 2))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
413 plot(msidata, pixel = 1:length(pixelnumber), main= "Average spectrum")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
414 plot(msidata, pixel =round(length(pixelnumber)/2, digits=0), main="Spectrum in middle of acquisition")
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
415 plot(msidata, pixel = highestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[highestmz_pixel,])))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
416 plot(msidata, pixel = secondhighestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[secondhighestmz_pixel,])))
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
417
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
418 dev.off()
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
419
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
420 ]]></configfile>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
421 </configfiles>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
422 <inputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
423 <param name="infile" type="data" format="imzml, rdata, analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
424 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
425 <param name="filename" type="text" value="" optional="true" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
426 <param name="inputpeptidefile" type="data" optional="true" format="txt, csv" label="Text file with peptidemasses and names"
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
427 help="first column peptide m/z, second column peptide name, tab separated file"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
428 <param name="plusminusinDalton" value="0.25" type="text" label="Mass range" help="plusminus mass window in Dalton"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
429 </inputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
430 <outputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
431 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label="${tool.name} on $infile.display_name"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
432 </outputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
433 <tests>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
434 <test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
435 <param name="infile" value="" ftype="imzml">
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
436 <composite_data value="Example_Continuous.imzML" ftype="imzml"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
437 <composite_data value="Example_Continuous.ibd" ftype="ibd"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
438 </param>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
439 <param name="inputpeptidefile" value="inputpeptides.csv" ftype="csv"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
440 <param name="plusminusinDalton" value="0.25"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
441 <param name="filename" value="Testfile_imzml"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
442 <output name="plots" file="Testfile_qualitycontrol_imzml.pdf" compare="sim_size" delta="20000"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
443 </test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
444 <test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
445 <param name="infile" value="" ftype="analyze75">
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
446 <composite_data value="Analyze75.hdr" ftype="hdr"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
447 <composite_data value="Analyze75.img" ftype="img"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
448 <composite_data value="Analyze75.t2m" ftype="t2m"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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449 </param>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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450 <param name="inputpeptidefile" value="inputpeptides.txt" ftype="txt"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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451 <param name="plusminusinDalton" value="0.5"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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452 <param name="filename" value="Testfile_analyze75"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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453 <output name="plots" file="Testfile_qualitycontrol_analyze75.pdf" compare="sim_size" delta="20000"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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454 </test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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455 <test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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456 <param name="infile" value="example_continousS042.RData" ftype="rdata"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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457 <param name="inputpeptidefile" value="inputpeptides.csv" ftype="txt"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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458 <param name="plusminusinDalton" value="0.1"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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459 <param name="filename" value="Testfile_rdata"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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460 <output name="plots" file="Testfile_qualitycontrol_rdata.pdf" compare="sim_size" delta="20000"/>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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461 </test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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462 </tests>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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463 <help>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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464 <![CDATA[
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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465 Quality control for maldi imaging mass spectrometry data.
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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466
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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467 Input data: 3 types of input data can be used:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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468
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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469 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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470 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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471 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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472
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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473 Only for continuous imzML so far.
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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474
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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475 The output of this tool contains key values and plots of the imaging data as pdf.
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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476
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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477 ]]>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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478 </help>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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479 <citations>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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480 <citation type="doi">10.1093/bioinformatics/btv146</citation>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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481 </citations>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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482 </tool>