Mercurial > repos > galaxyp > cardinal_filtering
annotate filtering.xml @ 0:a2988d8d4b77 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
author | galaxyp |
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date | Mon, 01 Oct 2018 01:04:17 -0400 |
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children | aac805a9d2ae |
rev | line source |
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0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.0"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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2 <description>tool for filtering mass spectrometry imaging data</description> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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3 <macros> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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4 <import>macros.xml</import> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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5 </macros> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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6 <expand macro="requirements"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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7 <requirement type="package" version="2.2.1">r-gridextra</requirement> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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8 <requirement type="package" version="2.2.1">r-ggplot2</requirement> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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9 </expand> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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10 <command detect_errors="exit_code"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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11 <![CDATA[ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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12 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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13 @INPUT_LINKING@ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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14 cat '${MSI_subsetting}' && |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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15 Rscript '${MSI_subsetting}' |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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16 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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17 ]]> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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18 </command> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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19 <configfiles> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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20 <configfile name="MSI_subsetting"><![CDATA[ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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21 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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22 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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23 ################################# load libraries and read file ################# |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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24 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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25 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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26 library(Cardinal) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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27 library(ggplot2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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28 library(gridExtra) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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29 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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30 @READING_MSIDATA@ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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31 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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32 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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33 ########################### QC numbers ######################## |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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34 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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35 ## Number of features (m/z) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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36 maxfeatures = length(features(msidata)) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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37 ## Range m/z |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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38 minmz = round(min(mz(msidata)), digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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39 maxmz = round(max(mz(msidata)), digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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40 ## Number of spectra (pixels) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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41 pixelcount = length(pixels(msidata)) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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42 ## Range x coordinates |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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43 minimumx = min(coord(msidata)[,1]) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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44 maximumx = max(coord(msidata)[,1]) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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45 ## Range y coordinates |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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46 minimumy = min(coord(msidata)[,2]) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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47 maximumy = max(coord(msidata)[,2]) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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48 ## Number of intensities > 0 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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49 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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50 ## Spectra multiplied with m/z (potential number of peaks) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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51 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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52 ## Percentage of intensities > 0 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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53 percpeaks = round(npeaks/numpeaks*100, digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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54 ## Number of empty TICs |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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55 TICs = colSums(spectra(msidata)[], na.rm=TRUE) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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56 NumemptyTIC = sum(TICs == 0) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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57 ## median TIC |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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58 medint = round(median(TICs), digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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59 ## Store features for QC plot |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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60 featuresinfile = mz(msidata) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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61 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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62 ## Next steps will only run if there are more than 0 intensities/pixels/features in the file |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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63 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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64 if (sum(spectra(msidata)[]>0, na.rm=TRUE) > 0) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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65 { |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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66 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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67 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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68 ## prepare dataframe for QC of pixel distribution (will be overwritten in filtering of pixels condition) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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69 position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata))) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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70 colnames(position_df)[3] = "annotation" |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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71 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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72 ###################################### Filtering of pixels ##################### |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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73 ################################################################################ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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74 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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75 ############ Pixels in two columns format: x and y in different columns ############# |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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76 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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77 #if str($pixels_cond.pixel_filtering) == "two_columns": |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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78 print("two columns") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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79 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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80 ## read tabular file |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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81 input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header, |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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82 stringsAsFactors = FALSE) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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83 numberpixels = nrow(input_list) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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84 inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y, $pixels_cond.column_names)] |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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85 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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86 ## rewrite into x = 1, y = 1 format and filter msidata, count validpixels |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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87 pixelvector = character() |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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88 for (pixel in 1:nrow(inputpixels)){ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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89 pixelvector[pixel] = paste0("x = ", inputpixels[pixel,1],", ", "y = ", inputpixels[pixel,2])} |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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90 pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector] |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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91 msidata = msidata[,pixelsofinterest] |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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92 validpixels=ncol(msidata) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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93 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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94 ## in case some pixels are left print annotation plot |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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95 colnames(inputpixels) = c("x", "y", "annotation") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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96 position_df = merge(coord(msidata)[,1:2], inputpixels, by=c("x", "y"), all.x=TRUE) |
a2988d8d4b77
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97 colnames(position_df)[3] = "annotation" |
a2988d8d4b77
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98 position_df\$annotation = factor(position_df\$annotation) |
a2988d8d4b77
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99 |
a2988d8d4b77
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100 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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101 ########### Pixels wihin x and y minima and maxima are kept ################### |
a2988d8d4b77
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102 |
a2988d8d4b77
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103 #elif str($pixels_cond.pixel_filtering) == "pixel_range": |
a2988d8d4b77
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104 print("pixel range") |
a2988d8d4b77
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105 |
a2988d8d4b77
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106 numberpixels = "range" |
a2988d8d4b77
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107 validpixels = "range" |
a2988d8d4b77
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108 |
a2988d8d4b77
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109 ## only filter pixels if at least one pixel will be left |
a2988d8d4b77
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110 if (sum(coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range) > 0 & sum(coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range) > 0){ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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111 |
a2988d8d4b77
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112 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range] |
a2988d8d4b77
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113 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range] |
a2988d8d4b77
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114 }else{ |
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115 msidata = msidata[,0] |
a2988d8d4b77
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116 print("no valid pixel found")} |
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117 |
a2988d8d4b77
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118 ## update position_df for filtered pixels |
a2988d8d4b77
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119 position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata))) |
a2988d8d4b77
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120 colnames(position_df)[3] = "annotation" |
a2988d8d4b77
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121 position_df\$annotation = factor(position_df\$annotation) |
a2988d8d4b77
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122 |
a2988d8d4b77
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123 #elif str($pixels_cond.pixel_filtering) == "none": |
a2988d8d4b77
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124 print("no pixel filtering") |
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125 |
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126 numberpixels = 0 |
a2988d8d4b77
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127 validpixels = 0 |
a2988d8d4b77
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128 |
a2988d8d4b77
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129 #end if |
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130 |
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131 }else{ |
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132 print("Inputfile has no intensities > 0") |
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133 } |
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134 |
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135 ################################# filtering of features ###################### |
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136 ############################################################################## |
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137 |
a2988d8d4b77
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138 ####################### Keep m/z from tabular file ######################### |
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139 |
a2988d8d4b77
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140 ## feature filtering only when pixels/features/intensities are left |
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141 npeaks_before_filtering= sum(spectra(msidata)[]>0, na.rm=TRUE) |
a2988d8d4b77
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142 |
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143 |
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144 if (npeaks_before_filtering > 0) |
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145 |
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146 { |
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147 |
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148 #if str($features_cond.features_filtering) == "features_list": |
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149 print("feature list") |
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150 |
a2988d8d4b77
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151 ## read tabular file, define starting row, extract and count valid features |
a2988d8d4b77
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152 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE) |
a2988d8d4b77
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153 extracted_features = input_features[,$features_cond.feature_column] |
a2988d8d4b77
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154 numberfeatures = length(extracted_features) |
a2988d8d4b77
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155 if (class(extracted_features) == "numeric"){ |
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156 ### max digits given in the input file will be used to match m/z but the maximum is 4 |
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157 max_digits = max(nchar(matrix(unlist(strsplit(as.character(extracted_features), "\\.")), ncol=2, byrow=TRUE)[,2])) |
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158 if (max_digits >4) |
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159 { |
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160 max_digits = 4 |
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161 } |
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162 |
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163 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits) |
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164 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)] |
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165 validmz = length(unique(featuresofinterest)) |
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166 }else{ |
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167 validmz = 0 |
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168 featuresofinterest = 0} |
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169 |
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170 ### filter msidata for valid features |
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171 msidata = msidata[featuresofinterest,] |
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172 |
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173 ############### features within a given range are kept ##################### |
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174 |
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175 #elif str($features_cond.features_filtering) == "features_range": |
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176 print("feature range") |
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177 |
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178 numberfeatures = "range" |
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179 validmz = "range" |
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180 |
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181 if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0){ |
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182 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,] |
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183 }else{ |
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184 msidata = msidata[0,] |
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185 print("no valid mz range")} |
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186 |
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187 ############### Remove m/z from tabular file ######################### |
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188 |
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189 #elif str($features_cond.features_filtering) == "remove_features": |
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190 print("remove features") |
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191 |
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192 ## read tabular file, define starting row, extract and count valid features |
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193 input_features = read.delim("$mz_tabular", header = $features_cond.removal_header, stringsAsFactors = FALSE) |
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194 extracted_features = input_features[,$features_cond.removal_column] |
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195 numberfeatures = length(extracted_features) |
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196 if (class(extracted_features) == "numeric"){ |
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197 print("input is numeric") |
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198 featuresofinterest = extracted_features |
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199 validmz = sum(featuresofinterest <= max(mz(msidata))& featuresofinterest >= min(mz(msidata))) |
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200 }else{featuresofinterest = 0 |
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201 validmz = 0} |
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202 |
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203 ### Here starts removal of features: |
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204 plusminus = $features_cond.removal_plusminus |
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205 |
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206 mass_to_remove = numeric() |
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207 if (sum(featuresofinterest) > 0){ |
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208 for (masses in featuresofinterest){ |
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209 #if str($features_cond.units_removal) == "ppm": |
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210 plusminus = masses * $features_cond.removal_plusminus/1000000 |
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211 #end if |
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212 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus)) |
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213 mass_to_remove = append(mass_to_remove, current_mass)} |
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214 msidata= msidata[-mass_to_remove, ] |
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215 }else{print("No features were removed as they were not fitting to m/z values and/or range")} |
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216 |
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217 |
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218 #elif str($features_cond.features_filtering) == "none": |
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219 |
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220 print("no feature filtering") |
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221 validmz = 0 |
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222 numberfeatures = 0 |
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223 |
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224 #end if |
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225 |
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226 ## save msidata as Rfile |
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227 save(msidata, file="$msidata_filtered") |
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228 ## Number of empty TICs |
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229 TICs2 = colSums(spectra(msidata)[], na.rm=TRUE) |
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230 }else{ |
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231 print("Inputfile or file filtered for pixels has no intensities > 0") |
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232 numberfeatures = NA |
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233 validmz = NA |
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234 ## Number of empty TICs |
a2988d8d4b77
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235 TICs2 = NA |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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236 } |
a2988d8d4b77
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237 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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238 #################### QC numbers ####################### |
a2988d8d4b77
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239 |
a2988d8d4b77
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240 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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241 ## Number of features (m/z) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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242 maxfeatures2 = length(features(msidata)) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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243 ## Range m/z |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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244 minmz2 = round(min(mz(msidata)), digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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245 maxmz2 = round(max(mz(msidata)), digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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246 ## Number of spectra (pixels) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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247 pixelcount2 = length(pixels(msidata)) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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248 ## Range x coordinates |
a2988d8d4b77
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249 minimumx2 = min(coord(msidata)[,1]) |
a2988d8d4b77
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250 maximumx2 = max(coord(msidata)[,1]) |
a2988d8d4b77
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251 ## Range y coordinates |
a2988d8d4b77
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252 minimumy2 = min(coord(msidata)[,2]) |
a2988d8d4b77
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253 maximumy2 = max(coord(msidata)[,2]) |
a2988d8d4b77
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254 ## Number of intensities > 0 |
a2988d8d4b77
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255 npeaks2= sum(spectra(msidata)[]>0, na.rm=TRUE) |
a2988d8d4b77
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256 ## Spectra multiplied with m/z (potential number of peaks) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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257 numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) |
a2988d8d4b77
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258 ## Percentage of intensities > 0 |
a2988d8d4b77
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259 percpeaks2 = round(npeaks2/numpeaks2*100, digits=2) |
a2988d8d4b77
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260 ## Number of empty TICs |
a2988d8d4b77
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261 NumemptyTIC2 = sum(TICs2 == 0) |
a2988d8d4b77
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262 ## median TIC |
a2988d8d4b77
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263 medint2 = round(median(TICs2), digits=2) |
a2988d8d4b77
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264 |
a2988d8d4b77
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265 properties = c("Number of m/z features", |
a2988d8d4b77
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266 "Range of m/z values", |
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267 "Number of pixels", |
a2988d8d4b77
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268 "Range of x coordinates", |
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269 "Range of y coordinates", |
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270 "Intensities > 0", |
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271 "Median TIC per pixel", |
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272 "Number of empty spectra", |
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273 "pixel overview", |
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274 "feature overview") |
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275 |
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276 before = c(paste0(maxfeatures), |
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277 paste0(minmz, " - ", maxmz), |
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278 paste0(pixelcount), |
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279 paste0(minimumx, " - ", maximumx), |
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280 paste0(minimumy, " - ", maximumy), |
a2988d8d4b77
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281 paste0(percpeaks, " %"), |
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282 paste0(medint), |
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283 paste0(NumemptyTIC), |
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284 paste0("input pixels: ", numberpixels), |
a2988d8d4b77
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285 paste0("input mz: ", numberfeatures)) |
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286 |
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287 filtered = c(paste0(maxfeatures2), |
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288 paste0(minmz2, " - ", maxmz2), |
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289 paste0(pixelcount2), |
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290 paste0(minimumx2, " - ", maximumx2), |
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291 paste0(minimumy2, " - ", maximumy2), |
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292 paste0(percpeaks2, " %"), |
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293 paste0(medint2), |
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294 paste0(NumemptyTIC2), |
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295 paste0("valid pixels: ", validpixels), |
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296 paste0("valid mz: ", validmz)) |
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297 |
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298 property_df = data.frame(properties, before, filtered) |
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299 |
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300 ############################### PDF QC ################################ |
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301 |
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302 |
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303 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12) |
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304 plot(0,type='n',axes=FALSE,ann=FALSE) |
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305 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name")) |
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306 grid.table(property_df, rows= NULL) |
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307 |
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308 ## QC report with more than value-table: only when pixels/features/intensities are left |
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309 if (npeaks2 > 0) |
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310 { |
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311 ### visual pixel control |
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312 |
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313 levels(position_df\$annotation) = factor(paste(1:length(levels(position_df\$annotation)), levels(position_df\$annotation), sep="_")) |
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314 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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315 pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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316 geom_tile(height = 1, width=1)+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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317 coord_fixed()+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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318 ggtitle("Spatial orientation of filtered pixels")+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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319 theme_bw()+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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320 theme(plot.title = element_text(hjust = 0.5))+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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321 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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322 theme(legend.position="bottom",legend.direction="vertical")+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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323 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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324 guides(fill=guide_legend(ncol=4,byrow=TRUE)) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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325 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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326 coord_labels = aggregate(cbind(x,y)~annotation, data=position_df, mean, na.rm=TRUE, na.action="na.pass") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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327 coord_labels\$file_number = 1:length(levels(position_df\$annotation)) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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328 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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329 for(file_count in 1:nrow(coord_labels)) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
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330 {pixel_image = pixel_image + annotate("text",x=coord_labels[file_count,"x"], |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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331 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} |
a2988d8d4b77
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332 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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333 print(pixel_image) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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334 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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335 ### control features which are removed |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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336 hist(mz(msidata), xlab="m/z", main="Kept m/z values") |
a2988d8d4b77
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337 #if str($features_cond.features_filtering) == "none": |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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338 print("no difference histogram as no m/z filtering took place") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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339 #else: |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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340 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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341 if (isTRUE(all.equal(featuresinfile, mz(msidata)))){ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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342 print("No difference in m/z values before and after filtering, no histogram drawn") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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343 }else{ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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344 hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")} |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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345 #end if |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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346 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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347 dev.off() |
a2988d8d4b77
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348 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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349 }else{ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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350 print("Inputfile or filtered file has no intensities > 0") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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351 dev.off() |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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352 } |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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353 ]]></configfile> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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354 </configfiles> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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355 <inputs> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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356 <expand macro="reading_msidata"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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357 <conditional name="pixels_cond"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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358 <param name="pixel_filtering" type="select" label="Select pixel filtering option"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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359 <option value="none" selected="True">none</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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360 <option value="two_columns">list of pixel coordinates (tabular file)</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
361 <option value="pixel_range">ranges for x and y (manually)</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
362 </param> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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363 <when value="none"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
364 <when value="two_columns"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
365 <expand macro="reading_pixel_annotations"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
366 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
367 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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368 <param name="two_columns_pixel" type="data" format="tabular" label="Tabular file with pixel coordinates" |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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369 help="Column with x values, another with y values, another with pixel annotations"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
370 <param name="pixel_column_x" data_ref="two_columns_pixel" label="Column with x values" type="data_column"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
371 <param name="pixel_column_y" data_ref="two_columns_pixel" label="Column with y values" type="data_column"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
372 <param name="annotation_column_xy" data_ref="two_columns_pixel" label="Column with annotations" type="data_column"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
373 <param name="pixel_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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374 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
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|
375 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
376 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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changeset
|
377 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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378 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
379 <when value="pixel_range"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
380 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
381 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
382 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
383 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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changeset
|
384 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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changeset
|
385 </conditional> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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changeset
|
386 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
387 <conditional name="features_cond"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
388 <param name="features_filtering" type="select" label="Select m/z feature filtering option"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
389 <option value="none" selected="True">none</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
390 <option value="features_list">keep a list of m/z (tabular file)</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
391 <option value="features_range">m/z range (manually)</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
392 <option value="remove_features">remove a list of m/z (tabular file)</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
393 </param> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
394 <when value="none"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
395 <when value="features_list"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
396 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to keep"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
397 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
398 <when value="features_range"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
399 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
400 <param name="max_mz" type="float" value="100" label="Maximum value for m/z"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
401 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
402 <when value="remove_features"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
403 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to remove"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
404 <param name="removal_plusminus" type="float" value="20" label="Window in which all m/z will be removed" help="This value is the half window size, it will be added and substracted from the given input value"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
405 <param name="units_removal" type="select" display="radio" optional ="False" label="units"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
406 <option value="ppm" selected="True">ppm</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
407 <option value="Da">Da</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
408 </param> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
409 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
410 </conditional> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
411 </inputs> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
412 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
413 <outputs> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
414 <data format="rdata" name="msidata_filtered" label="${tool.name} on ${on_string}"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
415 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
416 </outputs> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
417 <tests> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
418 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
419 <expand macro="infile_imzml"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
420 <param name="pixel_filtering" value="pixel_range"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
421 <param name="min_x_range" value="10"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
422 <param name="max_x_range" value="20"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
423 <param name="min_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
424 <param name="max_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
425 <output name="QC_overview" file="imzml_filtered2.pdf" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
426 <output name="msidata_filtered" file="imzml_filtered2.RData" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
427 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
428 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
429 <expand macro="infile_imzml"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
430 <param name="pixel_filtering" value="pixel_range"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
431 <param name="min_x_range" value="1"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
432 <param name="max_x_range" value="20"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
433 <param name="min_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
434 <param name="max_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
435 <param name="features_filtering" value="features_range"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
436 <param name="min_mz" value="350" /> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
437 <param name="max_mz" value="500"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
438 <output name="QC_overview" file="imzml_filtered3.pdf" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
439 <output name="msidata_filtered" file="imzml_filtered3.RData" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
440 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
441 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
442 <expand macro="infile_imzml"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
443 <param name="pixel_filtering" value="two_columns"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
444 <param name="annotation_file" ftype="tabular" value = "inputpixels_2column.tabular"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
445 <param name="column_x" value="1"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
446 <param name="column_y" value="3"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
447 <param name="column_names" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
448 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
449 <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
450 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
451 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
452 <expand macro="infile_imzml"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
453 <param name="pixel_filtering" value="pixel_range"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
454 <param name="min_x_range" value="0"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
455 <param name="max_x_range" value="10"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
456 <param name="min_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
457 <param name="max_y_range" value="20"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
458 <param name="features_filtering" value="features_list"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
459 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
460 <param name="feature_column" value="1"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
461 <param name="feature_header" value="0"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
462 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
463 <output name="msidata_filtered" file="imzml_filtered5.RData" compare="sim_size" /> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
464 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
465 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
466 <expand macro="infile_analyze75"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
467 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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468 <output name="msidata_filtered" file="analyze_filteredoutside.RData" compare="sim_size" /> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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469 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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470 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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471 <param name="infile" value="preprocessed.RData" ftype="rdata"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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472 <conditional name="outputs"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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473 <param name="outputs_select" value="no_quality_control"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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474 </conditional> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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475 <output name="msidata_filtered" file="rdata_notfiltered.RData" compare="sim_size"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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476 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" /> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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477 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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478 </tests> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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479 <help> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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480 <![CDATA[ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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481 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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482 @CARDINAL_DESCRIPTION@ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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483 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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484 ----- |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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485 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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486 This tool provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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487 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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488 @MSIDATA_INPUT_DESCRIPTION@ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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489 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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490 @SPECTRA_TABULAR_INPUT_DESCRIPTION@ |
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491 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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492 @MZ_TABULAR_INPUT_DESCRIPTION@ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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493 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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494 **Options** |
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495 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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496 - pixel filtering/annotation: either with a tabular file containing x and y coordinates and pixel annotations or by defining a range for x and y by hand (for the latter no annotation is possible). Pixel that are not present in the dataset are ignored. In case all pixels are not present in the dataset the output file will be empty and no further mz filtering will be performed. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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497 - m/z feature filtering: m/z values for filtering should be either imported as a tabular file containing containing m/z of interest or by defining a range for the m/z values. m/z that are not present in the dataset are ignored. If all given m/z values or the m/z range is outside the dataset, the output file will be empty. |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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498 - m/z feature removing: perturbing m/z features such as matrix contaminants can be removed by specifying their m/z in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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499 |
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500 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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501 **Tips** |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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502 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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503 - Numeric m/z features imported via a tabular file and m/z features of the dataset are rounded to 4 decimal points (or maximum number of decimal points of input m/z) and then matched. Therefore, it is recommended to use the filtering tool only for m/z which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool "Join two files on column allowing a small difference" should be used to find corresponding m/z values, which can then be used for filtering. |
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504 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes)) |
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505 |
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506 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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507 **Output** |
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508 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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509 - imzML file filtered for pixels and/or m/z |
a2988d8d4b77
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510 - pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z |
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511 |
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512 |
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513 ]]> |
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514 </help> |
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515 <expand macro="citations"/> |
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516 </tool> |