Mercurial > repos > galaxyp > maldi_quant_preprocessing
annotate maldi_quant_preprocessing.xml @ 2:3f3812d36027 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
author | galaxyp |
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date | Thu, 25 Oct 2018 07:23:20 -0400 |
parents | 18f04cc43f7e |
children | aa81463e21ea |
rev | line source |
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2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.2"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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2 <description> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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3 Preprocessing of mass-spectrometry imaging data |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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4 </description> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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5 <macros> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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6 <import>maldi_macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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7 </macros> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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8 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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9 <command detect_errors="exit_code"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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10 <![CDATA[ |
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3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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11 cat '${maldi_quant_preprocessing}' && |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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12 #if $infile.ext == 'imzml' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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13 cp '${infile.extra_files_path}/imzml' infile.imzML && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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14 cp '${infile.extra_files_path}/ibd' infile.ibd && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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15 #elif $infile.ext == 'analyze75' |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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16 cp '${infile.extra_files_path}/hdr' infile.hdr && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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17 cp '${infile.extra_files_path}/img' infile.img && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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18 cp '${infile.extra_files_path}/t2m' infile.t2m && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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19 du infile.hdr && |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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20 du infile.img && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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21 du -s -B1 infile.hdr && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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22 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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23 ln -s $infile infile.RData && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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24 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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25 Rscript "${maldi_quant_preprocessing}" && |
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3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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26 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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27 mkdir $outfile_imzml.files_path && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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28 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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29 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true && |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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30 echo "imzML file:" > $outfile_imzml && |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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31 ls -l "$outfile_imzml.files_path" >> $outfile_imzml |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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32 ]]> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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33 </command> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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34 <configfiles> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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35 <configfile name="maldi_quant_preprocessing"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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36 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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37 @R_IMPORTS@ |
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38 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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39 #if $restriction_conditional.restriction == 'restrict': |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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40 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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41 print('Reading mask region') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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42 ## Import imzML file |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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43 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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44 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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45 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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46 maldi_data = importImzMl('infile.imzML', |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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47 coordinates = coordinate_matrix) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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48 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2]) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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49 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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50 #else: |
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51 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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52 print('Reading entire file') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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53 #if $infile.ext == 'imzml' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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54 ## Import imzML file |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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55 maldi_data = import( 'infile.imzML', type="imzML" ) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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56 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data))) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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57 #elif $infile.ext == 'analyze75' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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58 ## Import analyze7.5 file |
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3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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59 maldi_data = importAnalyze( 'infile.hdr' ) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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60 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data))) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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61 #else |
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62 loadRData <- function(fileName){ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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63 #loads an RData file, and returns it |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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64 load(fileName) |
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65 get(ls()[ls() != "fileName"]) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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66 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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67 msidata = loadRData('infile.RData') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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68 ## save coordinates |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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69 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2]) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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70 ## save mz values |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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71 cardinal_mzs = Cardinal::mz(msidata) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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72 ## create MALDIquant MassSpectrum object |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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73 maldi_data = list() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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74 for(number_spectra in 1:ncol(msidata)){ |
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75 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra]) |
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76 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data))) |
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77 } |
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78 |
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79 #end if |
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80 |
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81 #end if |
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82 |
1
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83 ## Quality control plots during preprocessing |
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84 |
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85 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12) |
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86 plot(0,type='n',axes=FALSE,ann=FALSE) |
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87 |
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88 ## if no filename is given, name of file in Galaxy history is used |
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89 #set $filename = $infile.display_name |
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90 title(main=paste("$filename")) |
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91 |
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92 #if str($tabular_annotation.load_annotation) == 'yes_annotation': |
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93 print("use annotation file") |
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94 |
0
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95 ## read and extract x,y,annotation information |
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96 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE) |
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97 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)] |
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98 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation" |
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99 |
1
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100 ## merge with coordinate information (from above) of MSI data |
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101 colnames(coordinates_info)[3] = "pixel_index" |
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102 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE) |
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103 merged_annotation[is.na(merged_annotation)] = "NA" |
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104 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),] |
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105 samples = as.factor(merged_annotation\$annotation) |
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106 |
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107 ## print annotation overview into PDF output |
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108 |
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109 ## the more annotation groups a file has the smaller will be the legend |
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110 number_combined = length(levels(as.factor(merged_annotation\$annotation))) |
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111 if (number_combined<20){ |
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112 legend_size = 10 |
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113 }else if (number_combined>20 && number_combined<40){ |
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114 legend_size = 9 |
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115 }else if (number_combined>40 && number_combined<60){ |
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116 legend_size = 8 |
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117 }else if (number_combined>60 && number_combined<100){ |
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118 legend_size = 7 |
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119 }else{ |
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120 legend_size = 6 |
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121 } |
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122 |
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123 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+ |
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124 geom_tile() + |
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125 coord_fixed()+ |
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126 ggtitle("Spatial orientation of annotated data")+ |
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127 theme_bw()+ |
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128 theme(plot.title = element_text(hjust = 0.5))+ |
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129 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
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130 theme(legend.position="bottom",legend.direction="vertical")+ |
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131 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ |
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132 guides(fill=guide_legend(ncol=5,byrow=TRUE)) |
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133 |
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134 print(combine_plot) |
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135 |
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136 #end if |
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137 |
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138 #################### Preprocessing methods ##################################### |
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139 |
1
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140 ## QC plot on input file |
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141 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
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142 plot(avgSpectra, main="Average spectrum for input file") |
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143 |
1
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144 pixel_number = length(maldi_data) |
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145 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
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146 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
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147 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
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148 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
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149 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
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150 inputdata = c(minmz, maxmz,number_features,mean_features, medint) |
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151 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint)) |
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152 vectorofactions = "inputdata" |
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153 |
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154 |
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155 #for $method in $methods: |
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156 |
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157 #if str( $method.methods_conditional.method ) == 'Transformation': |
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158 |
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159 print('transforming') |
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160 ##transformation |
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161 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method") |
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162 ## QC plot and numbers |
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163 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
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164 plot(avgSpectra, main="Average spectrum after transformation") |
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165 pixel_number = length(maldi_data) |
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166 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
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167 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
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168 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
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169 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
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170 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
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171 transformed = c(minmz, maxmz,number_features,mean_features, medint) |
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172 QC_numbers= cbind(QC_numbers, transformed) |
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173 vectorofactions = append(vectorofactions, "transformed") |
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174 |
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175 |
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176 #elif str( $method.methods_conditional.method ) == 'Smoothing': |
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177 |
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178 print('smoothing') |
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179 ##smoothing |
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180 |
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181 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay': |
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182 print('SavitzkyGolay') |
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183 |
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184 maldi_data = smoothIntensity(maldi_data, |
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185 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial, |
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186 halfWindowSize=$method.methods_conditional.halfWindowSize) |
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187 |
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188 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage': |
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189 print('MovingAverage') |
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190 |
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191 maldi_data = smoothIntensity(maldi_data, |
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192 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted, |
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193 halfWindowSize=$method.methods_conditional.halfWindowSize) |
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194 |
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195 #end if |
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196 |
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197 ## QC plot and numbers |
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198 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
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199 plot(avgSpectra, main="Average spectrum after smoothing", sub="") |
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200 pixel_number = length(maldi_data) |
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201 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
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202 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
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203 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
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204 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
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205 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
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206 smoothed = c(minmz, maxmz,number_features,mean_features, medint) |
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207 QC_numbers= cbind(QC_numbers, smoothed) |
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208 vectorofactions = append(vectorofactions, "smoothed") |
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209 |
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210 |
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211 #elif str( $method.methods_conditional.method ) == 'Baseline': |
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212 |
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213 print('baseline removing') |
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214 ## Remove baseline |
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215 |
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216 #if str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'SNIP': |
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217 print('SNIP') |
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218 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE) |
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219 par(mfrow = c(2,2)) |
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220 for (random_sample in random_spectra){ |
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221 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]], |
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222 method="SNIP", iterations=$method.methods_conditional.methods_for_baseline.iterations) |
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223 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample)) |
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224 lines(maldi_data_baseline, col="blue", lwd=2)} |
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225 |
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226 maldi_data = removeBaseline(maldi_data, |
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227 method="SNIP", |
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228 iterations=$method.methods_conditional.methods_for_baseline.iterations) |
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229 |
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230 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'TopHat': |
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231 print('TopHat') |
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232 |
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233 maldi_data = removeBaseline(maldi_data, |
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234 method="TopHat", |
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235 halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize) |
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236 |
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237 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'ConvexHull': |
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238 print('ConvexHull') |
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239 |
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240 maldi_data = removeBaseline(maldi_data, |
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241 method="ConvecHull") |
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242 |
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243 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'median': |
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244 print('median') |
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245 |
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246 maldi_data = removeBaseline(maldi_data, |
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247 method="TopHat", |
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248 halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize) |
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249 |
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250 #end if |
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251 |
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252 ## QC plot and numbers |
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253 par(mfrow = c(1,1)) |
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254 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
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255 plot(avgSpectra, main="Average spectrum after baseline removal") |
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256 pixel_number = length(maldi_data) |
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257 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
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258 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
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259 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
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260 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
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261 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
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262 baseline_removed = c(minmz, maxmz,number_features,mean_features, medint) |
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263 QC_numbers= cbind(QC_numbers, baseline_removed) |
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264 vectorofactions = append(vectorofactions, "baseline_removed") |
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265 |
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266 |
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267 #elif str( $method.methods_conditional.method ) == 'Calibrate': |
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268 |
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269 print('calibrate') |
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270 ##calibrate |
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271 |
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272 #if str($method.methods_conditional.cond_calibration_range) == "yes": |
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273 ## calibrate only given m/z range |
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274 maldi_data = calibrateIntensity(maldi_data, |
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275 method="$method.methods_conditional.calibrate_method", |
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276 range=c($method.methods_conditional.cond_calibration_range.mass_start, $method.methods_conditional.cond_calibration_range.mass_end)) |
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277 #else: |
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278 maldi_data = calibrateIntensity(maldi_data, |
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279 method="$method.methods_conditional.calibrate_method") |
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280 #end if |
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281 ## QC plot and numbers |
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282 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
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283 plot(avgSpectra, main="Average spectrum after normalization") |
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284 pixel_number = length(maldi_data) |
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285 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
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286 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
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287 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
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288 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
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289 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
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290 intensity_calibrated = c(minmz, maxmz,number_features,mean_features, medint) |
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291 QC_numbers= cbind(QC_numbers, intensity_calibrated) |
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292 vectorofactions = append(vectorofactions, "intensity_calibrated ") |
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293 |
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294 |
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295 #elif str( $method.methods_conditional.method ) == 'Align': |
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296 |
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297 print('align') |
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298 ##align spectra |
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299 |
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300 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference': |
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301 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize, |
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302 SNR=$method.methods_conditional.snr, tolerance=$method.methods_conditional.tolerance, |
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303 allowNoMatches =$method.methods_conditional.allow_nomatch, emptyNoMatches = $method.methods_conditional.empty_nomatch, |
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304 warpingMethod="$method.methods_conditional.warping_method") |
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305 |
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306 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference': |
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307 ## create reference mass_vector from tabular file |
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308 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = $method.methods_conditional.reference_for_alignment.reference_header, stringsAsFactors = FALSE)[,1] |
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309 int_vector = rep(1,length(mass_vector)) |
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310 mass_list = createMassPeaks(mass_vector, int_vector) |
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311 |
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312 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize, |
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313 SNR=$method.methods_conditional.snr, |
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314 tolerance=$method.methods_conditional.tolerance, |
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315 warpingMethod="$method.methods_conditional.warping_method", |
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316 reference = mass_list, allowNoMatches =$method.methods_conditional.allow_nomatch, emptyNoMatches = $method.methods_conditional.empty_nomatch) |
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317 |
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318 #end if |
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319 |
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320 #if $method.methods_conditional.remove_empty: |
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321 print("remove empty spectra") |
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322 |
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323 #if $infile.ext == 'rdata' |
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324 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),] ## remove coordinates of empty spectra for Cardinal RData input |
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325 #end if |
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326 #if str($tabular_annotation.load_annotation) == 'yes_annotation': |
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327 merged_annotation = merged_annotation[-findEmptyMassObjects(maldi_data),] ## remove coordinate annotations for empty spectra |
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328 #end if |
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329 maldi_data = removeEmptyMassObjects(maldi_data) |
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330 #end if |
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331 |
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332 |
0
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333 ## QC plot |
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334 |
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335 if (length(maldi_data)>0){ |
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336 avgSpectra = averageMassSpectra(maldi_data,method="mean") |
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337 plot(avgSpectra, main="Average spectrum after alignment") |
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338 }else{"All spectra are empty"} |
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339 |
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340 pixel_number = length(maldi_data) |
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341 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4) |
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342 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4) |
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343 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2) |
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344 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2) |
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345 number_features = length(unique(unlist(lapply(maldi_data,mass)))) |
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346 spectra_aligned = c(minmz, maxmz,number_features,mean_features, medint) |
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347 QC_numbers= cbind(QC_numbers, spectra_aligned) |
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348 vectorofactions = append(vectorofactions, "spectra_aligned") |
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349 #end if |
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350 |
0
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351 #end for |
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352 |
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353 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# features", "median\nintensity") |
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354 plot(0,type='n',axes=FALSE,ann=FALSE) |
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355 grid.table(t(QC_numbers)) |
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356 |
0
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357 dev.off() |
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358 |
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359 ## export imzML file |
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360 if (length(maldi_data)>0){ |
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361 #if $infile.ext == 'rdata' |
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362 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates) |
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363 #else |
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364 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed) |
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365 #end if |
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366 |
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367 }else{"All spectra are empty, outputfiles will be empty,too."} |
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368 |
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369 ]]> |
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370 </configfile> |
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371 </configfiles> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
372 <inputs> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
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|
373 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML or Cardinal MSImageSet saved as RData" help="This file is in imzML format or Cardinal MSImageSet saved as RData. The file must be in profile mode, not centroided"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
374 <conditional name="restriction_conditional"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
375 <param name="restriction" type="select" label="Read in only spectra of interest" help="This option only works for imzML files"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
376 <option value="no_restriction" selected="True">Calculate on entire file</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
377 <option value="restrict">Restrict to coordinates of interest</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
378 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
379 <when value="restrict"> |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
380 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates" help="x-values in first column, y-values in second column"/> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
381 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
382 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
383 <when value="no_restriction"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
384 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
385 <conditional name="tabular_annotation"> |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
386 <param name="load_annotation" type="select" label="For Cardinal RData only: Use pixel annotation from tabular file to have updated annotation information in case empty spectra will be removed"> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
387 <option value="no_annotation" selected="True">use no annotation</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
388 <option value="yes_annotation">use pixel annotation from a tabular file</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
389 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
390 <when value="yes_annotation"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
391 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file" |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
392 help="Tabular file with three columns: x values, y values and pixel annotations"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
393 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
394 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
395 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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1
diff
changeset
|
396 <param name="tabular_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
397 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
398 <when value="no_annotation"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
399 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
400 <repeat name="methods" title="Method" min="1"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
401 <conditional name="methods_conditional"> |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
402 <param name="method" type="select" label="Select a method"> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
403 <option value="Transformation" selected="True">Transformation</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
404 <option value="Smoothing">Smoothing</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
405 <option value="Baseline">Baseline removal</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
406 <option value="Calibrate">Calibrate</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
407 <option value="Align">Align Spectra (warping/phase correction)</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
408 <validator type="empty_field" /> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
409 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
410 <when value="Transformation"> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
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|
411 <param name="transform_method" type="select" label="Select a transfprormation method"> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
412 <option value="sqrt" selected="True">sqrt</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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changeset
|
413 <option value="log">log</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
414 <option value="log2">log2</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
415 <option value="log10">log10</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
416 <validator type="empty_field" /> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
417 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
418 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
419 <when value="Smoothing"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
420 <conditional name="methods_for_smoothing"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
421 <param name="smooth_method" type="select" label="This method smoothes the intensity values of a MassSpectrum object"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
422 <option value="SavitzkyGolay" selected="True">SavitzkyGolay</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
423 <option value="MovingAverage">MovingAverage</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
424 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
425 <when value="SavitzkyGolay"> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
426 <param name="polynomial" value="3" type="text" label="PolynomialOrder argument to control the order of the filter" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
427 help="should be smaller than the resulting window"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
428 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
429 <when value="MovingAverage"> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
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|
430 <param name="weighted" type="boolean" label="Weighted average" help = "Indicates if the average should be equal weight or if it should have weights depending on the distance from the center as calculated as 1/2^abs(-halfWindowSize:halfWindowSize) with the sum of all weigths normalized to 1" truevalue="TRUE" falsevalue="FALSE"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
431 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
432 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
433 <param name="halfWindowSize" type="integer" value="10" |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
434 label="Half window size (number of data points)" |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
435 help="The resulting window reaches from |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
436 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize] |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
437 (window size is 2*halfWindowSize+1)."/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
438 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
439 <when value="Baseline"> |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
440 <conditional name="methods_for_baseline"> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
441 <param name="baseline_method" type="select" label="Baseline removal method"> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
442 <option value="SNIP" selected="True">SNIP</option> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
443 <option value="TopHat">TopHat</option> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
444 <option value="ConvexHull">ConvexHull</option> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
445 <option value="median">median</option> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
446 <validator type="empty_field" /> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
447 </param> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
448 <when value="SNIP"> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
449 <param name="iterations" type="integer" value="100" |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
450 label="Number of iterations" help="Corresponds to half window size: The resulting window reaches from mass[cur_index-iterations] to mass[cur_index+iterations]"/> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
451 </when> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
452 <when value="TopHat"> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
453 <param name="tophat_halfWindowSize" type="integer" value="10" |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
454 label="Half window size (number of data points)" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
455 help="The resulting window reaches from |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
456 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
457 </when> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
458 <when value="ConvexHull"/> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
459 <when value="median"> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
460 <param name="median_halfWindowSize" type="integer" value="10" |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
461 label="Half window size (number of data points)" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
462 help="The resulting window reaches from |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
463 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
464 </when> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
465 </conditional> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
466 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
467 <when value="Calibrate"> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
468 <param name="calibrate_method" type="select" label="Intensity calibration (normalization) method"> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
469 <option value="TIC" selected="True">TIC</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
470 <option value="PQN">PQN</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
471 <option value="median">median</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
472 <validator type="empty_field" /> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
473 </param> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
474 <conditional name="cond_calibration_range"> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
475 <param name="calibration_range" type="select" label="Instead of the whole m/z range, a specified m/z range can be used to calculate the scaling factor"> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
476 <option value="no" selected="True">complete m/z range</option> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
477 <option value="yes">specify a m/z range</option> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
478 </param> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
479 <when value="no"/> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
480 <when value="yes"> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
481 <param name="mass_start" type="integer" value="800" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
482 label="Start of m/z range, has to be inside m/z range" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
483 help="Scaling factor is calculated on the mass range and applied to the whole spectrum."/> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
484 <param name="mass_end" type="integer" value="3000" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
485 label="End of m/z range, has to be inside m/z range"/> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
486 </when> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
487 </conditional> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
488 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
489 <when value="Align"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
490 <param name="warping_method" type="select" label="Warping methods"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
491 <option value="lowess" selected="True">Lowess</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
492 <option value="linear">Linear</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
493 <option value="quadratic">Quadratic</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
494 <option value="cubic">Cubic</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
495 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
496 |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
497 <param name="tolerance" type="float" value="0.00005" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
498 label="Tolerance = abs(mz1 - mz2)/mz2" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
499 help="Maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 50e-6" /> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
500 |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
501 <param name="halfWindowSize" type="integer" value="20" |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
502 label="Half window size (number of data points)" |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
503 help="The resulting window reaches from |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
504 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize] |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
505 (window size is 2*halfWindowSize+1). |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
506 The best size differs depending on the selected smoothing method."/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
507 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
508 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
509 <param name="allow_nomatch" type="boolean" label="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
510 <param name="empty_nomatch" type="boolean" label="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/> |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
511 <param name="remove_empty" type="boolean" label="Should empty spectra be removed" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
512 |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
513 <conditional name="reference_for_alignment"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
514 <param name="align_ref" type="select" label="Reference to which the samples should be aligned" help="Use internal calibrants to perform m/z calibration"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
515 <option value="no_reference" selected="True">no reference</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
516 <option value="yes_reference">reference from tabular file</option> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
517 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
518 <when value="no_reference"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
519 <when value="yes_reference"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
520 <param name="reference_file" type="data" format="tabular" |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
521 label="Tabular file with m/z (MassPeaks) which should be used for spectra alignment" |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
522 help="At least 2 reference m/z per spectrum are needed"/> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
523 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
524 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
525 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
526 </when> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
527 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
528 </repeat> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
529 <param name="export_processed" type="boolean" label="Export file as processed imzML" help="otherwise continuous imzML will be exported" truevalue="TRUE" falsevalue="FALSE"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
530 </inputs> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
531 <outputs> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
532 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}" /> |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
533 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="${tool.name} on ${on_string}: QC"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
534 </outputs> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
535 <tests> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
536 <test> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
537 <param name="infile" value="" ftype="imzml"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
538 <composite_data value="Example_Continuous.imzML"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
539 <composite_data value="Example_Continuous.ibd"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
540 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
541 <conditional name="restriction_conditional"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
542 <param name="restriction" value="restrict"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
543 <param name="coordinates_file" value="restricted_pixels.tabular"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
544 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
545 <conditional name="methods_conditional"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
546 <param name="method" value="Transformation"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
547 <param name="transform_method" value="log2"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
548 <param name="method" value="Smoothing"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
549 <param name="smooth_method" value="SavitzkyGolay"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
550 <param name="method" value="Basline"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
551 <param name="baseline_method" value ="TopHat"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
552 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
553 <output name="outfile_imzml" file="outfile1.imzML" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
554 <output name="outfile_imzml" file="outfile1.ibd" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
555 <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
556 </test> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
557 <test> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
558 <param name="infile" value="msidata_1.RData" ftype="rdata"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
559 <conditional name="methods_conditional"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
560 <param name="method" value="Calibrate"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
561 <param name="calibrate_method" value="PQN"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
562 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
563 <output name="outfile_imzml" file="outfile2.imzML" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
564 <output name="outfile_imzml" file="outfile2.ibd" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
565 <output name="plots" file="Preprocessing2_QC.pdf" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
566 </test> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
567 <test> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
568 <param name="infile" value="" ftype="imzml"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
569 <composite_data value="Example_Continuous.imzML"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
570 <composite_data value="Example_Continuous.ibd"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
571 </param> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
572 <conditional name="tabular_annotation"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
573 <param name="load_annotation" value="yes_annotation"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
574 <param name="annotation_file" value="pixel_annotations.tabular"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
575 <param name="column_x" value="1"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
576 <param name="column_y" value="2"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
577 <param name="column_names" value="3"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
578 <param name="tabular_header" value="TRUE"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
579 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
580 <conditional name="methods_conditional"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
581 <param name="method" value="Align"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
582 <param name="warping_method" value="linear"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
583 <param name="halfWindowSize" value="1"/> |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
584 <param name="tolerance" value="0.002"/> |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
585 <param name="allow_nomatch" value="TRUE"/> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
586 <param name="remove_empty" value="TRUE"/> |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
587 <param name="empty_nomatch" value="TRUE"/> |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
588 <conditional name="reference_for_alignment"> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
589 <param name="align_ref" value="yes_reference"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
590 <param name="reference_file" value="align_reference_test2.tabular" ftype="tabular"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
591 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
592 </conditional> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
593 <output name="outfile_imzml" file="outfile3.imzML" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
594 <output name="outfile_imzml" file="outfile3.ibd" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
595 <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
596 </test> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
597 </tests> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
598 <help><![CDATA[ |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
599 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
600 @MADLI_QUANT_DESCRIPTION@ |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
601 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
602 ----- |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
603 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
604 **Input data** |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
605 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
606 - MSI data: 2 types of input data can be used: |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
607 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
608 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
609 - Cardinal "MSImageSet" data saved as .RData |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
610 - Only for Cardinal RData files and when remove empty spectra is chosen: Tabular file with coordinates annotations. Separate columns for x and y coordinates and a third column with pixel annotations. Tabular files with any header name or no header at all are supported |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
611 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. The file has to contain x values in the first column and y values in the second columns. Further columns are allowed. Tabular files with any header name or no header at all are supported. |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
612 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
613 :: |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
614 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
615 x_coord y_coord |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
616 1 1 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
617 2 1 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
618 3 1 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
619 ... |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
620 ... |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
621 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
622 - Optional: Tabular file with reference m/z for the spectra align function. At least 2 m/z values of the input list must be present in every spectrum to peform the alignment. First column must contain m/z values, without empty fields or letters. Tabular files with any header name or no header at all are supported. |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
623 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
624 :: |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
625 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
626 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
627 m/z |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
628 100.0 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
629 100.01 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
630 100.02 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
631 ... |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
632 ... |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
633 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
634 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
635 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
636 **Options** |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
637 |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
638 - Transformation: Variance stabilization through intensity transformation:'log', 'log2', 'log10' and 'squareroot' (sqrt) are available |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
639 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are 'SavitzkyGolay' and 'Moving Average' |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
640 |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
641 - For all smoothing methods: The larger the 'Half window size'f, the stronger the smoothing. The resulting window should be smaller than the FWHM (full width at half maximum) of the typical peaks. Moving average needs smaller window size than SavitzkyGolay. |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
642 - Moving average: Recommended for broader peaks/high m/z range spectra. Weighted moving average: Points in the center get larger weight factors than points away from the center. |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
643 - SavitzkyGolay: Recommended for sharp peaks/low m/z range, preserves the shape of the local maxima. The PolynomialOrder should be smaller than the resulting window. Negative values will be replaced with 0. |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
644 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
645 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets). |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
646 |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
647 - Available methods are SNIP, TopHat,ConvexHull and median: |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
648 - SNIP is the default baseline reduction method in MALDIquant. |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
649 - ConvexHull is not appropriate for MALDI-TOF baseline removal. |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
650 - The moving median may generate negative intensities. |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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diff
changeset
|
651 - Except for the ConvexHull all methods have a parameter for the 'Half window size' (in SNIP it is called 'iterations'). The smaller the window the more baseline will be removed but also parts of the peaks. Wider windows preserve the peak height better and produce a smoother baseline, but some local background variation will remain. |
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
652 |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
653 - Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN) |
2
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
654 |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
655 - TIC and median are local calibration methods: each spectrum is normalized on its own (each peak is divided by the TIC or median of the spectrum) |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
656 - PQN is a global calibration method: In PQN all spectra are calibrated using the TIC calibration first. Subsequently, a median reference spectrum is created and the intensities in all spectra are standardized using the reference spectrum and a spectrum-specific median is calculated for each spectrum. Finally, each spectrum is rescaled by the median of the ratios of its intensity values and that of the reference spectrum |
3f3812d36027
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
1
diff
changeset
|
657 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
658 - Spectra alignment (warping): alignment for (re)calibration of m/z values, at least two m/z per spectrum are needed for the alignment. This requirement can be skipped by setting "Don't throw an error when less than 2 reference m/z were found in a spectrum" to yes. If the not aligned spectra should be set to zero select yes in "logical, if TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero". In order to remove such empty spectra set "Should empty spectra be removed" to yes. |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
659 |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
660 |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
661 **Output** |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
662 |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff
changeset
|
663 - imzML file (imzML format can be continuous or processed) |
1
18f04cc43f7e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
0
diff
changeset
|
664 - PDF with average mass spectra after each preprocessing step |
0
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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665 |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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666 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/ |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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667 |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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668 ]]> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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669 </help> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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670 <expand macro="citation"/> |
24d15e9d4a5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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671 </tool> |