Mercurial > repos > galaxyp > cardinal_filtering
annotate filtering.xml @ 8:a8157342d9a3 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
author | galaxyp |
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date | Wed, 13 May 2020 14:11:34 -0400 |
parents | 1d4a6fe69a40 |
children | e92efed83208 |
rev | line source |
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7
1d4a6fe69a40
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
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1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.0"> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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2 <description>tool for filtering mass spectrometry imaging data</description> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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3 <macros> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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4 <import>macros.xml</import> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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5 </macros> |
7
1d4a6fe69a40
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
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6 <expand macro="requirements"> |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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7 <requirement type="package" version="2.3">r-gridextra</requirement> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
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8 <requirement type="package" version="3.2.1">r-ggplot2</requirement> |
7
1d4a6fe69a40
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
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9 </expand> |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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10 <expand macro="print_version"/> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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11 <command detect_errors="exit_code"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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12 <![CDATA[ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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13 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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14 @INPUT_LINKING@ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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15 cat '${MSI_subsetting}' && |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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16 Rscript '${MSI_subsetting}' && |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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17 mkdir $outfile_imzml.files_path && |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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18 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true && |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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19 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true && |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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20 echo "imzML file:" > $outfile_imzml && |
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
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21 ls -l "$outfile_imzml.files_path" >> $outfile_imzml |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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22 ]]> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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23 </command> |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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24 |
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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25 |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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26 <configfiles> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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27 <configfile name="MSI_subsetting"><![CDATA[ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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28 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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29 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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30 ################################# load libraries and read file ################# |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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31 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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32 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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33 library(Cardinal) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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34 library(ggplot2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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35 library(gridExtra) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
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36 |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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37 |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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38 |
7
1d4a6fe69a40
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
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39 @READING_MSIDATA_FULLY_COMPATIBLE@ |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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40 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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41 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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42 ########################### QC numbers ######################## |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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43 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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44 ## Number of features (m/z) |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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45 maxfeatures = nrow(msidata) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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46 ## Range m/z |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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47 minmz = round(min(mz(msidata)), digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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48 maxmz = round(max(mz(msidata)), digits=2) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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49 ## Number of spectra (pixels) |
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d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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50 pixelcount = ncol(msidata) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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51 ## Range x coordinates |
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d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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52 minimumx = min(coord(msidata)\$x) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
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53 maximumx = max(coord(msidata)\$x) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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54 ## Range y coordinates |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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55 minimumy = min(coord(msidata)\$y) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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56 maximumy = max(coord(msidata)\$y) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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57 ## Store features for QC plot |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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58 featuresinfile = mz(msidata) |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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59 |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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60 all_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, rep("removed pixels", times=ncol(msidata))) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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61 colnames(all_df) = c("x", "y", "annotation") |
4
58376f5a6319
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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62 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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63 ## Next steps will only run if there are more than 0 pixels/features in the file |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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64 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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65 if (ncol(msidata)>0 & nrow(msidata) >0) |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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66 { |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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67 ###################################### Filtering of pixels ##################### |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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68 ################################################################################ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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69 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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70 ############ Pixels in two columns format: x and y in different columns ############# |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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71 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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72 #if str($pixels_cond.pixel_filtering) == "two_columns": |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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73 print("two columns") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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74 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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75 ## read tabular file |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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76 input_list = read.delim("$pixels_cond.annotation_file", header = $pixels_cond.tabular_header, |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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77 stringsAsFactors = FALSE) |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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78 inputpixels = input_list[,c($pixels_cond.column_x, $pixels_cond.column_y)] |
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79 input_pixels = paste(inputpixels[,1], inputpixels[,2], sep="_") |
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80 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_") |
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81 pixelsofinterest = dataset_pixels %in% input_pixels |
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82 |
2
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83 tryCatch( |
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84 { |
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85 msidata = msidata[,pixelsofinterest] |
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86 if (ncol(msidata) == 0) |
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87 { |
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88 stop(call.=FALSE) |
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89 } |
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90 }, |
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91 error=function(cond) { |
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92 ## in case all coordinates were outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data |
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93 message("Error during pixel filtering") |
6
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94 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool") |
2
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95 stop(call.=FALSE) |
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96 } |
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97 ) |
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98 |
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99 ## QC values: |
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100 numberpixels = nrow(input_list) |
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101 validpixels=ncol(msidata) |
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102 |
2
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103 ########### Pixels wihin x and y minima and maxima are kept ################# |
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104 |
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105 #elif str($pixels_cond.pixel_filtering) == "pixel_range": |
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106 print("pixel range") |
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107 |
2
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108 ## QC values: |
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109 numberpixels = "range" |
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110 validpixels = "range" |
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111 |
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112 tryCatch( |
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113 { |
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114 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range] |
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115 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range] |
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116 if (ncol(msidata) == 0) |
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117 { |
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118 stop(call.=FALSE) |
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119 } |
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120 }, |
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121 error=function(cond) { |
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122 ## in case one of the ranges was outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data |
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123 message("Error during pixel filtering") |
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124 message("Check that both x and y ranges were inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields") |
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125 stop(call.=FALSE) |
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126 } |
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127 ) |
1
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128 |
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129 ######################## no pixel filtering ################################ |
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130 |
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131 #elif str($pixels_cond.pixel_filtering) == "none": |
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132 print("no pixel filtering") |
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133 |
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134 ## QC values: |
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135 numberpixels = 0 |
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136 validpixels = 0 |
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137 |
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138 #end if |
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139 |
2
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140 ############################# QC data ##################################### |
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141 |
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142 ## dataframe for QC of pixel distribution |
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143 |
6
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144 remaining_df = data.frame(as.numeric(coord(msidata)\$x), as.numeric(coord(msidata)\$y), rep("remaining pixels", times=ncol(msidata))) |
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145 colnames(remaining_df) = c("x", "y", "annotation") |
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146 position_df = rbind(all_df, remaining_df) |
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147 position_df[row.names(unique(position_df[,c("x", "y")])),] |
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148 position_df\$annotation = factor(position_df\$annotation) |
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149 gc() |
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150 |
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151 }else{ |
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152 print("Inputfile has no intensities > 0") |
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153 } |
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154 |
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155 ################################# filtering of features ###################### |
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156 ############################################################################## |
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157 |
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158 ####################### Keep m/z from tabular file ######################### |
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159 |
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160 ## feature filtering only when pixels/features/intensities are left |
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161 |
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162 |
1
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163 if (ncol(msidata) > 0){ |
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164 if (nrow(msidata) > 0) |
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165 { |
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166 |
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167 #if str($features_cond.features_filtering) == "features_list": |
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168 print("feature list") |
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169 |
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170 ## read tabular file, define starting row, extract and count valid features |
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171 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE) |
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172 extracted_features = input_features[,$features_cond.feature_column] |
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173 numberfeatures = length(extracted_features) |
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174 |
1
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175 if (class(extracted_features) == "numeric"){ |
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176 ### max digits given in the input file will be used to match m/z but the maximum is 4 |
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177 max_digits = max(nchar(sapply(strsplit(as.character(extracted_features), "\\."),`[`,2)), na.rm=TRUE) |
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178 |
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179 if (max_digits >4) |
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180 { |
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181 max_digits = 4 |
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182 } |
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183 |
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184 validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits) |
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185 featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)] |
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186 validmz = length(unique(featuresofinterest)) |
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187 |
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188 }else{ |
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189 validmz = 0 |
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190 featuresofinterest = 0} |
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191 |
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192 ### filter msidata for valid features |
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193 |
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194 tryCatch( |
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195 { |
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196 msidata = msidata[featuresofinterest,] |
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197 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data |
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198 if (nrow(msidata) == 0) |
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199 { |
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200 stop(call.=FALSE) |
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201 } |
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202 }, |
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203 error=function(cond) { |
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204 ## in case all provided m/z values were outside the m/z range |
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205 ## tool is stopped to avoid continuing with wrong data |
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206 message("Error during m/z filtering") |
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207 message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset (this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)") |
2
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208 stop(call.=FALSE) |
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209 } |
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210 ) |
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211 |
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212 |
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213 ############### features within a given range are kept ##################### |
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214 |
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215 #elif str($features_cond.features_filtering) == "features_range": |
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216 print("feature range") |
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217 |
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218 numberfeatures = "range" |
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219 validmz = "range" |
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220 |
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221 tryCatch( |
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222 { |
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223 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,] |
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224 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data |
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225 if (nrow(msidata) == 0) |
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226 { |
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227 stop(call.=FALSE) |
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228 } |
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229 }, |
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230 error=function(cond) { |
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231 ## in case all m/z features were outside the dataset leading to zero m/z features, tool is stopped to avoid continuing with wrong data |
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232 message("Error during m/z filtering") |
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233 message("Check that the entered m/z range is inside the dataset coordinates (can be checked with the 'MSI qualitycontrol' tool) or if any not numeric character was entered into the input fields") |
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234 stop(call.=FALSE) |
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235 } |
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236 ) |
1
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237 |
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238 ############### Remove m/z from tabular file ######################### |
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239 |
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240 #elif str($features_cond.features_filtering) == "remove_features": |
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241 print("remove features") |
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242 |
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243 ## read tabular file, define starting row, extract and count valid features |
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244 input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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245 extracted_features = input_features[,$features_cond.feature_column] |
1
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246 numberfeatures = length(extracted_features) |
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247 if (class(extracted_features) == "numeric"){ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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248 print("input is numeric") |
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249 featuresofinterest = extracted_features |
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250 }else{featuresofinterest = 0} |
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251 |
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252 ### Here starts removal of features: |
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253 plusminus = $features_cond.removal_plusminus |
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254 |
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255 tryCatch( |
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256 { |
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257 mass_to_remove = numeric() |
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258 for (masses in featuresofinterest){ |
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259 #if str($features_cond.units_removal) == "ppm": |
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260 plusminus = masses * $features_cond.removal_plusminus/1000000 |
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261 #end if |
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262 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus)) |
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263 mass_to_remove = append(mass_to_remove, current_mass)} |
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264 mass_to_keep = setdiff(1:nrow(msidata),mass_to_remove) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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265 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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266 msidata= msidata[mass_to_keep, ] |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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267 validmz = maxfeatures - nrow(msidata) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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268 |
2
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269 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data |
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270 if (nrow(msidata) == 0) |
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271 { |
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272 stop(call.=FALSE) |
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273 } |
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274 }, |
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275 error=function(cond) { |
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276 message("Error during removal of m/z features") |
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277 stop(call.=FALSE) |
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278 } |
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279 ) |
0
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280 |
a2988d8d4b77
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281 |
2
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282 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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283 ######################## No m/z filtering ############################## |
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284 |
1
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285 #elif str($features_cond.features_filtering) == "none": |
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286 |
1
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287 print("no feature filtering") |
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288 validmz = 0 |
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289 numberfeatures = 0 |
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290 |
1
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291 #end if |
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292 |
1
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293 }else{ |
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294 print("Inputfile has no m/z features") |
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295 numberfeatures = NA |
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296 validmz = NA |
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297 } |
0
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298 }else{ |
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299 print("Inputfile or file filtered for pixels has no pixels") |
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300 numberfeatures = NA |
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301 validmz = NA |
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302 } |
2
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303 gc() |
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304 |
2
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305 #################### QC numbers ####################### |
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306 |
2
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307 ## Number of features (m/z) |
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308 maxfeatures2 = nrow(msidata) |
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309 ## Range m/z |
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310 minmz2 = round(min(mz(msidata)), digits=2) |
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311 maxmz2 = round(max(mz(msidata)), digits=2) |
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312 ## Number of spectra (pixels) |
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313 pixelcount2 = ncol(msidata) |
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314 ## Range x coordinates |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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315 minimumx2 = min(coord(msidata)\$x) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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316 maximumx2 = max(coord(msidata)\$x) |
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317 ## Range y coordinates |
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318 minimumy2 = min(coord(msidata)\$y) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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319 maximumy2 = max(coord(msidata)\$y) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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320 |
2
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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321 properties = c("Number of m/z features", |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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322 "Range of m/z values", |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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323 "Number of pixels", |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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324 "Range of x coordinates", |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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325 "Range of y coordinates", |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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326 "pixel overview", |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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327 "feature overview") |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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328 |
2
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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329 before = c(paste0(maxfeatures), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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330 paste0(minmz, " - ", maxmz), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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331 paste0(pixelcount), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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332 paste0(minimumx, " - ", maximumx), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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333 paste0(minimumy, " - ", maximumy), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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334 paste0("input pixels: ", numberpixels), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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335 paste0("input mz: ", numberfeatures)) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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336 |
2
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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337 filtered = c(paste0(maxfeatures2), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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338 paste0(minmz2, " - ", maxmz2), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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339 paste0(pixelcount2), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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340 paste0(minimumx2, " - ", maximumx2), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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341 paste0(minimumy2, " - ", maximumy2), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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342 paste0("valid pixels: ", validpixels), |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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343 paste0("valid mz: ", validmz)) |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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344 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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345 property_df = data.frame(properties, before, filtered) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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346 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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347 ########################### PDF QC and MSI output ########################### |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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348 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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349 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12) |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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350 plot(0,type='n',axes=FALSE,ann=FALSE) |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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351 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.element_identifier")) |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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352 grid.table(property_df, rows= NULL) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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353 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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354 ## QC report only when pixels/features are left |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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355 if (ncol(msidata)>0 & nrow(msidata) >0) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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356 { |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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357 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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358 ### visual pixel control |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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359 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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360 pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+ |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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361 geom_tile(height = 1, width=1)+ |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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362 coord_fixed()+ |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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363 ggtitle("Spatial orientation of filtered pixels")+ |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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364 theme_bw()+ |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
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365 theme(plot.title = element_text(hjust = 0.5))+ |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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366 theme(legend.position="bottom",legend.direction="vertical")+ |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
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367 guides(fill=guide_legend(ncol=5,byrow=TRUE)) |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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368 print(pixel_image) |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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369 |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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370 |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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371 ### visual mz feature control |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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372 |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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373 kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata))) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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374 colnames(kept_df) = c("mz", "legend") |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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375 |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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376 mz_removed = setdiff(featuresinfile, mz(msidata)) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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377 removed_df = data.frame(mz_removed, rep("removed m/z", length(mz_removed))) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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378 colnames(removed_df) = c("mz", "legend") |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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379 histogram_df = rbind(removed_df,kept_df) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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380 |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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381 histogram_mz= ggplot(histogram_df, aes(x=mz, fill=legend)) + |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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382 geom_histogram()+ theme_bw()+ |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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383 theme(plot.title = element_text(hjust = 0.5))+ |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
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diff
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384 theme(legend.position="bottom",legend.direction="vertical")+ |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
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385 labs(title="Overview of filtered m/z", x="m/z", y = "count") + |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
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386 guides(fill=guide_legend(ncol=5,byrow=TRUE)) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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387 print(histogram_mz) |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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388 |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
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|
389 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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1
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390 dev.off() |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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changeset
|
391 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
392 ## save msidata as imzML file, will only work if there is at least 1 m/z left |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
393 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
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diff
changeset
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394 if (maxfeatures2 > 0){ |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
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|
395 ## make sure that coordinates are integers |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
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396 coord(msidata)\$y = as.integer(coord(msidata)\$y) |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
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|
397 coord(msidata)\$x = as.integer(coord(msidata)\$x) |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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398 writeImzML(msidata, "out")} |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
399 |
1
aac805a9d2ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
400 |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
401 }else{ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
402 print("Inputfile or filtered file has no intensities > 0") |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
403 dev.off() |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
404 } |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
405 |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
406 ]]></configfile> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
407 </configfiles> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
408 <inputs> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
409 <expand macro="reading_msidata"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
410 <conditional name="pixels_cond"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
411 <param name="pixel_filtering" type="select" label="Select pixel filtering option"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
412 <option value="none" selected="True">none</option> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
413 <option value="two_columns">coordinates from tabular file</option> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
414 <option value="pixel_range">ranges for x and y (manually)</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
415 </param> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
416 <when value="none"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
417 <when value="two_columns"> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
418 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates" |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
419 help="Tabular file with two columns: x values and y values"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
420 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
421 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
422 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
423 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
424 <when value="pixel_range"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
425 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
426 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
427 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
428 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
429 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
430 </conditional> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
431 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
432 <conditional name="features_cond"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
433 <param name="features_filtering" type="select" label="Select m/z feature filtering option"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
434 <option value="none" selected="True">none</option> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
435 <option value="features_list">keep m/z (tabular file)</option> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
436 <option value="features_range">m/z range (manually)</option> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
437 <option value="remove_features">remove m/z (tabular file)</option> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
438 </param> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
439 <when value="none"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
440 <when value="features_list"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
441 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to keep"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
442 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
443 <when value="features_range"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
444 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
445 <param name="max_mz" type="float" value="100" label="Maximum value for m/z"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
446 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
447 <when value="remove_features"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
448 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to remove"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
449 <param name="removal_plusminus" type="float" value="20" label="Window in which all m/z will be removed" help="This value is the half window size, it will be added and substracted from the given input value"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
450 <param name="units_removal" type="select" display="radio" optional ="False" label="units"> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
451 <option value="ppm" selected="True">ppm</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
452 <option value="Da">Da</option> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
453 </param> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
454 </when> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
455 </conditional> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
456 </inputs> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
457 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
458 <outputs> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
459 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
460 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
461 </outputs> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
462 <tests> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
463 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
464 <expand macro="infile_imzml"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
465 <param name="pixel_filtering" value="pixel_range"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
466 <param name="min_x_range" value="1"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
467 <param name="max_x_range" value="20"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
468 <param name="min_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
469 <param name="max_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
470 <param name="features_filtering" value="features_range"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
471 <param name="min_mz" value="350"/> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
472 <param name="max_mz" value="500"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
473 <output name="QC_overview" file="imzml_filtered3.pdf" compare="sim_size"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
474 <output name="outfile_imzml" ftype="imzml" file="out3.imzml.txt" compare="sim_size"> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
475 <extra_files type="file" file="out3.imzml" name="imzml" lines_diff="6"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
476 <extra_files type="file" file="out3.ibd" name="ibd" compare="sim_size"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
477 </output> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
478 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
479 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
480 <expand macro="infile_imzml"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
481 <param name="pixel_filtering" value="two_columns"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
482 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
483 <param name="column_x" value="1"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
484 <param name="column_y" value="3"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
485 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
486 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size"> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
487 <extra_files type="file" file="out4.imzml" name="imzml" lines_diff="6"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
488 <extra_files type="file" file="out4.ibd" name="ibd" compare="sim_size"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
489 </output> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
490 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
491 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
492 <expand macro="infile_imzml"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
493 <param name="pixel_filtering" value="pixel_range"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
494 <param name="min_x_range" value="0"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
495 <param name="max_x_range" value="10"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
496 <param name="min_y_range" value="2"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
497 <param name="max_y_range" value="20"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
498 <param name="features_filtering" value="features_list"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
499 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
500 <param name="feature_column" value="1"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
501 <param name="feature_header" value="0"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
502 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
503 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size"> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
504 <extra_files type="file" file="out5.imzml" name="imzml" lines_diff="6"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
505 <extra_files type="file" file="out5.ibd" name="ibd" compare="sim_size"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
506 </output> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
507 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
508 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
509 <expand macro="infile_analyze75"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
510 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
511 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size"> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
512 <extra_files type="file" file="out6.imzml" name="imzml" lines_diff="6"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
513 <extra_files type="file" file="out6.ibd" name="ibd" compare="sim_size"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
514 </output> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
515 </test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
516 <test> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
517 <param name="infile" value="preprocessed.RData" ftype="rdata"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
518 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" /> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
519 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size"> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
520 <extra_files type="file" file="out7.imzml" name="imzml" lines_diff="6"/> |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
521 <extra_files type="file" file="out7.ibd" name="ibd" compare="sim_size"/> |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
522 </output> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
523 </test> |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
524 <test> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
525 <expand macro="processed_infile_imzml"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
526 <conditional name="processed_cond"> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
527 <param name="processed_file" value="processed"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
528 <param name="accuracy" value="100"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
529 <param name="units" value="ppm"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
530 </conditional> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
531 <param name="pixel_filtering" value="two_columns"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
532 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
533 <param name="column_x" value="1"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
534 <param name="column_y" value="3"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
535 <param name="features_filtering" value="remove_features"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
536 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
537 <param name="feature_column" value="1"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
538 <param name="feature_header" value="0"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
539 <param name="removal_plusminus" value="100"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
540 <param name="units_removal" value="ppm"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
541 <output name="QC_overview" file="imzml_filtered8.pdf" compare="sim_size"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
542 <output name="outfile_imzml" ftype="imzml" file="out8.imzml.txt" compare="sim_size"> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
543 <extra_files type="file" file="out8.imzml" name="imzml" lines_diff="6"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
544 <extra_files type="file" file="out8.ibd" name="ibd" compare="sim_size"/> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
545 </output> |
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
546 </test> |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
547 </tests> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
548 <help> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
549 <![CDATA[ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
550 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
551 @CARDINAL_DESCRIPTION@ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
552 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
553 ----- |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
554 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
555 This tool provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data. |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
556 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
557 @MSIDATA_INPUT_DESCRIPTION@ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
558 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
559 - Optional file with pixel coordinates and annotation: |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
560 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
561 - Tabular file: One column with x values, one column with y values |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
562 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
563 - Pixel with coordinates outside the coordinates of the input file are ignored |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
564 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
565 :: |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
566 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
567 x_coord y_coord |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
568 1 1 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
569 2 1 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
570 3 1 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
571 ... |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
572 ... |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
573 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
574 @MZ_TABULAR_INPUT_DESCRIPTION@ |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
575 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
576 **Options** |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
577 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
578 - Pixel filtering/annotation: |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
579 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
580 - Either with a tabular file containing x and y coordinates or by entering x-min, x-max, y-min, y-max manually |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
581 - Pixel that are not present in the dataset are ignored |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
582 - An error occurs if the input for filtering (tabular file, x-range or y-range) contains not a single coordinate that occurs in the input dataset |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
583 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
584 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
585 - m/z feature filtering: |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
586 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
587 - Either with a tabular file containing m/z values or by entering m/z-min and m/z-max manually |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
588 - m/z values that are not present in the dataset are ignored |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
589 - An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
590 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
591 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
592 - m/z feature removing: |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
593 |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
594 - Perturbing m/z features such as matrix contaminants, tryptic peptides and internal calibrants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
595 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
596 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
597 **Tips** |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
598 |
2
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
599 - m/z feautre filtering with a tabular file: |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
600 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
601 - For matching the m/z features of the input dataset are rounded to the number of decimal points of the m/z values from the tabular file. In case the input had more than 4 digits m/z values of dataset and tabular file are rounded to 4 digits. |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
602 - Therefore, it is recommended to use the filtering tool only for m/z features which have been extracted from the same dataset. If the m/z values are from a different dataset, the tool 'Join two files on column allowing a small difference' should be used to find corresponding m/z values, which can then be used for filtering. |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
603 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
604 - Problems to select tabular file: |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
605 |
0c4579390f73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
606 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from 'tabular' - datatype can be changed by pressing the pen button of the dataset (edit attributes) |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
607 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
608 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
609 **Output** |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
610 |
6
d2ccd8348018
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
4
diff
changeset
|
611 - MSI data as (continuous) imzML file |
4
58376f5a6319
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
2
diff
changeset
|
612 - pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z |
0
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
613 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
614 |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
615 ]]> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
616 </help> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
617 <expand macro="citations"/> |
a2988d8d4b77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
618 </tool> |