Mercurial > repos > galaxyp > cardinal_single_ion_segmentation
annotate macros.xml @ 2:db423b7bce78 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author | galaxyp |
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date | Thu, 04 Jul 2024 13:43:40 +0000 |
parents | 4cb6c83d3777 |
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rev | line source |
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0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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1 <macros> |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
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0
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2 <token name="@TOOL_VERSION@">3.4.3</token> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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3 <token name="@VERSION_SUFFIX@">0</token> |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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4 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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5 <xml name="requirements"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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6 <requirements> |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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7 <requirement type="package" version="@TOOL_VERSION@">bioconductor-cardinal</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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8 <requirement type="package" version="2.3">r-gridextra</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
diff
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9 <requirement type="package" version="3.5.1">r-ggplot2</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
diff
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10 <requirement type="package" version="0.14.1">r-maldiquantforeign</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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11 <requirement type="package" version="1.22.2">r-maldiquant</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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12 <requirement type="package" version="3.50.0">bioconductor-sva</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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13 <requirement type="package" version="1.1.0.1">r-randomcolor</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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14 <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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15 <requirement type="package" version="2.23_24">r-kernsmooth</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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16 <requirement type="package" version="1.3.0">r-scales</requirement> |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
0
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17 <requirement type="package" version="1.0.12">r-pheatmap</requirement> |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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18 <yield/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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19 </requirements> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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20 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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21 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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22 <xml name="print_version"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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23 <version_command><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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24 echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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25 ]]></version_command> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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26 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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27 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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28 <token name="@INPUT_LINKING@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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29 #if $infile.ext == 'imzml' |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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30 cp '${infile.extra_files_path}/imzml' infile.imzML && |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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31 cp '${infile.extra_files_path}/ibd' infile.ibd && |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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32 #elif $infile.ext == 'analyze75' |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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33 cp '${infile.extra_files_path}/hdr' infile.hdr && |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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34 cp '${infile.extra_files_path}/img' infile.img && |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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35 cp '${infile.extra_files_path}/t2m' infile.t2m && |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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36 #else |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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37 ln -s $infile infile.RData && |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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38 #end if |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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39 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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40 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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41 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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42 <token name="@READING_MSIDATA@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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43 ## importing MSI data files |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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44 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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45 ## read RData files (MSI and other data) independent of filename |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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46 loadRData <- function(fileName){ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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47 load(fileName) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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48 get(ls()[ls() != "fileName"]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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49 } |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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50 |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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51 |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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52 #if $infile.ext == 'imzml' |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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53 #if str($processed_cond.processed_file) == "processed": |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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54 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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55 centroided(msidata) = $centroids |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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56 #else |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents:
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57 msidata <- readImzML('infile') |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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58 centroided(msidata) = $centroids |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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59 #end if |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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60 #elif $infile.ext == 'analyze75' |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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61 msidata = readAnalyze('infile', attach.only=TRUE) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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62 centroided(msidata) = $centroids |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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63 #else |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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64 msidata = loadRData('infile.RData') |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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65 #end if |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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66 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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67 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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68 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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69 <token name="@DATA_PROPERTIES@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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70 ## Number of features (mz) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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71 maxfeatures = length(features(msidata)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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72 ## Range mz |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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73 minmz = round(min(mz(msidata)), digits=2) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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74 maxmz = round(max(mz(msidata)), digits=2) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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75 ## Number of spectra (pixels) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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76 pixelcount = length(pixels(msidata)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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77 ## Range x coordinates |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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78 minimumx = min(coord(msidata)[,1]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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79 maximumx = max(coord(msidata)[,1]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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80 ## Range y coordinates |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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81 minimumy = min(coord(msidata)[,2]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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82 maximumy = max(coord(msidata)[,2]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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83 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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84 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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85 properties = c("Number of m/z features", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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86 "Range of m/z values", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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87 "Number of pixels", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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88 "Range of x coordinates", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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89 "Range of y coordinates") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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90 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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91 values = c(paste0(maxfeatures), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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92 paste0(minmz, " - ", maxmz), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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93 paste0(pixelcount), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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94 paste0(minimumx, " - ", maximumx), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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95 paste0(minimumy, " - ", maximumy)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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96 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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97 property_df = data.frame(properties, values) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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98 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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99 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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100 <token name="@READING_MSIDATA_FULLY_COMPATIBLE@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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101 ## importing MSI data files |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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102 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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103 #if $infile.ext == 'imzml' |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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104 #if str($processed_cond.processed_file) == "processed": |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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105 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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106 centroided(msidata) = $centroids |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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107 #else |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
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108 msidata <- readImzML('infile') |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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109 centroided(msidata) = $centroids |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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110 #end if |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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111 #elif $infile.ext == 'analyze75' |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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112 msidata = readAnalyze('infile', attach.only=TRUE) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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113 centroided(msidata) = $centroids |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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114 #else |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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115 ## function to read RData files independent of filename |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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116 loadRData <- function(fileName){ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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117 load(fileName) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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118 get(ls()[ls() != "fileName"]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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119 } |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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120 msidata = loadRData('infile.RData') |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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121 msidata = as(msidata, "MSImagingExperiment") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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122 run(msidata) = "infile" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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123 #end if |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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124 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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125 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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126 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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127 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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128 ########################### QC numbers ######################## |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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129 ## including intensity calculations which need data in RAM |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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130 int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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131 ## Number of NA in spectra matrix |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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132 NAcount = sum(is.na(int_matrix)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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133 ## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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134 int_matrix[is.na(int_matrix)] <- 0 |
2
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
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135 |
db423b7bce78
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
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136 |
0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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137 ## Number of features (mz) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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138 maxfeatures = length(features(msidata)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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139 ## Range mz |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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140 minmz = round(min(mz(msidata)), digits=2) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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141 maxmz = round(max(mz(msidata)), digits=2) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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142 ## Number of spectra (pixels) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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143 pixelcount = length(pixels(msidata)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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144 ## Range x coordinates |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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145 minimumx = min(coord(msidata)[,1]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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146 maximumx = max(coord(msidata)[,1]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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147 ## Range y coordinates |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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148 minimumy = min(coord(msidata)[,2]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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149 maximumy = max(coord(msidata)[,2]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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150 ## Range of intensities |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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151 minint = round(min(int_matrix), digits=2) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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152 maxint = round(max(int_matrix), digits=2) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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153 ## Number of intensities > 0, for if conditions |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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154 npeaks= sum(int_matrix>0) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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155 ## Number of NA in spectra matrix |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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156 infcount = sum(is.infinite(int_matrix)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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157 ## Number of duplicated coordinates |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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158 dupl_coord = sum(duplicated(coord(msidata))) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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159 properties = c("Number of m/z features", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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160 "Range of m/z values", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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161 "Number of pixels", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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162 "Range of x coordinates", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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163 "Range of y coordinates", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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164 "Range of intensities", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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165 "Number of NA intensities", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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166 "Number of Inf intensities", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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167 "Number of duplicated coordinates") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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168 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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169 values = c(paste0(maxfeatures), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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170 paste0(minmz, " - ", maxmz), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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171 paste0(pixelcount), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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172 paste0(minimumx, " - ", maximumx), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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173 paste0(minimumy, " - ", maximumy), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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174 paste0(minint, " - ", maxint), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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175 paste0(NAcount), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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176 paste0(infcount), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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177 paste0(dupl_coord)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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178 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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179 property_df = data.frame(properties, values) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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180 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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181 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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182 <token name="@CARDINAL_DESCRIPTION@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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183 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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184 `More information on Cardinal <http://cardinalmsi.org/>`_ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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185 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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186 <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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187 **Input data** |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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188 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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189 - MSI data: 3 types of input data can be used: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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190 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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191 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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192 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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193 - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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194 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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195 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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196 - Optional tabular file with m/z values: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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197 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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198 - One column with numeric m/z values (without empty fields or letters) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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199 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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200 - m/z features outside the m/z range of the input file are ignored |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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201 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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202 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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203 :: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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204 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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205 m/z |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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206 100.0 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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207 100.01 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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208 100.02 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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209 ... |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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210 ... |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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211 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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212 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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213 <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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214 - Tabular file with m/z values: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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215 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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216 - One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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217 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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218 - m/z features outside the m/z range of the input file are ignored |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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219 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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220 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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221 :: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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222 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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223 m/z name |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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224 100.0 analyte1 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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225 100.01 analyte2 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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226 100.02 analyte3 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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227 ... |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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228 ... |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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229 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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230 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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231 <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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232 - Optional file with pixel coordinates and annotation: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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233 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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234 - Tabular file: One column with x values, one column with y values and one column with annotations |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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235 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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236 - Pixel with coordinates outside the coordinates of the input file are ignored |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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237 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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238 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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239 :: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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240 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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241 x_coord y_coord annotation |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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242 1 1 healthy |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
243 2 1 healthy |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
244 3 1 disease |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
245 ... |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
246 ... |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
247 ]]></token> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
248 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
249 <xml name="reading_msidata"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
250 <param name="infile" type="data" format="imzml,rdata,analyze75" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
251 label="MSI data" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
252 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
253 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
254 <conditional name="processed_cond"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
255 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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256 <option value="no_processed" selected="True">no</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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257 <option value="processed">yes</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
258 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
259 <when value="no_processed"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
260 <when value="processed"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
261 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
262 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
263 <option value="mz" >mz</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
264 <option value="ppm" selected="True" >ppm</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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265 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
266 </when> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
267 </conditional> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
268 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
269 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
270 <xml name="pdf_filename"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
271 <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
272 <sanitizer invalid_char=""> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
273 <valid initial="string.ascii_letters,string.digits"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
274 <add value="_"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
275 <add value=" "/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
276 </valid> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
277 </sanitizer> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
278 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
279 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
280 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
281 <xml name="sanitizer_multiple_digits"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
282 <sanitizer invalid_char=""> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
283 <valid initial="string.digits"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
284 <add value=":" /> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
285 <add value="," /> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
286 </valid> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
287 </sanitizer> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
288 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
289 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
290 <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
291 <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
292 <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
293 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
294 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
295 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
296 <xml name="reading_2_column_mz_tabular" token_optional="false"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
297 <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
298 label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
299 <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
300 <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
301 <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
302 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
303 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
304 <xml name="reading_pixel_annotations"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
305 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
306 help="Tabular file with three columns: x values, y values and pixel annotations"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
307 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
308 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
309 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
310 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
311 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
312 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
313 <xml name="citations"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
314 <citations> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
315 <citation type="doi">10.1093/bioinformatics/btv146</citation> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
316 <citation type="doi">10.1093/gigascience/giz143</citation> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
changeset
|
317 </citations> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
318 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
319 <xml name="infile_analyze75"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
320 <param name="infile" value="" ftype="analyze75"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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|
321 <composite_data value="Analyze75.hdr"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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322 <composite_data value="Analyze75.img"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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323 <composite_data value="Analyze75.t2m"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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324 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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325 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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326 <xml name="infile_imzml"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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327 <param name="infile" value="" ftype="imzml"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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328 <composite_data value="Example_Continuous.imzML"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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329 <composite_data value="Example_Continuous.ibd"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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330 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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331 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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332 <xml name="processed_infile_imzml"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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333 <param name="infile" value="" ftype="imzml"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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334 <composite_data value="Example_Processed.imzML"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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335 <composite_data value="Example_Processed.ibd"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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336 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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337 </xml> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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338 </macros> |