Mercurial > repos > galaxyp > cardinal_preprocessing

comparison macros.xml @ 8:87bb011a4ee8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
author galaxyp
date Wed, 13 May 2020 14:21:48 -0400
parents 44a4b31fcbf3
children ca727a6dede6
comparison
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7:44a4b31fcbf3 8:87bb011a4ee8
29 ]]></token> 29 ]]></token>
30 30
31 31
32 <token name="@READING_MSIDATA@"><![CDATA[ 32 <token name="@READING_MSIDATA@"><![CDATA[
33 ## importing MSI data files 33 ## importing MSI data files
34
35 ## read RData files (MSI and other data) independent of filename
36 loadRData <- function(fileName){
37 load(fileName)
38 get(ls()[ls() != "fileName"])
39 }
34 40
35 #if $infile.ext == 'imzml' 41 #if $infile.ext == 'imzml'
36 #if str($processed_cond.processed_file) == "processed": 42 #if str($processed_cond.processed_file) == "processed":
37 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units") 43 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units")
38 msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous 44 msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous
43 #end if 49 #end if
44 #elif $infile.ext == 'analyze75' 50 #elif $infile.ext == 'analyze75'
45 msidata = readAnalyze('infile', attach.only=TRUE) 51 msidata = readAnalyze('infile', attach.only=TRUE)
46 centroided(msidata) = $centroids 52 centroided(msidata) = $centroids
47 #else 53 #else
48 ## function to read RData files independent of filename
49 loadRData <- function(fileName){
50 load(fileName)
51 get(ls()[ls() != "fileName"])
52 }
53 msidata = loadRData('infile.RData') 54 msidata = loadRData('infile.RData')
54 #end if 55 #end if
55 56
56 ]]></token> 57 ]]></token>
57 58