Mercurial > repos > galaxyp > cardinal_combine

comparison combine.xml @ 8:525f201b86c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
author galaxyp
date Wed, 13 May 2020 14:08:25 -0400
parents 392b2dfd261d
children 7e18fcb92a6a
comparison
equal deleted inserted replaced
7:392b2dfd261d 8:525f201b86c1
1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0"> 1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1">
2 <description> 2 <description>
3 combine several mass spectrometry imaging datasets into one 3 combine several mass spectrometry imaging datasets into one
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
84 84
85 ## read and manipulate MSI data 85 ## read and manipulate MSI data
86 86
87 #if $infile.ext == 'imzml' 87 #if $infile.ext == 'imzml'
88 #if str($processed_cond.processed_file) == "processed": 88 #if str($processed_cond.processed_file) == "processed":
89 msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE, as="MSImageSet") 89 msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
90 ##msidata_$i = collect(msidata_$i, as.matrix=TRUE) ##coercion to continuous 90 msidata_$i = collect(msidata_$i, as.matrix=TRUE) ##coercion to continuous
91 centroided(msidata_$i) = $centroids 91 centroided(msidata_$i) = $centroids
92 #else 92 #else
93 msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as="MSImageSet") 93 msidata_$i <- readImzML('infile_${i}', attach.only=TRUE)
94 centroided(msidata_$i) = $centroids 94 centroided(msidata_$i) = $centroids
95 #end if 95 #end if
96 #elif $infile.ext == 'analyze75' 96 #elif $infile.ext == 'analyze75'
97 msidata_$i = readAnalyze('infile_${i}', attach.only=TRUE, as="MSImageSet") 97 msidata_$i = readAnalyze('infile_${i}', attach.only=TRUE)
98 centroided(msidata_$i) = $centroids 98 centroided(msidata_$i) = $centroids
99 #else 99 #else
100 ## function to read RData files independent of filename 100 ## function to read RData files independent of filename
101 loadRData <- function(fileName){ 101 loadRData <- function(fileName){
102 load(fileName) 102 load(fileName)
109 msidata_$i\$column3 = NULL 109 msidata_$i\$column3 = NULL
110 msidata_$i\$column4 = NULL 110 msidata_$i\$column4 = NULL
111 msidata_$i\$column5 = NULL 111 msidata_$i\$column5 = NULL
112 msidata_$i\$combined_sample = NULL 112 msidata_$i\$combined_sample = NULL
113 #end if 113 #end if
114
115 ## coercion into MSImageSet
116 msidata_$i = as(msidata_$i, "MSImageSet")
114 117
115 ## remove duplicated coordinates, otherwise combine will fail 118 ## remove duplicated coordinates, otherwise combine will fail
116 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) 119 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
117 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))] 120 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]
118 121