Mercurial > repos > galaxyp > cardinal_combine
diff combine.xml @ 8:edb351764624 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
| author | galaxyp |
|---|---|
| date | Wed, 13 May 2020 17:53:43 +0000 |
| parents | a93991a9db04 |
| children | 11d9b3ebbabd |
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--- a/combine.xml Thu Apr 23 11:54:58 2020 +0000 +++ b/combine.xml Wed May 13 17:53:43 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0"> +<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1"> <description> combine several mass spectrometry imaging datasets into one </description> @@ -86,15 +86,15 @@ #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": - msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE, as="MSImageSet") - ##msidata_$i = collect(msidata_$i, as.matrix=TRUE) ##coercion to continuous + msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) + msidata_$i = collect(msidata_$i, as.matrix=TRUE) ##coercion to continuous centroided(msidata_$i) = $centroids #else - msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as="MSImageSet") + msidata_$i <- readImzML('infile_${i}', attach.only=TRUE) centroided(msidata_$i) = $centroids #end if #elif $infile.ext == 'analyze75' - msidata_$i = readAnalyze('infile_${i}', attach.only=TRUE, as="MSImageSet") + msidata_$i = readAnalyze('infile_${i}', attach.only=TRUE) centroided(msidata_$i) = $centroids #else ## function to read RData files independent of filename @@ -112,6 +112,9 @@ msidata_$i\$combined_sample = NULL #end if + ## coercion into MSImageSet + msidata_$i = as(msidata_$i, "MSImageSet") + ## remove duplicated coordinates, otherwise combine will fail print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]