Mercurial > repos > galaxyp > cardinal_combine
diff combine.xml @ 7:392b2dfd261d draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
| author | galaxyp |
|---|---|
| date | Thu, 23 Apr 2020 08:04:25 -0400 |
| parents | bb1ac6b47a6c |
| children | 525f201b86c1 |
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--- a/combine.xml Wed Mar 25 07:02:41 2020 -0400 +++ b/combine.xml Thu Apr 23 08:04:25 2020 -0400 @@ -1,17 +1,15 @@ -<tool id="cardinal_combine" name="MSI combine" version="2.2.6.1"> +<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0"> <description> combine several mass spectrometry imaging datasets into one </description> <macros> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="2.2.6">bioconductor-cardinal</requirement> - <requirement type="package" version="3.6.1">r-base</requirement> + <expand macro="requirements"> <requirement type="package" version="3.2.1">r-ggplot2</requirement> <requirement type="package" version="0.12">r-maldiquantforeign</requirement> <requirement type="package" version="1.19.3">r-maldiquant</requirement> - </requirements> + </expand> <command detect_errors="exit_code"> <![CDATA[ #for $i, $infile in enumerate($infiles): @@ -54,6 +52,7 @@ library(MALDIquantForeign) library(MALDIquant) + ## read tabular file for xy_shift option #if str( $combine_conditional.combine_method ) == 'xy_shifts': input_list = read.delim("$combine_conditional.coordinates_file", header = $combine_conditional.xy_header, @@ -85,18 +84,24 @@ ## read and manipulate MSI data - #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 = c("MSImageSet")) + #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 + centroided(msidata_$i) = $centroids + #else + msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as="MSImageSet") + centroided(msidata_$i) = $centroids + #end if + #elif $infile.ext == 'analyze75' + msidata_$i = readAnalyze('infile_${i}', attach.only=TRUE, as="MSImageSet") centroided(msidata_$i) = $centroids #else - msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as = c("MSImageSet")) - centroided(msidata_$i) = $centroids - #end if - #elif $infile.ext == 'analyze75' - msidata_$i <- readAnalyze('infile_${i}', attach.only=TRUE, as = c("MSImageSet")) - centroided(msidata_$i) = $centroids - #else + ## function to read RData files independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } msidata_$i = loadRData('infile_${i}.RData') ## keep compatibility with old .RData files: msidata_$i\$column1 = NULL @@ -105,8 +110,7 @@ msidata_$i\$column4 = NULL msidata_$i\$column5 = NULL msidata_$i\$combined_sample = NULL - - #end if + #end if ## remove duplicated coordinates, otherwise combine will fail print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) @@ -563,5 +567,6 @@ <citations> <citation type="doi">10.1093/bioinformatics/btv146</citation> <citation type="doi">10.1007/978-3-319-45809-0_6</citation> + <citation type="doi">10.1093/gigascience/giz143</citation> </citations> </tool>