Mercurial > repos > galaxyp > cardinal_filtering
diff filtering.xml @ 7:1d4a6fe69a40 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
| author | galaxyp |
|---|---|
| date | Thu, 23 Apr 2020 08:10:44 -0400 |
| parents | d2ccd8348018 |
| children | e92efed83208 |
line wrap: on
line diff
--- a/filtering.xml Wed Mar 25 08:05:39 2020 -0400 +++ b/filtering.xml Thu Apr 23 08:10:44 2020 -0400 @@ -1,14 +1,12 @@ -<tool id="cardinal_filtering" name="MSI filtering" version="2.4.0.0"> +<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.0"> <description>tool for filtering mass spectrometry imaging data</description> <macros> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="2.4.0">bioconductor-cardinal</requirement> - <requirement type="package" version="3.6.1">r-base</requirement> + <expand macro="requirements"> <requirement type="package" version="2.3">r-gridextra</requirement> <requirement type="package" version="3.2.1">r-ggplot2</requirement> - </requirements> + </expand> <expand macro="print_version"/> <command detect_errors="exit_code"> <![CDATA[ @@ -38,27 +36,7 @@ -## function to read RData files independent of filename -loadRData <- function(fileName){ -load(fileName) -get(ls()[ls() != "fileName"]) -} - -#if $infile.ext == 'imzml' - #if str($processed_cond.processed_file) == "processed": - msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) - centroided(msidata) = $centroids - #else - msidata <- readImzML('infile', attach.only=TRUE) - centroided(msidata) = $centroids - #end if -#elif $infile.ext == 'analyze75' - msidata = readAnalyze('infile', attach.only=TRUE) - centroided(msidata) = $centroids -#else - msidata = loadRData('infile.RData') - msidata = as(msidata, "MSImagingExperiment") -#end if +@READING_MSIDATA_FULLY_COMPATIBLE@ ########################### QC numbers ########################