Mercurial > repos > galaxyp > cardinal_preprocessing
diff macros.xml @ 18:83aac7741200 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
| author | galaxyp |
|---|---|
| date | Thu, 04 Jul 2024 13:38:14 +0000 |
| parents | 798da6bdff3d |
| children |
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--- a/macros.xml Wed Apr 19 22:46:23 2023 +0000 +++ b/macros.xml Thu Jul 04 13:38:14 2024 +0000 @@ -1,10 +1,20 @@ <macros> - <token name="@VERSION@">2.10.0</token> + <token name="@TOOL_VERSION@">3.4.3</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> - <!--requirement type="package" version="3.6.1">r-base</requirement--> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-cardinal</requirement> + <requirement type="package" version="2.3">r-gridextra</requirement> + <requirement type="package" version="3.5.1">r-ggplot2</requirement> + <requirement type="package" version="0.14.1">r-maldiquantforeign</requirement> + <requirement type="package" version="1.22.2">r-maldiquant</requirement> + <requirement type="package" version="3.50.0">bioconductor-sva</requirement> + <requirement type="package" version="1.1.0.1">r-randomcolor</requirement> + <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement> + <requirement type="package" version="2.23_24">r-kernsmooth</requirement> + <requirement type="package" version="1.3.0">r-scales</requirement> + <requirement type="package" version="1.0.12">r-pheatmap</requirement> <yield/> </requirements> </xml> @@ -17,12 +27,12 @@ <token name="@INPUT_LINKING@"><![CDATA[ #if $infile.ext == 'imzml' - ln -s '${infile.extra_files_path}/imzml' infile.imzML && - ln -s '${infile.extra_files_path}/ibd' infile.ibd && + cp '${infile.extra_files_path}/imzml' infile.imzML && + cp '${infile.extra_files_path}/ibd' infile.ibd && #elif $infile.ext == 'analyze75' - ln -s '${infile.extra_files_path}/hdr' infile.hdr && - ln -s '${infile.extra_files_path}/img' infile.img && - ln -s '${infile.extra_files_path}/t2m' infile.t2m && + cp '${infile.extra_files_path}/hdr' infile.hdr && + cp '${infile.extra_files_path}/img' infile.img && + cp '${infile.extra_files_path}/t2m' infile.t2m && #else ln -s $infile infile.RData && #end if @@ -38,13 +48,13 @@ get(ls()[ls() != "fileName"]) } + #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units") - msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous centroided(msidata) = $centroids #else - msidata <- readImzML('infile', attach.only=TRUE) + msidata <- readImzML('infile') centroided(msidata) = $centroids #end if #elif $infile.ext == 'analyze75' @@ -95,7 +105,7 @@ msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) centroided(msidata) = $centroids #else - msidata <- readImzML('infile', attach.only=TRUE) + msidata <- readImzML('infile') centroided(msidata) = $centroids #end if #elif $infile.ext == 'analyze75' @@ -117,13 +127,13 @@ <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ ########################### QC numbers ######################## ## including intensity calculations which need data in RAM - int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use ## Number of NA in spectra matrix NAcount = sum(is.na(int_matrix)) ## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata int_matrix[is.na(int_matrix)] <- 0 - + + ## Number of features (mz) maxfeatures = length(features(msidata)) ## Range mz