diff macros.xml @ 17:91f0f5922011 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c

--- a/macros.xml	Wed Apr 19 22:47:48 2023 +0000
+++ b/macros.xml	Thu Jul 04 13:36:52 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