# HG changeset patch
# User galaxyp
# Date 1589393305 14400
# Node ID 525f201b86c151f65df1346675a890f0b0533aac
# Parent  392b2dfd261dc673a96e3ef6ef5cb82111585de4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"

diff -r 392b2dfd261d -r 525f201b86c1 combine.xml
--- a/combine.xml	Thu Apr 23 08:04:25 2020 -0400
+++ b/combine.xml	Wed May 13 14:08:25 2020 -0400
@@ -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}))]
diff -r 392b2dfd261d -r 525f201b86c1 macros.xml
--- a/macros.xml	Thu Apr 23 08:04:25 2020 -0400
+++ b/macros.xml	Wed May 13 14:08:25 2020 -0400
@@ -32,6 +32,12 @@
     <token name="@READING_MSIDATA@"><![CDATA[
         ## importing MSI data files
 
+            ## read RData files (MSI and other data) 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=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units")
@@ -45,11 +51,6 @@
             msidata = readAnalyze('infile', attach.only=TRUE)
             centroided(msidata) = $centroids
         #else
-            ## function to read RData files independent of filename
-            loadRData <- function(fileName){
-            load(fileName)
-            get(ls()[ls() != "fileName"])
-            }
             msidata = loadRData('infile.RData')
         #end if
 
diff -r 392b2dfd261d -r 525f201b86c1 test-data/QC_analyze75.pdf
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diff -r 392b2dfd261d -r 525f201b86c1 test-data/QC_empty_spectra.pdf
Binary file test-data/QC_empty_spectra.pdf has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/QC_imzml.pdf
Binary file test-data/QC_imzml.pdf has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/QC_rdata.pdf
Binary file test-data/QC_rdata.pdf has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results1.ibd
Binary file test-data/preprocessing_results1.ibd has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results1.imzml
--- a/test-data/preprocessing_results1.imzml	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results1.imzml	Wed May 13 14:08:25 2020 -0400
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="722d404b-4188-40b4-a3b2-3764ebbdecad" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c5aded0bab57fd7317901ff7709f2395fc91152e" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="25fb4349-d529-4b12-8523-a6aa0306ecf4" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7f41f9f5efcb31248caefc91b7d6edce87d7f42c" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results1.imzml.txt
--- a/test-data/preprocessing_results1.imzml.txt	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results1.imzml.txt	Wed May 13 14:08:25 2020 -0400
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli   216 Mär 24 10:39 ibd
--rw-r--r-- 1 meli meli 18090 Mär 24 10:39 imzml
+-rw-r--r-- 1 meli meli   216 Mai 10 17:37 ibd
+-rw-r--r-- 1 meli meli 18090 Mai 10 17:37 imzml
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results1.pdf
Binary file test-data/preprocessing_results1.pdf has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results2.ibd
Binary file test-data/preprocessing_results2.ibd has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results2.imzml
--- a/test-data/preprocessing_results2.imzml	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results2.imzml	Wed May 13 14:08:25 2020 -0400
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e536d1e2-427b-4c5b-9743-8210ae52a564" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7cea783e9d345946b874fc1f25d40ce90bffd2f9" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="fa59b434-12e0-47fe-b338-814c92daa7d6" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5764be27b51a23d8c23e4c93befb9d8e57161bd9" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results2.imzml.txt
--- a/test-data/preprocessing_results2.imzml.txt	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results2.imzml.txt	Wed May 13 14:08:25 2020 -0400
@@ -1,4 +1,4 @@
 imzML file:
 total 64
--rw-r--r-- 1 meli meli 37404 Mär 24 10:40 ibd
--rw-r--r-- 1 meli meli 22796 Mär 24 10:40 imzml
+-rw-r--r-- 1 meli meli 37404 Mai 10 17:38 ibd
+-rw-r--r-- 1 meli meli 22796 Mai 10 17:38 imzml
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results2.pdf
Binary file test-data/preprocessing_results2.pdf has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results3.ibd
Binary file test-data/preprocessing_results3.ibd has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results3.imzml
--- a/test-data/preprocessing_results3.imzml	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results3.imzml	Wed May 13 14:08:25 2020 -0400
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="df9dd256-6485-4954-8338-ddb0c760d4dc" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ea9ad44f2615ef4d24b92d3ceb38dfa8ec47a978" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="d11b7693-3397-4d1f-9e67-29d952701100" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94906879d47bbdcf97126d50c906dfd76e6681e4" />
 			<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results3.imzml.txt
--- a/test-data/preprocessing_results3.imzml.txt	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results3.imzml.txt	Wed May 13 14:08:25 2020 -0400
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli   960 Apr 22 15:36 ibd
--rw-r--r-- 1 meli meli 18112 Apr 22 15:36 imzml
+-rw-r--r-- 1 meli meli   960 Mai 10 17:39 ibd
+-rw-r--r-- 1 meli meli 18112 Mai 10 17:39 imzml
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results3.pdf
Binary file test-data/preprocessing_results3.pdf has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results4.ibd
Binary file test-data/preprocessing_results4.ibd has changed
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results4.imzml
--- a/test-data/preprocessing_results4.imzml	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results4.imzml	Wed May 13 14:08:25 2020 -0400
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="db79298c-8368-42d7-84fc-18cad6ef1924" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="18bae3cc87b4c9aab2577cffe2fbc7425a93270b" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c6122884-ceb5-46b6-9160-5d28e8862946" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="03e4b58b8e63517605164e90b85fe93a851a9c5b" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results4.imzml.txt
--- a/test-data/preprocessing_results4.imzml.txt	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results4.imzml.txt	Wed May 13 14:08:25 2020 -0400
@@ -1,4 +1,4 @@
 imzML file:
 total 84
--rw-r--r-- 1 meli meli 63256 Mär 24 11:35 ibd
--rw-r--r-- 1 meli meli 18199 Mär 24 11:35 imzml
+-rw-r--r-- 1 meli meli 63256 Mai 10 17:40 ibd
+-rw-r--r-- 1 meli meli 18199 Mai 10 17:40 imzml
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results4.pdf
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diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results5.ibd
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diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results5.imzml
--- a/test-data/preprocessing_results5.imzml	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results5.imzml	Wed May 13 14:08:25 2020 -0400
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="1cb5b7df-bc82-4588-9a14-1dd58a3983a7" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a16bf7a9d9d4064ce94821e3e7df2681725a497b" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="3aff713c-00ec-422d-b63d-efd45fbdd7cc" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9316138c1e7484662943bb206c79c2d074121530" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results5.imzml.txt
--- a/test-data/preprocessing_results5.imzml.txt	Thu Apr 23 08:04:25 2020 -0400
+++ b/test-data/preprocessing_results5.imzml.txt	Wed May 13 14:08:25 2020 -0400
@@ -1,4 +1,4 @@
 imzML file:
 total 428
--rw-r--r-- 1 meli meli 415936 Apr 19 21:07 ibd
--rw-r--r-- 1 meli meli  18569 Apr 19 21:07 imzml
+-rw-r--r-- 1 meli meli 415936 Mai 10 17:40 ibd
+-rw-r--r-- 1 meli meli  18569 Mai 10 17:40 imzml
diff -r 392b2dfd261d -r 525f201b86c1 test-data/preprocessing_results5.pdf
Binary file test-data/preprocessing_results5.pdf has changed