# HG changeset patch
# User galaxyp
# Date 1551364073 18000
# Node ID 58c4aef16eb0ca576cfbb266201e94634fde0719
# Parent  3642ed221eb2d84b5a331dceebf8be53bccbb8c1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2

diff -r 3642ed221eb2 -r 58c4aef16eb0 spectra_plots.xml
--- a/spectra_plots.xml	Fri Feb 15 10:23:28 2019 -0500
+++ b/spectra_plots.xml	Thu Feb 28 09:27:53 2019 -0500
@@ -56,7 +56,7 @@
     #if str($processed_cond.processed_file) == "processed":
         ##processed file needs to be converted into matrix to be able to replace NAs
         iData(msidata) <- iData(msidata)[]
-        spectra(msidata)[][is.na(spectra(msidata)[])] = 0
+        spectra(msidata)[is.na(spectra(msidata))] = 0
     #else
         spectra(msidata)[is.na(spectra(msidata))] = 0
     #end if
@@ -101,7 +101,7 @@
 
             ##################### III) plot full mass spectrum #################
 
-                    plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
+                    plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), main="Mass spectrum of full m/z range")
 
             ##################### IV) plot zoom-in mass spectrum ###############
 
@@ -199,9 +199,9 @@
                         key_legend = TRUE
                     }else{key_legend = FALSE}
 
-            plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE)
+            plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE, main="Average mass spectrum of full m/z range")
         }else{
-            plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
+            plot(msidata, pixel=1:ncol(msidata), key=TRUE, main="Average mass spectrum of full m/z range")}
 
         ##################### II) Sample: plot zoom-in mass spectrum ##########
 
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.ibd
Binary file test-data/preprocessing_results1.ibd has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.imzml
--- a/test-data/preprocessing_results1.imzml	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results1.imzml	Thu Feb 28 09:27:53 2019 -0500
@@ -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="{002DF5BA-0549-44DF-A8BB-27DA3E197EB7}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0379019A6F9D0B55F9217420030633F7163AF9D3" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{728FBFFE-E6FC-4283-8068-393A66F6BD5C}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="375094460F3B80674CB2F541DCD9928B3D61B2FF" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.imzml.txt
--- a/test-data/preprocessing_results1.imzml.txt	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results1.imzml.txt	Thu Feb 28 09:27:53 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli    96 Feb 12 21:24 ibd
--rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml
+-rw-r--r-- 1 meli meli    96 Feb 24 14:11 ibd
+-rw-r--r-- 1 meli meli 16714 Feb 24 14:11 imzml
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results1.pdf
Binary file test-data/preprocessing_results1.pdf has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.ibd
Binary file test-data/preprocessing_results2.ibd has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.imzml
--- a/test-data/preprocessing_results2.imzml	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results2.imzml	Thu Feb 28 09:27:53 2019 -0500
@@ -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="{84BEACDD-B841-4730-81A0-A19A28C7B48A}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1BC49DCCC566E7A6938CE3DE62090650C2A04798" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{40F230A1-1893-4A8C-BAE2-A8BBEF24DB20}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="417ADF38FBC4D0304A9B75B4C85799137846DD2F" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.imzml.txt
--- a/test-data/preprocessing_results2.imzml.txt	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results2.imzml.txt	Thu Feb 28 09:27:53 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 80
--rw-r--r-- 1 meli meli 54720 Feb 12 21:25 ibd
--rw-r--r-- 1 meli meli 21132 Feb 12 21:25 imzml
+-rw-r--r-- 1 meli meli 54720 Feb 24 14:12 ibd
+-rw-r--r-- 1 meli meli 21132 Feb 24 14:12 imzml
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results2.pdf
Binary file test-data/preprocessing_results2.pdf has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results3.ibd
Binary file test-data/preprocessing_results3.ibd has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results3.imzml
--- a/test-data/preprocessing_results3.imzml	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results3.imzml	Thu Feb 28 09:27:53 2019 -0500
@@ -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="{4C387879-DE12-49A4-878F-6980D6F7C6F0}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94ED775BCF16644D23DACFCA1E62D28D5C755178" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{D767424F-5E74-45AB-AF1B-0D25244B435B}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="445E32981D0B3D08ED2BA74E11500A3A08CDB9B7" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results3.imzml.txt
--- a/test-data/preprocessing_results3.imzml.txt	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results3.imzml.txt	Thu Feb 28 09:27:53 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 36
--rw-r--r-- 1 meli meli 14216 Feb 12 21:26 ibd
--rw-r--r-- 1 meli meli 16824 Feb 12 21:26 imzml
+-rw-r--r-- 1 meli meli 14216 Feb 24 14:12 ibd
+-rw-r--r-- 1 meli meli 16824 Feb 24 14:12 imzml
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results3.pdf
Binary file test-data/preprocessing_results3.pdf has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results4.ibd
Binary file test-data/preprocessing_results4.ibd has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results4.imzml
--- a/test-data/preprocessing_results4.imzml	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results4.imzml	Thu Feb 28 09:27:53 2019 -0500
@@ -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="{26018306-9D72-49F5-89CB-68E4DDE0527C}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="BA6411EC5A5A59ABE5BD7005F4ED8FCEBA775A8E" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{FE932E04-42E4-4D89-B721-2A6CE83250B6}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="36C7C916C176DD85CBBF4B7FA969C92B9403768D" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results4.imzml.txt
--- a/test-data/preprocessing_results4.imzml.txt	Fri Feb 15 10:23:28 2019 -0500
+++ b/test-data/preprocessing_results4.imzml.txt	Thu Feb 28 09:27:53 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 28
--rw-r--r-- 1 meli meli  6376 Feb 12 21:29 ibd
--rw-r--r-- 1 meli meli 16801 Feb 12 21:29 imzml
+-rw-r--r-- 1 meli meli  6376 Feb 24 14:13 ibd
+-rw-r--r-- 1 meli meli 16801 Feb 24 14:13 imzml
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results4.pdf
Binary file test-data/preprocessing_results4.pdf has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results5.RData
Binary file test-data/preprocessing_results5.RData has changed
diff -r 3642ed221eb2 -r 58c4aef16eb0 test-data/preprocessing_results5.pdf
Binary file test-data/preprocessing_results5.pdf has changed