# HG changeset patch
# User galaxyp
# Date 1630221914 0
# Node ID d333733dd571ba713953c675ea2453d5d6efc10f
# Parent  1693b2126f308772c57909d6b470523f26590445
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"

diff -r 1693b2126f30 -r d333733dd571 macros.xml
--- a/macros.xml	Wed Dec 23 22:28:42 2020 +0000
+++ b/macros.xml	Sun Aug 29 07:25:14 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.6.0</token>
+    <token name="@VERSION@">2.10.0</token>
 
     <xml name="requirements">
         <requirements>
diff -r 1693b2126f30 -r d333733dd571 spectra_plots.xml
--- a/spectra_plots.xml	Wed Dec 23 22:28:42 2020 +0000
+++ b/spectra_plots.xml	Sun Aug 29 07:25:14 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.3">
+<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0">
     <description>
         mass spectrometry imaging mass spectra plots
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
+        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
         <requirement type="package" version="2.3">r-gridextra</requirement>
         <requirement type="package" version="1.1.1">r-scales</requirement>
     </expand>
diff -r 1693b2126f30 -r d333733dd571 test-data/QC_imzml_shortreport.pdf
Binary file test-data/QC_imzml_shortreport.pdf has changed
diff -r 1693b2126f30 -r d333733dd571 test-data/pixels_test6.tabular
--- a/test-data/pixels_test6.tabular	Wed Dec 23 22:28:42 2020 +0000
+++ b/test-data/pixels_test6.tabular	Sun Aug 29 07:25:14 2021 +0000
@@ -1,25 +1,25 @@
-pixel names	x	y	predicted condition
-xy_1_1	1	1	A
-xy_2_1	2	1	A
-xy_3_1	3	1	B
-xy_4_1	4	1	C
-xy_1_2	1	2	C
-xy_2_2	2	2	C
-xy_3_2	3	2	A
-xy_4_2	4	2	A
-xy_1_3	1	3	A
-xy_2_3	2	3	B
-xy_3_3	3	3	C
-xy_4_3	4	3	A
-xy_10_1	10	1	C
-xy_11_1	11	1	C
-xy_12_1	12	1	C
-xy_13_1	13	1	B
-xy_10_2	10	2	C
-xy_11_2	11	2	B
-xy_12_2	12	2	C
-xy_13_2	13	2	C
-xy_10_3	10	3	C
-xy_11_3	11	3	C
-xy_12_3	12	3	B
-xy_13_3	13	3	C
+pixel names	x	y	predicted condition	A	B	C
+xy_1_1	1	1	A	0.434439526064797	0.195646317191818	0.369914156743386
+xy_2_1	2	1	A	0.38219998209377	0.242372158141275	0.375427859764956
+xy_3_1	3	1	B	0.312531499299517	0.385612104162858	0.301856396537625
+xy_4_1	4	1	C	0.393153488582866	0.191107087820634	0.4157394235965
+xy_1_2	1	2	C	0.366986470447772	0.216121568441093	0.416891961111135
+xy_2_2	2	2	C	0.381682206547616	0.213188918797062	0.405128874655322
+xy_3_2	3	2	A	0.376695037169723	0.260689491088564	0.362615471741713
+xy_4_2	4	2	A	0.42305935188829	0.174038449100755	0.402902199010954
+xy_1_3	1	3	A	0.382420991383021	0.249364697048677	0.368214311568302
+xy_2_3	2	3	B	0.272145998315727	0.446525938567718	0.281328063116555
+xy_3_3	3	3	C	0.36296987427851	0.255631013944556	0.381399111776934
+xy_4_3	4	3	A	0.444812272103175	0.132274264153212	0.422913463743613
+xy_10_1	10	1	C	0.376216993893763	0.227584528606788	0.39619847749945
+xy_11_1	11	1	C	0.358430578177403	0.236120068794936	0.405449353027661
+xy_12_1	12	1	C	0.359751662628136	0.218620985552221	0.421627351819643
+xy_13_1	13	1	B	0.101486342705225	0.813997511218961	0.0845161460758142
+xy_10_2	10	2	C	0.354612526523361	0.272635192773437	0.372752280703202
+xy_11_2	11	2	B	0.291635599769993	0.444466545540823	0.263897854689184
+xy_12_2	12	2	C	0.36763798979782	0.203911653614431	0.428450356587749
+xy_13_2	13	2	C	0.344608135177236	0.304026642707691	0.351365222115073
+xy_10_3	10	3	C	0.37046458150651	0.205561286708086	0.423974131785404
+xy_11_3	11	3	C	0.358113833435286	0.262878459144526	0.379007707420187
+xy_12_3	12	3	B	0.180921926305915	0.66902588624642	0.150052187447665
+xy_13_3	13	3	C	0.378266307042675	0.20859472985319	0.413138963104135
diff -r 1693b2126f30 -r d333733dd571 test-data/preprocessing_results4.ibd
Binary file test-data/preprocessing_results4.ibd has changed
diff -r 1693b2126f30 -r d333733dd571 test-data/preprocessing_results4.imzml
--- a/test-data/preprocessing_results4.imzml	Wed Dec 23 22:28:42 2020 +0000
+++ b/test-data/preprocessing_results4.imzml	Sun Aug 29 07:25:14 2021 +0000
@@ -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="48842eaf-40e5-4a3f-831c-2d7a3b7e04b9" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2010ba5b7d44695d891cfe3b6674a5699fa610c0" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="04431b64-9f3d-44b4-9e63-81b9e4924aec" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="38a4fadd32374bdf0e4b2bb7d976f6067d542a29" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.6.0">
+		<software id="Cardinal" version="2.10.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
diff -r 1693b2126f30 -r d333733dd571 test-data/preprocessing_results4.imzml.txt
--- a/test-data/preprocessing_results4.imzml.txt	Wed Dec 23 22:28:42 2020 +0000
+++ b/test-data/preprocessing_results4.imzml.txt	Sun Aug 29 07:25:14 2021 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 84
--rw-rw-r-- 1 meli meli 62696 Oct  5 19:58 ibd
--rw-rw-r-- 1 meli meli 18199 Oct  5 19:58 imzml
+-rw-rw-r-- 1 meli meli 62696 Aug 28 16:41 ibd
+-rw-rw-r-- 1 meli meli 18200 Aug 28 16:41 imzml
diff -r 1693b2126f30 -r d333733dd571 test-data/preprocessing_results4.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test1.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test2.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test3.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test4.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test5.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test6.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test6.rdata
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diff -r 1693b2126f30 -r d333733dd571 test-data/test7.pdf
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diff -r 1693b2126f30 -r d333733dd571 test-data/test7.rdata
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