# HG changeset patch
# User galaxyp
# Date 1551363943 18000
# Node ID 773a24b240e18f6c754a37f746ee8b06283b66d1
# Parent  27a4c660bbcad49dbeda7fa1a4c2673017a2ebf0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2

diff -r 27a4c660bbca -r 773a24b240e1 mz_images.xml
--- a/mz_images.xml	Fri Feb 15 10:20:01 2019 -0500
+++ b/mz_images.xml	Thu Feb 28 09:25:43 2019 -0500
@@ -102,7 +102,7 @@
             print("svg pixel image")
             ## reverse y axis for svg output = correct order and nice svg image
             coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1
-            svg(file="svg_pixel_output.svg")
+            svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
             par(mar=c(0,0,0,0))
             image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing")
             dev.off()
@@ -144,12 +144,12 @@
         <expand macro="reading_2_column_mz_tabular"/>
 
 
-        <param name="image_contrast" type="select" label="Select a contrast enhancement function for the heatmap images" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
+        <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
             <option value="none" selected="True">none</option>
             <option value="suppression">suppression</option>
             <option value="histogram">histogram</option>
         </param>
-        <param name="image_smoothing" type="select" label="Select an image smoothing function for the heatmap images" help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges">
+        <param name="image_smoothing" type="select" label="Image smoothing" help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges">
             <option value="none" selected="True">none</option>
             <option value="gaussian">gaussian</option>
             <option value="adaptive">adaptive</option>
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results1.ibd
Binary file test-data/preprocessing_results1.ibd has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results1.imzml
--- a/test-data/preprocessing_results1.imzml	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results1.imzml	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results1.imzml.txt
--- a/test-data/preprocessing_results1.imzml.txt	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results1.imzml.txt	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results1.pdf
Binary file test-data/preprocessing_results1.pdf has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results2.ibd
Binary file test-data/preprocessing_results2.ibd has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results2.imzml
--- a/test-data/preprocessing_results2.imzml	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results2.imzml	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results2.imzml.txt
--- a/test-data/preprocessing_results2.imzml.txt	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results2.imzml.txt	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results2.pdf
Binary file test-data/preprocessing_results2.pdf has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results3.ibd
Binary file test-data/preprocessing_results3.ibd has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results3.imzml
--- a/test-data/preprocessing_results3.imzml	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results3.imzml	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results3.imzml.txt
--- a/test-data/preprocessing_results3.imzml.txt	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results3.imzml.txt	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results3.pdf
Binary file test-data/preprocessing_results3.pdf has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results4.ibd
Binary file test-data/preprocessing_results4.ibd has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results4.imzml
--- a/test-data/preprocessing_results4.imzml	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results4.imzml	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results4.imzml.txt
--- a/test-data/preprocessing_results4.imzml.txt	Fri Feb 15 10:20:01 2019 -0500
+++ b/test-data/preprocessing_results4.imzml.txt	Thu Feb 28 09:25:43 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 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results4.pdf
Binary file test-data/preprocessing_results4.pdf has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results5.RData
Binary file test-data/preprocessing_results5.RData has changed
diff -r 27a4c660bbca -r 773a24b240e1 test-data/preprocessing_results5.pdf
Binary file test-data/preprocessing_results5.pdf has changed