Mercurial > repos > galaxyp > cardinal_mz_images

diff mz_images.xml @ 3:773a24b240e1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
author galaxyp
date Thu, 28 Feb 2019 09:25:43 -0500
parents 27a4c660bbca
children 5e6f8fb2df07
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--- 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>