Mercurial > repos > galaxyp > cardinal_mz_images

comparison 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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2:27a4c660bbca 3:773a24b240e1
100 ## optional svg output with original coordinates 100 ## optional svg output with original coordinates
101 #if $svg_pixelimage: 101 #if $svg_pixelimage:
102 print("svg pixel image") 102 print("svg pixel image")
103 ## reverse y axis for svg output = correct order and nice svg image 103 ## reverse y axis for svg output = correct order and nice svg image
104 coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1 104 coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1
105 svg(file="svg_pixel_output.svg") 105 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
106 par(mar=c(0,0,0,0)) 106 par(mar=c(0,0,0,0))
107 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") 107 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")
108 dev.off() 108 dev.off()
109 #end if 109 #end if
110 110
142 <expand macro="reading_msidata"/> 142 <expand macro="reading_msidata"/>
143 <expand macro="pdf_filename"/> 143 <expand macro="pdf_filename"/>
144 <expand macro="reading_2_column_mz_tabular"/> 144 <expand macro="reading_2_column_mz_tabular"/>
145 145
146 146
147 <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"> 147 <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">
148 <option value="none" selected="True">none</option> 148 <option value="none" selected="True">none</option>
149 <option value="suppression">suppression</option> 149 <option value="suppression">suppression</option>
150 <option value="histogram">histogram</option> 150 <option value="histogram">histogram</option>
151 </param> 151 </param>
152 <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"> 152 <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">
153 <option value="none" selected="True">none</option> 153 <option value="none" selected="True">none</option>
154 <option value="gaussian">gaussian</option> 154 <option value="gaussian">gaussian</option>
155 <option value="adaptive">adaptive</option> 155 <option value="adaptive">adaptive</option>
156 </param> 156 </param>
157 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window"/> 157 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window"/>