Mercurial > repos > galaxyp > cardinal_mz_images
comparison mz_images.xml @ 3:773a24b240e1 draft
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"/> |