Mercurial > repos > galaxyp > msi_ion_images
comparison msi_ion_images.xml @ 6:5a5b5a8fa8a0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
author | galaxyp |
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date | Tue, 19 Jun 2018 18:07:40 -0400 |
parents | 2b9fa240e261 |
children | db0cf8eb4395 |
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5:2b9fa240e261 | 6:5a5b5a8fa8a0 |
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1 <tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.1"> | 1 <tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.2"> |
2 <description> | 2 <description> |
3 mass spectrometry imaging m/z heatmaps | 3 mass spectrometry imaging m/z heatmaps |
4 </description> | 4 </description> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> | 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> |
33 library(lattice) | 33 library(lattice) |
34 | 34 |
35 ## Read MALDI Imaging dataset | 35 ## Read MALDI Imaging dataset |
36 | 36 |
37 #if $infile.ext == 'imzml' | 37 #if $infile.ext == 'imzml' |
38 msidata = readImzML('infile') | 38 msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") |
39 #elif $infile.ext == 'analyze75' | 39 #elif $infile.ext == 'analyze75' |
40 msidata = readAnalyze('infile') | 40 msidata = readAnalyze('infile') |
41 #else | 41 #else |
42 load('infile.RData') | 42 load('infile.RData') |
43 #end if | 43 #end if |
128 title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename")) | 128 title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename")) |
129 | 129 |
130 ############################# I) numbers #################################### | 130 ############################# I) numbers #################################### |
131 | 131 |
132 properties = c("Number of m/z features", | 132 properties = c("Number of m/z features", |
133 "Range of m/z values [Da]", | 133 "Range of m/z values", |
134 "Number of pixels", | 134 "Number of pixels", |
135 "Range of x coordinates", | 135 "Range of x coordinates", |
136 "Range of y coordinates", | 136 "Range of y coordinates", |
137 "Range of intensities", | 137 "Range of intensities", |
138 "Median of intensities", | 138 "Median of intensities", |
179 | 179 |
180 #if str($image_cond.image_type) == "standard_image": | 180 #if str($image_cond.image_type) == "standard_image": |
181 print("standard image") | 181 print("standard image") |
182 | 182 |
183 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", | 183 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", |
184 smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey, | 184 smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy), |
185 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} | 185 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} |
186 | 186 |
187 | 187 |
188 ###lattice image | 188 ###lattice image |
189 | 189 |
192 | 192 |
193 #if str($strip) =="TRUE": | 193 #if str($strip) =="TRUE": |
194 | 194 |
195 print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), | 195 print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), |
196 lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", | 196 lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", |
197 colorkey=$colorkey, | 197 colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy), |
198 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} | 198 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} |
199 | 199 |
200 #elif str($strip) =="FALSE": | 200 #elif str($strip) =="FALSE": |
201 | 201 |
202 print(image(msidata, mz=inputmz[mass], strip = $strip, | 202 print(image(msidata, mz=inputmz[mass], strip = $strip, |
217 ]]></configfile> | 217 ]]></configfile> |
218 </configfiles> | 218 </configfiles> |
219 <inputs> | 219 <inputs> |
220 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" | 220 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" |
221 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> | 221 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> |
222 <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> | |
223 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> | |
224 <option value="mz" >mz</option> | |
225 <option value="ppm" selected="True" >ppm</option> | |
226 </param> | |
222 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/> | 227 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/> |
223 <param name="massfile" type="data" format="tabular" label="Tabular file with m/z and names" | 228 <param name="massfile" type="data" format="tabular" label="Tabular file with m/z and names" |
224 help="first column m/z, second column m/z name, tab separated file"/> | 229 help="first column m/z, second column m/z name, tab separated file"/> |
225 <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"> | 230 <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"> |
226 <option value="none" selected="True">none</option> | 231 <option value="none" selected="True">none</option> |