Mercurial > repos > galaxyp > msi_ion_images

comparison msi_ion_images.xml @ 9:3aac627bd3ee draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_ion_images commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author galaxyp
date Wed, 22 Aug 2018 13:42:32 -0400
parents 6cd561bbb7ee
children
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8:6cd561bbb7ee 9:3aac627bd3ee
1 <tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.4"> 1 <tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.10.0.5">
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>
42 msidata <- readImzML('infile', attach.only=TRUE) 42 msidata <- readImzML('infile', attach.only=TRUE)
43 #end if 43 #end if
44 #elif $infile.ext == 'analyze75' 44 #elif $infile.ext == 'analyze75'
45 msidata = readAnalyze('infile', attach.only=TRUE) 45 msidata = readAnalyze('infile', attach.only=TRUE)
46 #else 46 #else
47 load('infile.RData') 47 loadRData <- function(fileName){
48 load(fileName)
49 get(ls()[ls() != "fileName"])
50 }
51 msidata = loadRData('infile.RData')
48 #end if 52 #end if
49 53
50 54
51 ###################################### file properties in numbers ############## 55 ###################################### file properties in numbers ##############
52 56
261 <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"> 265 <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">
262 <option value="none" selected="True">none</option> 266 <option value="none" selected="True">none</option>
263 <option value="gaussian">gaussian</option> 267 <option value="gaussian">gaussian</option>
264 <option value="adaptive">adaptive</option> 268 <option value="adaptive">adaptive</option>
265 </param> 269 </param>
266 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window in Dalton"/> 270 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window"/>
267 <param name="strip" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/> 271 <param name="strip" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
268 <param name="colorkey" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> 272 <param name="colorkey" type="boolean" checked="True" display="radio" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
269 <conditional name="image_cond"> 273 <conditional name="image_cond">
270 <param name="image_type" type="select" label="Select the image type"> 274 <param name="image_type" type="select" label="Select the image type">
271 <option value="standard_image" selected="True">standard</option> 275 <option value="standard_image" selected="True">standard</option>