Mercurial > repos > galaxyp > cardinal_single_ion_segmentation
annotate spatial_DGMM.xml @ 0:4cb6c83d3777 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
author | galaxyp |
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date | Tue, 22 Feb 2022 20:51:09 +0000 |
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children | db423b7bce78 |
rev | line source |
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0
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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1 <tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@VERSION@.0"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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2 <description>mass spectrometry imaging spatial DGMM</description> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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3 <macros> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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4 <import>macros.xml</import> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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5 </macros> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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6 <expand macro="requirements"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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7 <requirement type="package" version="2.3">r-gridextra</requirement> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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8 </expand> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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9 <command detect_errors="exit_code"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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10 <![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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11 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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12 @INPUT_LINKING@ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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13 cat '${MSI_spatial_DGMM}' && |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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14 Rscript '${MSI_spatial_DGMM}' |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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15 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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16 ]]> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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17 </command> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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18 <configfiles> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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19 <configfile name="MSI_spatial_DGMM"><![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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20 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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21 ################################# load libraries and read file ################# |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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22 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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23 library(Cardinal) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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24 library(gridExtra) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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25 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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26 @READING_MSIDATA_FULLY_COMPATIBLE@ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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27 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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28 #if str($sample_groups.group) == "multiple_groups": |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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29 ## read and extract x,y,annotation information |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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30 input_tabular <- read.delim("$sample_groups.annotation_file", header = $sample_groups.tabular_header, stringsAsFactors = FALSE) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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31 annotation_input <- input_tabular[,c($sample_groups.column_x, $sample_groups.column_y, $sample_groups.column_names)] |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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32 annotation_name <- colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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33 colnames(annotation_input) <- c("x", "y", "annotation") ## rename annotations header to default name "annotation" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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34 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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35 ## merge with coordinate information of msidata |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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36 msidata_coordinates <- data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata))) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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37 colnames(msidata_coordinates) <- c("x", "y", "pixel_index") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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38 merged_annotation <- merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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39 merged_annotation[is.na(merged_annotation)] <- "NA" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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40 merged_annotation <- merged_annotation[order(merged_annotation\$pixel_index),] |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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41 msidata\$annotation <- as.character(merged_annotation[,4]) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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42 #end if |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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43 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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44 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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45 @DATA_PROPERTIES_INRAM@ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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46 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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47 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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48 ## remove duplicated coordinates |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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49 msidata <- msidata[,!duplicated(coord(msidata))] |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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50 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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51 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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52 ######################################## PDF ################################### |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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53 ################################################################################ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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54 ################################################################################ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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55 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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56 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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57 pdf("single_ion_segmentation.pdf", fonts = "Times", pointsize = 12) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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58 plot(0,type='n',axes=FALSE,ann=FALSE) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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59 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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60 title(main=paste0("Single ion segmentation for file: \n\n", "$infile.display_name")) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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61 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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62 grid.table(property_df, rows= NULL) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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63 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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64 if (npeaks > 0) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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65 { |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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66 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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67 ## set seed to make analysis reproducible |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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68 set.seed($setseed) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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69 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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70 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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71 ## single ion segmentation |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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72 dgmm <- spatialDGMM(msidata, |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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73 r = c($r), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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74 k = c($k), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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75 #if str($sample_groups.group) == 'single_group': |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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76 groups = as.factor(rep("$infile.display_name", ncol(msidata))), |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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77 #else |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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78 groups = msidata\$annotation, |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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79 #end if |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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80 method = "$method", |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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81 dist = "$dist", |
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82 annealing = $annealing, |
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83 init = "$init", |
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84 p0 = $p0, |
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85 iter.max = $iter_max, |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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86 tol = $tol) |
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87 |
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88 ## Summary results table |
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89 dgmm_summary <- as.data.frame(summary(dgmm)) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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90 colnames(dgmm_summary) <- c('r', 'k', 'Feature', 'Classes/group') |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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91 dgmm_summary\$'m/z' <- mz(msidata) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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92 feature_n <- dgmm_summary\$Feature |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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93 dgmm_summary\$Feature <- NULL |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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94 dgmm_summary\$Feature <- feature_n |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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95 write.table(dgmm_summary, file="$dgmm_summary", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") |
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96 |
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97 ## Results images |
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98 for (dgmm_repeat in 1:nrow(dgmm_summary)){ |
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99 print(image(dgmm, values="class", model=dgmm_repeat))} |
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100 dev.off() ## closes pdf file |
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101 |
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102 ## optional outputs |
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103 pixel_names <- paste0("xy_", coord(dgmm)\$x, "_", coord(dgmm)\$y) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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104 |
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105 #if $output_probability: |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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106 dir.create("DGMM_probability") |
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107 for (dgmm_repeat in 1:nrow(dgmm_summary)){ |
4cb6c83d3777
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108 name_repeat <- file.path(paste0("DGMM_probability/probability_r", dgmm_summary\$r[dgmm_repeat], "_k", dgmm_summary\$k[dgmm_repeat], "_mz", dgmm_summary\$`m/z`[dgmm_repeat], ".tabular")) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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109 prob_df <- data.frame(coord(dgmm)\$x, coord(dgmm)\$y, pixel_names, resultData(dgmm, dgmm_repeat, "class"), resultData(dgmm, dgmm_repeat, "probability")) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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110 colnames(prob_df)[1:4] <- c("x", "y", "pixel_names", "class") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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111 write.table(prob_df, file=name_repeat, quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") |
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112 } |
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113 #end if |
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114 |
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115 #if $output_estimates: |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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116 dir.create("DGMM_estimates") |
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117 for (dgmm_repeat in 1:nrow(dgmm_summary)){ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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118 name_repeat <- file.path(paste0("DGMM_estimates/estimates_r", dgmm_summary\$r[dgmm_repeat], "_k", dgmm_summary\$k[dgmm_repeat], "_mz", dgmm_summary\$`m/z`[dgmm_repeat], ".tabular")) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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119 est_df <- resultData(dgmm, dgmm_repeat, "estimates") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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120 write.table(est_df, file=name_repeat, quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") |
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121 } |
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122 #end if |
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123 |
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124 #if $output_plots: |
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125 dir.create("DGMM_plots") |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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126 for (dgmm_repeat in 1:nrow(dgmm_summary)){ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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127 name_repeat <- file.path(paste0("DGMM_plots/plot_r", dgmm_summary\$r[dgmm_repeat], "_k", dgmm_summary\$k[dgmm_repeat], "_mz", dgmm_summary\$`m/z`[dgmm_repeat], ".png")) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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128 png(file=name_repeat) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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129 print(plot(dgmm, model=dgmm_repeat, lwd=2)) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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130 dev.off() |
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131 } |
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132 #end if |
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133 |
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134 ## optional output as .RData |
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135 #if $output_rdata: |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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136 ## save as (.RData) |
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137 save(dgmm, file="$dgmm_rdata") |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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138 #end if |
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139 |
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140 }else{ |
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141 print("Inputfile has no intensities > 0") |
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142 } |
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143 |
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144 ]]></configfile> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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145 </configfiles> |
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146 <inputs> |
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147 <expand macro="reading_msidata"/> |
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148 <conditional name="sample_groups"> |
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149 <param name="group" type="select" label="Dataset groups" help="Pixels from different groups will be segmented separately. For the validity of |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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150 downstream statistical analysis, it is important that each distinct observational unit (e.g., tissue sample) is assigned to a unique group"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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151 <option value="single_group" selected="True">Dataset is a single group</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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152 <option value="multiple_groups">Dataset contains multiple groups</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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153 </param> |
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154 <when value="single_group"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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155 <when value="multiple_groups"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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156 <expand macro="reading_pixel_annotations"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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157 </when> |
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158 </conditional> |
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159 <param name="r" type="text" value="2" |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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160 label="r" help="The spatial neighborhood radius of nearby pixels to consider. Only a single value is allowed"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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161 <expand macro="sanitizer_multiple_digits"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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162 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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163 <param name="k" type="text" value="5" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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164 label="k" help="The maximum number of segments (clusters). The final number of segments may differ. Only a single value is allowed."> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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165 <expand macro="sanitizer_multiple_digits"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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166 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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167 <param name="method" type="select" display="radio" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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168 label="weights method" help="The method to use to calculate the spatial smoothing weights. The 'gaussian' method refers to spatially-aware (SA) weights, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) weights"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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169 <option value="gaussian" selected="True">gaussian</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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170 <option value="adaptive">adaptive</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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171 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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172 <param name="dist" type="select" display="radio" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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173 label="distance metric" help="The type of distance metric to use when calculating neighboring pixels based on r. The options are ‘radial’, ‘manhattan’, ‘minkowski’, and ‘chebyshev’ (the |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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174 default)."> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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175 <option value="chebyshev" selected="True">chebyshev</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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176 <option value="manhattan">manhattan</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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177 <option value="radial">radial</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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178 <option value="minkowski">minkowski</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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179 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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180 <param name="annealing" type="boolean" label="annealing" help="Should simulated annealing be used during the optimization process to improve parameter estimates?" truevalue="TRUE" falsevalue="FALSE" /> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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181 <param name="init" type="select" display="radio" |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff
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182 label="init" help="Should the parameter estimates be initialized using k-means (’kmeans’) or Gaussian mixture model (’gmm’)?"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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183 <option value="kmeans" selected="True">kmeans</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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184 <option value="gmm">gmm</option> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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185 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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186 <param name="p0" type="float" value="0.05" label="p0" help="A regularization parameter applied to estimated posterior class probabilities to avoid singularities. Must be positive for successful gradient descent optimization.Changing this value (within reason) should have only minimal impact on values of parameter estimates, but may greatly affect the algorithm’s speed and stability." /> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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187 <param name="iter_max" type="integer" value="100" label="iter.max" help="The maximum number of EM-algorithm iterations." /> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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188 <param name="tol" type="float" value="0.05" label="tolerance" help="The tolerance convergence criterion for the EM-algorithm. Corresponds to the |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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189 change in log-likelihood."/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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190 <param name="setseed" type="integer" value="1" label="set seed" help="Use same value to reproduce previous results"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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191 <param name="output_estimates" type="boolean" label="Generate estimates results"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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192 <param name="output_probability" type="boolean" label="Generate probability and class results"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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193 <param name="output_plots" type="boolean" label="Generate plots results"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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194 <param name="output_rdata" type="boolean" label="Results as .RData output"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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195 </inputs> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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196 <outputs> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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197 <data format="tabular" name="dgmm_summary" label="${tool.name} on ${on_string}: summary"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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198 <data format="pdf" name="file_info" from_work_dir="single_ion_segmentation.pdf" label = "${tool.name} on ${on_string}: file_info"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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199 <data format="rdata" name="dgmm_rdata" label="${tool.name} on ${on_string}: dgmm.RData"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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200 <filter>output_rdata</filter> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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201 </data> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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202 <collection name="estimates_output" type="list" label="${tool.name} logs: ${on_string}: estimates"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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203 <filter>output_estimates</filter> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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204 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_estimates" format="tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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205 </collection> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
206 <collection name="probability_output" type="list" label="${tool.name} logs: ${on_string}: probability"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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207 <filter>output_probability</filter> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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208 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_probability" format="tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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209 </collection> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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210 <collection name="plots_output" type="list" label="${tool.name} logs: ${on_string}: plots"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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211 <filter>output_plots</filter> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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212 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_plots" format="tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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213 </collection> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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214 </outputs> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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215 <tests> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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216 <test> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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217 <param name="infile" value="" ftype="imzml"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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218 <composite_data value="spatial_DGMM_input.imzML"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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219 <composite_data value="spatial_DGMM_input.ibd"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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220 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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221 <param name="r" value="1"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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222 <param name="k" value="6"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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223 <param name="method" value="adaptive"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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224 <param name="dist" value="radial"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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225 <param name="annealing" value="TRUE"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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226 <param name="output_estimates" value="True"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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227 <param name="output_probability" value="True"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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228 <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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229 <output name="dgmm_summary" file="dgmm_summary1.tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
230 <output_collection name="estimates_output" type="list" count="10"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
231 <element name="estimates_r1_k6_mz1135.93347167969" file="estimates_r1_k6_mz1135.93347167969.tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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|
232 </output_collection> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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233 <output_collection name="probability_output" type="list" count="10"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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234 <element name="probability_r1_k6_mz1023.70806884766" file="probability_r1_k6_mz1023.70806884766.tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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235 </output_collection> |
4cb6c83d3777
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236 </test> |
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237 <test> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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238 <param name="infile" value="" ftype="imzml"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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239 <composite_data value="spatial_DGMM_input.imzML"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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240 <composite_data value="spatial_DGMM_input.ibd"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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241 </param> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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242 <conditional name="sample_groups"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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243 <param name="group" value="multiple_groups"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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244 <param name="annotation_file" value="DGMM_annotations.tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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245 <param name="column_x" value="1"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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246 <param name="column_y" value="2"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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247 <param name="column_names" value="3"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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248 <param name="tabular_header" value="True"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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249 </conditional> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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250 <param name="r" value="2"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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251 <param name="k" value="10"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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252 <param name="annealing" value="TRUE"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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253 <param name="output_estimates" value="True"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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254 <param name="output_probability" value="True"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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255 <param name="output_plots" value="True"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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256 <param name="output_rdata" value="True"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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257 <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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258 <output name="dgmm_summary" file="dgmm_summary2.tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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259 <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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260 <output_collection name="estimates_output" type="list" count="10"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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261 <element name="estimates_r2_k10_mz1200.46533203125" file="estimates_r2_k10_mz1200.46533203125.tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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262 </output_collection> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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263 <output_collection name="probability_output" type="list" count="10"> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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264 <element name="probability_r2_k10_mz1135.93347167969" file="probability_r2_k10_mz1135.93347167969.tabular"/> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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265 </output_collection> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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266 </test> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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267 </tests> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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268 <help> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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269 <![CDATA[ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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270 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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271 @CARDINAL_DESCRIPTION@ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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272 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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273 ----- |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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274 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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275 This tool fits spatially-aware Dirichlet Gaussian mixture models (DGMM) to each feature and each run in an mass spectrometry imaging |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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276 experiment. Each image is segmented and the means and variances of all Gaussian components are estimated. A linear filter with a spatial kernel is applied to the component probabilities to achieve |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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277 spatial smoothing. Simulated annealing is used in the EM-algorithm to avoid local optima and achieve more accurate parameter estimates. |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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278 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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279 @MSIDATA_INPUT_DESCRIPTION@ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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280 - NA intensities are not allowed |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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281 - duplicated coordinates will be removed |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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282 - It is highly recommended to use a dataset that is reduced for the number of m/z features e.g. pre-processed, binned, filtered for m/z of interest in order to keep computational times reasonable. In addition, it is beneficial to run the tool first without generating all possible results data and upon inspection of the summary of the results decide on the best tool parameters and m/z features (which can be filtered in the MSI filtering tool). |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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283 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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284 @SPECTRA_TABULAR_INPUT_DESCRIPTION@ |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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285 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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286 **Tips** |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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287 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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288 - The input dataset should contain as few m/z features as possible to keep computational times reasonable. In addition, it is beneficial to run the tool first without generating all possible results data and upon inspection of the summary of the results decide on the best tool parameters and m/z features (which can be filtered in the MSI filtering tool). |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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289 - Pixels from distinct ovbservational units (e.g. sample, patient) should be assigned to a unique group via the annotation file and segmented separately for the validity of downstream statistical analysis. |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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290 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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291 **Output** |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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292 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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293 - Pdf with file info and an image of the clusters for each m/z feature |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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294 - Tabular file summarizing spatial DGMM performance for each feature |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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295 - (optional) Tabular files for each spatial DGMM run and feature with |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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296 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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297 - probabilities (The probability of class membership for each Gaussian component) and classes (The predicted Gaussian component) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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298 - estimates (A list giving the parameter estimates for the means and variances for each Gaussian component) |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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299 - (optional) Visualization of features density plots |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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300 - (optional) .RData file which contains the segmentation results and can be used for further exploration in R using the Cardinal package |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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301 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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302 ]]> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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303 </help> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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304 <citations> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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305 <citation type="doi">10.1093/bioinformatics/btv146</citation> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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306 <citation type="doi">10.1093/bioinformatics/btz345</citation> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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307 </citations> |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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308 |
4cb6c83d3777
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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309 </tool> |