Mercurial > repos > galaxyp > cardinal_colocalization

annotate colocalization.xml @ 1:4257fc095049 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
author galaxyp
date Wed, 19 Apr 2023 22:43:26 +0000
parents d3ca64dafdef
children 8ad8061e18c4
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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1 <tool id="cardinal_colocalization" name="MSI colocalization" version="@VERSION@.0">
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2 <description>mass spectrometry imaging colocalization</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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6 <expand macro="requirements">
d3ca64dafdef "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>
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8 </expand>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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12 @INPUT_LINKING@
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13 cat '${MSI_colocalization}' &&
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14 Rscript '${MSI_colocalization}'
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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16 ]]>
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17 </command>
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18 <configfiles>
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19 <configfile name="MSI_colocalization"><![CDATA[
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d3ca64dafdef "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 #################
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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23 library(Cardinal)
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24 library(gridExtra)
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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26 @READING_MSIDATA_FULLY_COMPATIBLE@
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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28 #if str($reference_type.reference) == "roi_ref":
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29 ## read and extract x,y,annotation information
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30 input_tabular <- read.delim("$reference_type.annotation_file", header = $reference_type.tabular_header, stringsAsFactors = FALSE)
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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31 annotation_input <- input_tabular[,c($reference_type.column_x, $reference_type.column_y, $reference_type.column_names)]
d3ca64dafdef "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
d3ca64dafdef "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"
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d3ca64dafdef "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
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36 msidata_coordinates <- data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
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37 colnames(msidata_coordinates) <- c("x", "y", "pixel_index")
d3ca64dafdef "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)
d3ca64dafdef "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"
d3ca64dafdef "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),]
d3ca64dafdef "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])
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42 reference_group <- msidata\$annotation == "$reference_type.ref_name"
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43 #end if
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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45 ## remove duplicated coordinates
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46 msidata <- msidata[,!duplicated(coord(msidata))]
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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49 @DATA_PROPERTIES_INRAM@
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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52 ######################################## PDF ###################################
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53 ################################################################################
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54 ################################################################################
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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57 pdf("colocalization.pdf", fonts = "Times", pointsize = 12)
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58 plot(0,type='n',axes=FALSE,ann=FALSE)
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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60 title(main=paste0("Colocalization for file: \n\n", "$infile.display_name"))
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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62 grid.table(property_df, rows= NULL)
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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65 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0)
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66 {
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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67
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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68 ## colocalization analysis
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69 col_results <- colocalized(msidata,
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70 #if str($reference_type.reference) == "mz_ref":
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71 mz = $reference_type.mz_value,
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72 #else
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73 ref = reference_group,
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74 #end if
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75 n = $n_tophits,
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76 sort.by = "$sort_by",
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77 threshold = median)
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78
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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79 ## Summary results table
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80 col_results_df <- as.data.frame(col_results)
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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82 write.table(col_results_df, file="$coloc_results", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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84 ## visualize top 10 m/z features
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d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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86 if (nrow(col_results_df) <= 10)
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87 {
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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88 for (mass in col_results_df\$mz){
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
89 par(oma=c(0,0,0,1))## margin for image legend
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
90 print(image(msidata, mz=mass, plusminus=0.25,
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
91 main= paste0(round(mass, digits = 2)),
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
92 contrast.enhance = "histogram", strip=FALSE, ylim= c(maximumy,minimumy)))
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
93 }
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
94 }else{
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
95 for (mass in col_results_df\$mz[1:10]){
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
96 par(oma=c(0,0,0,1))## margin for image legend
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
97 print(image(msidata, mz=mass, plusminus=0.25,
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
98 main= paste0(round(mass, digits = 2)),
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
99 contrast.enhance = "histogram", strip=FALSE, ylim= c(maximumy,minimumy)))
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
100 }
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
101 }
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
102
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
103
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
104 dev.off()
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
105
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
106 }else{
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
107 print("Inputfile has no intensities > 0")
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
108 }
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
109
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
110 ]]></configfile>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
111 </configfiles>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
112 <inputs>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
113 <expand macro="reading_msidata"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
114 <conditional name="reference_type">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
115 <param name="reference" type="select" label="Reference type" help="Region of interest (selected spectra) or m/z feature.">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
116 <option value="mz_ref" selected="True">m/z feature</option>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
117 <option value="roi_ref">Region of interest (spectra)</option>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
118 </param>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
119 <when value="mz_ref">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
120 <param name="mz_value" type="float" value="1000" label="m/z feature" help="The m/z closest to this m/z value will be used as a reference."/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
121 </when>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
122 <when value="roi_ref">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
123 <expand macro="reading_pixel_annotations"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
124 <param name="ref_name" type="text" value="reference" label="Reference name" help="Name has to match exactly on of the annotation names in the annotation file"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
125 </when>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
126 </conditional>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
127 <param name="n_tophits" type="integer" value="10" label="Top hits" help="The number of top-ranked colocalized features to return in the tabular file." />
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
128 <param name="sort_by" type="select" display="radio"
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
129 label="sort.by" help="The colocalization measure used to rank colocalized features. Possible options
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
130 include Pearson’s correlation and Manders’ colocalization coefficients.">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
131 <option value="correlation" selected="True">Pearson's correlation</option>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
132 <option value="M1">Manders' colocalization coefficient 1</option>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
133 <option value="M2">Manders' colocalization coefficient 2</option>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
134 </param>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
135 </inputs>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
136 <outputs>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
137 <data format="pdf" name="coloc_pdf" from_work_dir="colocalization.pdf" label = "${tool.name} on ${on_string}: results"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
138 <data format="tabular" name="coloc_results" label="${tool.name} on ${on_string}: summary"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
139 </outputs>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
140 <tests>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
141 <test>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
142 <param name="infile" value="" ftype="imzml">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
143 <composite_data value="spatial_DGMM_input.imzML"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
144 <composite_data value="spatial_DGMM_input.ibd"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
145 </param>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
146 <conditional name="reference_type">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
147 <param name="reference" value="mz_ref"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
148 <param name="mz_value" value="1000"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
149 </conditional>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
150 <output name="coloc_pdf" file="coloc1.pdf" compare="sim_size" delta="2000"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
151 <output name="coloc_results" file="coloc_table1.tabular"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
152 </test>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
153 <test>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
154 <param name="infile" value="" ftype="imzml">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
155 <composite_data value="spatial_DGMM_input.imzML"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
156 <composite_data value="spatial_DGMM_input.ibd"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
157 </param>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
158 <conditional name="reference_type">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
159 <param name="reference" value="roi_ref"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
160 <param name="annotation_file" value="DGMM_annotations.tabular"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
161 <param name="column_x" value="1"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
162 <param name="column_y" value="2"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
163 <param name="column_names" value="3"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
164 <param name="tabular_header" value="True"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
165 <param name="ref_name" value="circle"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
166 </conditional>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
167 <param name="n_tophits" value="5"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
168 <param name="sort_by" value="M2"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
169 <output name="coloc_pdf" file="coloc2.pdf" compare="sim_size" delta="2000"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
170 <output name="coloc_results" file="coloc_table2.tabular"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
171 </test>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
172 <test>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
173 <param name="infile" value="123_combined.RData" ftype="rdata"/>
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
174 <conditional name="reference_type">
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
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175 <param name="reference" value="mz_ref"/>
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176 <param name="mz_value" value="102.0"/>
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177 </conditional>
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178 <param name="n_tophits" value="50"/>
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179 <param name="sort_by" value="correlation"/>
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180 <output name="coloc_pdf" file="coloc3.pdf" compare="sim_size" delta="2000"/>
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181 <output name="coloc_results" file="coloc_table3.tabular"/>
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182 </test>
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183 </tests>
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184 <help>
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185 <![CDATA[
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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186
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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187 @CARDINAL_DESCRIPTION@
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188
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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189 -----
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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190
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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191 This tool finds colocalized features in an imaging dataset. Use it to find m/z features that are colocalized with another m/z feature or regions of interests.
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192
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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193 @MSIDATA_INPUT_DESCRIPTION@
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194
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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195 - NA intensities are not allowed
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196 - duplicated coordinates will be removed
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197 - it is highly recommended to use a dataset that is reduced for the number of m/z features e.g. pre-processed and optionally filtered for m/z of interest in order to keep computational times reasonable.
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198
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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199
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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200 **Options**
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201
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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202 - The reference can be either a single m/z feature or a region of interest provided via the annotation file.
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203
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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204 - For single m/z features the closest m/z to the m/z value that is used as reference is used
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205 - For regions of interest as a reference the name of the region that should be used as a reference has to be written exactly in the way in which it appears in the annotation file input.
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206 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
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207
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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208 - By default, pearson correlation is used to rank the colocalized features. Manders’ colocalization coefficients (M1 and M2) are also provided.
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209
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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210 **Output**
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211
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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212 - Pdf with file info and the ion images of the top 10 m/z features (to plot the ion images for more m/z features use the MSI mz images tool)
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213 - Tabular file with the top m/z features and their correlation values (pearson, Manders 1 and Manders 2) with the reference
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214
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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215
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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216 ]]>
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217 </help>
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218 <citations>
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219 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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220 </citations>
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221
d3ca64dafdef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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222 </tool>