Mercurial > repos > galaxyp > cardinal_mz_images

annotate mz_images.xml @ 0:2ba12c97f7cc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
author galaxyp
date Mon, 01 Oct 2018 01:06:41 -0400
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2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0">
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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2 <description>
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3 mass spectrometry imaging m/z heatmaps
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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4 </description>
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5 <macros>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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6 <import>macros.xml</import>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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7 </macros>
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8 <expand macro="requirements">
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9 <requirement type="package" version="2.2.1">r-gridextra</requirement>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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10 <requirement type="package" version="0.20-35">r-lattice</requirement>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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11 </expand>
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12 <command detect_errors="aggressive">
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13 <![CDATA[
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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14 @INPUT_LINKING@
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15 cat '${MSI_heatmaps}' &&
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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16 Rscript '${MSI_heatmaps}'
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <configfile name="MSI_heatmaps"><![CDATA[
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21
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22 ################################# load libraries and read file #################
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23
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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24 library(Cardinal)
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25 library(gridExtra)
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26 library(lattice)
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28 @READING_MSIDATA@
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30 @DATA_PROPERTIES@
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32 ##################################### read and filter input m/z ##############
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34 input_list = read.delim("$calibrant_file", header = $calibrant_header, stringsAsFactors = FALSE)
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35 input_list = input_list[,c($mz_column, $name_column)]
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37 ### calculate how many input m/z are valid:
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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38 inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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39 inputmz = as.numeric(inputmasses[,1])
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40 inputnames = as.character(inputmasses[,2])
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43 ############################## PDF #############################################
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44 ################################################################################
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46 pdf("heatmaps.pdf", fonts = "Times", pointsize = 12)
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47 plot(0,type='n',axes=FALSE,ann=FALSE)
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48 #if not $filename:
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49 #set $filename = $infile.display_name
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50 #end if
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51 title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename"))
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52
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53 new_row = data.frame(paste0(length(inputmz), "/", length(input_list[,1])), paste0("# valid m/z in \n", "$calibrant_file.display_name"))
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54 colnames(new_row) = c("properties", "values")
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55 property_df = rbind(property_df, new_row)
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57 grid.table(property_df, rows= NULL)
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59 ############################# II) images ####################################
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61 ### only plot images when file has peaks and valid input m/z:
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63 if (npeaks > 0){
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64 if (length(inputmz) != 0){
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65 for (mass in 1:length(inputmz)){
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67 ###standard image
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69 #if str($image_type) == "standard_image":
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70 print("standard image")
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72 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast",
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73 smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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74 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}
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75
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77 ###lattice image
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79 #elif str($image_type) == "lattice_image":
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80 print("lattice image")
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82 #if str($strip) =="TRUE":
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84 print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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85 lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing",
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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86 colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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87 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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88
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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89 #elif str($strip) =="FALSE":
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galaxyp
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90
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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91 print(image(msidata, mz=inputmz[mass], strip = $strip,
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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92 lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing",
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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93 colorkey=$colorkey,
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94 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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95
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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96 #end if
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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97
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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98 #end if
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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99
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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100 ## optional svg output with original coordinates
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101 #if $svg_pixelimage:
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102 print("svg pixel image")
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103 svg(file="svg_pixel_output.svg")
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104 par(mar=c(0,0,0,0))
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105 image(msidata, mz = inputmz[1],strip=FALSE, ylim=c(maximumy, minimumy), plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing")
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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106 dev.off()
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107 #end if
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108
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109 } else {print("The input m/z were invalid")}
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110 dev.off()
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111 }else{
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112 print("inputfile has no intensities > 0")
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113 dev.off()
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114 }
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115
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116
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117 ]]></configfile>
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118 </configfiles>
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119 <inputs>
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120 <expand macro="reading_msidata"/>
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121 <expand macro="pdf_filename"/>
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122 <expand macro="reading_2_column_mz_tabular"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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123
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124
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125 <param name="image_contrast" type="select" label="Select a contrast enhancement function for the heatmap images" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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126 <option value="none" selected="True">none</option>
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127 <option value="suppression">suppression</option>
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128 <option value="histogram">histogram</option>
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129 </param>
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130 <param name="image_smoothing" type="select" label="Select an image smoothing function for the heatmap images" help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges">
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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131 <option value="none" selected="True">none</option>
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132 <option value="gaussian">gaussian</option>
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133 <option value="adaptive">adaptive</option>
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134 </param>
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135 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
136 <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
137 <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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138 <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image"
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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139 label="Standard image" help="No: lattice function is used to display image"/>
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140 <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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141 </inputs>
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142 <outputs>
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143 <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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144 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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145 <filter>svg_pixelimage</filter>
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146 </data>
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147 </outputs>
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148 <tests>
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149 <test>
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150 <expand macro="infile_imzml"/>
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151 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
152 <param name="mz_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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153 <param name="name_column" value="2"/>
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154 <param name="plusminus_dalton" value="0.25"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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155 <param name="filename" value="Testfile_imzml"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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156 <param name="image_contrast" value="histogram"/>
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157 <param name="strip" value="True"/>
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158 <param name="colorkey" value="True"/>
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159 <param name="image_type" value="lattice_image"/>
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160 <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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161 </test>
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162 <test>
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163 <expand macro="infile_analyze75"/>
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164 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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165 <param name="mz_column" value="1"/>
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166 <param name="name_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
167 <param name="plusminus_dalton" value="0.5"/>
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168 <param name="filename" value="Testfile_analyze75"/>
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169 <param name="image_smoothing" value="gaussian"/>
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170 <param name="strip" value="False"/>
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171 <param name="colorkey" value="True"/>
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172 <param name="svg_pixelimage" value="True"/>
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173 <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
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174 <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
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175 </test>
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176 <test>
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177 <param name="infile" value="preprocessed.rdata" ftype="rdata"/>
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178 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
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179 <param name="mz_column" value="1"/>
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180 <param name="name_column" value="2"/>
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181 <param name="plusminus_dalton" value="0.5"/>
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182 <param name="strip" value="True"/>
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183 <param name="colorkey" value="True"/>
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184 <param name="image_type" value="lattice_image"/>
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185 <param name="filename" value="Testfile_rdata"/>
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186 <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>
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187 </test>
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188 <test>
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189 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
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190 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
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191 <param name="mz_column" value="1"/>
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192 <param name="name_column" value="1"/>
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193 <param name="plusminus_dalton" value="0.5"/>
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194 <param name="strip" value="True"/>
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195 <param name="colorkey" value="False"/>
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196 <param name="filename" value="Testfile_rdata"/>
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197 <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>
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198 </test>
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199 </tests>
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200 <help><![CDATA[
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201
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202
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203 @CARDINAL_DESCRIPTION@
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204
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205 -----
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206
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207 This tool uses the Cardinal image function to plot the intensity distribution of m/z feature of mass spectrometry imaging data.
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208
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209 @MSIDATA_INPUT_DESCRIPTION@
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210
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211 @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@
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212
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213 **Tips**
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214
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215 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes))
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216 - No heatmaps are plotted when the input mass spectrometry imaging file has no intensities > 0 or all chosen m/z features are not present in the MSI dataset
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217 - The contrast enhance and image smoothing functions require a certain number (about 2%) of m/z features with intensities > 0 across all spectra
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218 - The standard image function should work for all files while the lattice function works not perfectly on every file
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219
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220 **Output**
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221
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222 - Pdf with the heatmap images
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223 - optional: svg file with the heatmap of the first valid m/z in the tabular file
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224
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225
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226 ]]>
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227 </help>
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228 <expand macro="citations"/>
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229 </tool>