Mercurial > repos > galaxyp > cardinal_mz_images

annotate mz_images.xml @ 2:27a4c660bbca draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:20:01 -0500
parents 4d5f798a7a18
children 773a24b240e1
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2">
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2 <description>
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3 mass spectrometry imaging m/z heatmaps
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements">
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9 <requirement type="package" version="2.3">r-gridextra</requirement>
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10 <requirement type="package" version="0.20_35">r-lattice</requirement>
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11 </expand>
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12 <command detect_errors="aggressive">
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13 <![CDATA[
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14 @INPUT_LINKING@
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15 cat '${MSI_heatmaps}' &&
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16 Rscript '${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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22 ################################# load libraries and read file #################
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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:
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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
1
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53 new_row = data.frame(paste0("# valid m/z in \n", "$calibrant_file.display_name"), paste0(length(inputmz), "/", length(input_list[,1])))
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54 colnames(new_row) = c("properties", "values")
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55 property_df = rbind(property_df, new_row)
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57 grid.table(property_df, rows= NULL)
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59 ############################# II) images ####################################
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2
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61 ### only plot images when file has features and pixels:
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62
2
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63 if (ncol(msidata)>0 & nrow(msidata) >0){
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64 if (length(inputmz) != 0){
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65 for (mass in 1:length(inputmz)){
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67 ###standard image
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69 #if str($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",
2
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73 smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.2*maximumy,minimumy-1),
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74 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}
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77 ###lattice image
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79 #elif str($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)),
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85 lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing",
2
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86 colorkey=$colorkey,ylim=c(maximumy+0.2*maximumy,minimumy-1),
0
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87 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}
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88
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89 #elif str($strip) =="FALSE":
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90
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91 print(image(msidata, mz=inputmz[mass], strip = $strip,
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92 lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing",
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93 colorkey=$colorkey,
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94 main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}
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95
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96 #end if
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97
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98 #end if
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99
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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")
2
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103 ## reverse y axis for svg output = correct order and nice svg image
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104 coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1
0
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105 svg(file="svg_pixel_output.svg")
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106 par(mar=c(0,0,0,0))
2
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107 image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing")
0
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108 dev.off()
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109 #end if
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110
2
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111 ## optional overlay all input m/z in one image
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112 #if str($overlay_cond.overlay_selection) == "yes_overlay":
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113
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114 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours])
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115 colourvector = c($color_string)
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116
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117 image(msidata, mz=inputmz,
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118 plusminus = $plusminus_dalton,
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119 col=colourvector,
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120 contrast.enhance = "$image_contrast",
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121 normalize.image="linear",
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122 smooth.image = "$image_smoothing",
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123 superpose=TRUE, main="overlay of all m/z",
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124 ylim= c(maximumy+0.2*maximumy,minimumy-1))
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125
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126 legend("topright",
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127 fill=colourvector,
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128 legend=as.numeric(sort(as.character(inputmz))))
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129 #end if
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130
0
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131 } else {print("The input m/z were invalid")}
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132 dev.off()
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133 }else{
2
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134 print("input file has no features or pixels left")
0
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135 dev.off()
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136 }
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137
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138
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139 ]]></configfile>
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140 </configfiles>
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141 <inputs>
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142 <expand macro="reading_msidata"/>
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143 <expand macro="pdf_filename"/>
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144 <expand macro="reading_2_column_mz_tabular"/>
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145
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146
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147 <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">
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148 <option value="none" selected="True">none</option>
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149 <option value="suppression">suppression</option>
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150 <option value="histogram">histogram</option>
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151 </param>
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152 <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">
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153 <option value="none" selected="True">none</option>
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154 <option value="gaussian">gaussian</option>
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155 <option value="adaptive">adaptive</option>
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156 </param>
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157 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window"/>
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158 <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
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159 <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
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160 <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image"
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161 label="Standard image" help="No: lattice function is used to display image"/>
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162 <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
2
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163 <conditional name="overlay_cond">
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164 <param name="overlay_selection" type="select" label="Overlay image">
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165 <option value="no_overlay" selected="True">no</option>
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166 <option value="yes_overlay">yes</option>
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167 </param>
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168 <when value="no_overlay"/>
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169 <when value="yes_overlay">
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170 <repeat name="colours" title="Colours for the plots" min="1" max="50">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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171 <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of m/z in tabular file">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
172 <sanitizer>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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173 <valid initial="string.letters,string.digits">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
174 <add value="#" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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175 </valid>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
176 </sanitizer>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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177 </param>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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178 </repeat>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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179 </when>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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180 </conditional>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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181 </inputs>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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182 <outputs>
2
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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183 <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}: results"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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184 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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185 <filter>svg_pixelimage</filter>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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186 </data>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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187 </outputs>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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188 <tests>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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189 <test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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190 <expand macro="infile_imzml"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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191 <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
galaxyp
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192 <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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193 <param name="name_column" value="2"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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194 <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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195 <param name="filename" value="Testfile_imzml"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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196 <param name="image_contrast" value="histogram"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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197 <param name="strip" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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198 <param name="colorkey" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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199 <param name="image_type" value="lattice_image"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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200 <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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201 </test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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202 <test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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203 <expand macro="infile_analyze75"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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204 <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
galaxyp
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205 <param name="mz_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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206 <param name="name_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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207 <param name="plusminus_dalton" value="0.5"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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208 <param name="filename" value="Testfile_analyze75"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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209 <param name="image_smoothing" value="gaussian"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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210 <param name="strip" value="False"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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211 <param name="colorkey" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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212 <param name="svg_pixelimage" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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213 <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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214 <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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215 </test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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216 <test>
2
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217 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
0
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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218 <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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219 <param name="mz_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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220 <param name="name_column" value="2"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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221 <param name="plusminus_dalton" value="0.5"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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222 <param name="strip" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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223 <param name="colorkey" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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224 <param name="image_type" value="lattice_image"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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225 <param name="filename" value="Testfile_rdata"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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226 <output name="plots" file="Heatmaps_rdata.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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227 </test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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228 <test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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229 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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230 <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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231 <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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232 <param name="name_column" value="1"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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233 <param name="plusminus_dalton" value="0.5"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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234 <param name="strip" value="True"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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235 <param name="colorkey" value="False"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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236 <param name="filename" value="Testfile_rdata"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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237 <output name="plots" file="Heatmaps_LM8_file16.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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238 </test>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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239 </tests>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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240 <help><![CDATA[
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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241
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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242
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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243 @CARDINAL_DESCRIPTION@
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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244
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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245 -----
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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246
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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247 This tool uses the Cardinal image function to plot the intensity distribution of m/z feature of mass spectrometry imaging data.
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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248
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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249 @MSIDATA_INPUT_DESCRIPTION@
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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250
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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251 @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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252
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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253 **Tips**
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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254
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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255 - 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))
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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256 - 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
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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257 - The contrast enhance and image smoothing functions require a certain number (about 2%) of m/z features with intensities > 0 across all spectra
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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258 - The standard image function should work for all files while the lattice function works not perfectly on every file
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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259
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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260 **Output**
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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261
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262 - Pdf with the heatmap images
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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263 - optional: svg file with the heatmap of the first valid m/z in the tabular file
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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264
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265
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266 ]]>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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267 </help>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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268 <expand macro="citations"/>
2ba12c97f7cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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269 </tool>