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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 91a79a90a63fc6f14b8a99aaa224d1dfd74c9f68
author bgruening
date Wed, 29 Oct 2025 10:25:34 +0000
parents 04fe94223792
children
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00372f57c454 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 3a7c1e056d37cf5c5a4eca3d9c86d0f27acaac19
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1 <tool id="wordcloud" name="Generate a word cloud" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>with highly customizable appearance</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.9.4</token>
3
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5 <token name="@VERSION_SUFFIX@">4</token>
0
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6 <token name="@PROFILE@">23.0</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">wordcloud</requirement>
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10 </requirements>
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11 <version_command>wordcloud_cli --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 wordcloud_cli
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14 --imagefile 'output.png'
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15 --text $text
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16 #if $stopwords
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17 --stopwords $stopwords
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18 #end if
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19
00372f57c454 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 3a7c1e056d37cf5c5a4eca3d9c86d0f27acaac19
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20 #if $fonts.fonts_selector == 'cached':
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21 --fontfile ${fonts.fonts_select.fields.path}
00372f57c454 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 3a7c1e056d37cf5c5a4eca3d9c86d0f27acaac19
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22 #elif $fonts.fonts_selector == 'history':
00372f57c454 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 3a7c1e056d37cf5c5a4eca3d9c86d0f27acaac19
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23 --fontfile ${fonts.fontfile}
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24 #end if
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25
00372f57c454 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 3a7c1e056d37cf5c5a4eca3d9c86d0f27acaac19
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26 #if $min_font_size
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27 --min_font_size $min_font_size
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28 #end if
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29 #if $max_font_size
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30 --max_font_size $max_font_size
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31 #end if
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32 #if $font_step
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33 --font_step $font_step
00372f57c454 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 3a7c1e056d37cf5c5a4eca3d9c86d0f27acaac19
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34 #end if
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35 #if $min_word_length
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36 --min_word_length $min_word_length
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37 #end if
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38 #if str($max_words):
00372f57c454 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 3a7c1e056d37cf5c5a4eca3d9c86d0f27acaac19
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39 --max_words $max_words
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40 #end if
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41 #if str($width):
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42 --width $width
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43 #end if
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44 #if str($height):
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45 --height $height
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46 #end if
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47 #if str($margin):
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48 --margin $margin
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49 #end if
2
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50 --mode $background_options.mode
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51 #if str($background_options.mode) == 'RGB'
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52 --background '$background_options.background_color'
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53 #if str($background_options.cloud_shape.cloud_shape_options) == 'mask'
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54 --mask $background_options.cloud_shape.mask
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55 --contour_width $background_options.cloud_shape.contour_width
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56 --contour_color '$background_options.cloud_shape.contour_color'
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57 #end if
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58 #else
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59 --background None
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60 #if str($background_options.cloud_shape.cloud_shape_options) == 'mask'
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61 --mask $background_options.cloud_shape.mask
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62 #end if
0
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63 #end if
2
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64 #if $color_choice.color_option == "color":
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65 --color '$color_choice.color'
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66 #else if $color_choice.color_option == "colormask":
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67 --colormask $color_choice.colormask
3
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68 #else if $color_choice.colormap == "colormap":
e00cb408785a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 91a79a90a63fc6f14b8a99aaa224d1dfd74c9f68
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69 --colormap $color_choice.colormap
0
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70 #end if
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71 #if str($prefer_horizontal):
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72 --prefer_horizontal $prefer_horizontal
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73 #end if
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74 #if str($scale):
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75 --scale $scale
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76 #end if
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77 #if str($relative_scaling):
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78 --relative_scaling $relative_scaling
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79 #end if
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80 $no_collocations
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81 $include_numbers
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82 $no_normalize_plurals
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83 $repeat
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84 #if str($random_state):
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85 --random_state $random_state
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86 #end if
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87 ]]>
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88 </command>
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89 <inputs>
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90 <param argument="--text" type="data" format="txt" label="Input file" help="Input file to process"/>
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91 <param argument="--stopwords" type="data" format="txt" optional="true" label="Stopwords file" help="Specify file of stopwords (containing one word per line) to remove from the given text after parsing"/>
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92
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93 <conditional name="fonts">
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94 <param name="fonts_selector" type="select" label="Do you want to select a special font?" help="You can pass a specific file from your history or select a few prebuild fonts. By default DroidSansMono is used.">
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95 <option value="none">Use the default DroidSansMono font</option>
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96 <option value="cached">Select from a list of fonts</option>
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97 <option value="history">Choose a font from your history</option>
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98 </param>
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99 <when value="none"/>
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100 <when value="cached">
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101 <param name="fonts_select" type="select" label="Select font from list">
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102 <options from_data_table="fonts">
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103 <filter type="sort_by" column="2" />
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104 <validator type="no_options" message="No fonts are available" />
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105 </options>
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106 </param>
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107 </when>
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108 <when value="history">
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109 <param argument="--fontfile" type="data" format="binary" optional="true" label="Font file you wish to use" help="The font file you want to use"/>
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110 </when>
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111 </conditional>
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112
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113 <param argument="--min_font_size" type="integer" min="1" value="4" optional="true" label=" Smallest font size to use" />
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114 <param argument="--max_font_size" type="integer" min="1" optional="true" label="Maximum font size for the largest word" />
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115 <param argument="--font_step" type="integer" value="1" label="Step size for the font" help="Font_step &gt; 1 might speed up computation but give a worse fit"/>
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116 <param argument="--min_word_length" type="integer" value="0" optional ="True" label="Minimum number of letters a word must have to be included"/>
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117 <param argument="--max_words" type="integer" min="1" value="200" optional="true" label="Maximum number of words"/>
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118 <param argument="--width" type="integer" min="1" value="400" optional="true" label="Define output image width"/>
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119 <param argument="--height" type="integer" min="1" value="200" optional="true" label="Define output image height"/>
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120 <param argument="--margin" type="integer" value="2" label="Spacing to leave around words"/>
2
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121 <conditional name="background_options">
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122 <param argument="--mode" type="select" label="Use RGB or RGBA for transparent background">
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123 <option value="RGB" selected="true">RGB</option>
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124 <option value="RGBA">RGBA</option>
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125 </param>
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126 <when value="RGB">
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127 <param argument="--background_color" type="color" value="#000000" optional="true" label="Use given color as background color for the image">
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128 <validator type="regex" message="Please select a valid RGB color">[#][0-9A-Fa-f]{6}</validator>
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129 </param>
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130 <conditional name="cloud_shape">
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131 <param name="cloud_shape_options" type="select" label="Choose word cloud shape">
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132 <option value="rectangle" selected="true">Default - Rectangle</option>
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133 <option value="mask">Mask from image input</option>
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134 </param>
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135 <when value="rectangle"/>
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136 <when value="mask">
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137 <param argument="--mask" type="data" format="png" optional="true" label="Mask to use for the image form"/>
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138 <param argument="--contour_width" type="float" min="0" value="0" optional="true" label="Contour width" help="Use given color as mask contour color"/>
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139 <param argument="--contour_color" type="color" value="#000000" optional="true" label="Contour color">
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140 <validator type="regex" message="Please select a valid RGB color">[#][0-9A-Fa-f]{6}</validator>
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141 </param>
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142 </when>
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143 </conditional>
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144 </when>
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145 <when value="RGBA">
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146 <conditional name="cloud_shape">
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147 <param name="cloud_shape_options" type="select" label="Choose word cloud shape">
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148 <option value="rectangle" selected="true">Default - Rectangle</option>
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149 <option value="mask">Mask from image input</option>
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150 </param>
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151 <when value="rectangle"/>
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152 <when value="mask">
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153 <param argument="--mask" type="data" format="png" optional="true" label="Mask to use for the image form"/>
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154 </when>
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155 </conditional>
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156 </when>
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157 </conditional>
0
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158 <conditional name="color_choice" label="Choose color option">
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159 <param name="color_option" type="select" label="Color option">
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160 <option value="color">Color</option>
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161 <option value="colormask">Color Mask</option>
3
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162 <option value="colormap">Colormap</option>
0
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163 </param>
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164 <when value="color">
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165 <param argument="--color" type="color" value="#00ff00" optional="true" label="Use given color as coloring for the image">
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166 <validator type="regex" message="Please select a valid RGB color">[#][0-9A-Fa-f]{6}</validator>
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167 </param>
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168 </when>
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169 <when value="colormask">
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170 <param argument="--colormask" type="data" format="png" optional="true" label="Color Mask" help="Upload a color mask image"/>
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171 </when>
3
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172 <when value="colormap">
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173 <param argument="--colormap" type="select" value="viridis" optional="true" label="Matplotlib colormap name">
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174 <option value="viridis">viridis</option>
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175 <option value="plasma">plasma</option>
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176 <option value="inferno">inferno</option>
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177 <option value="magma">magma</option>
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178 <option value="cividis">cividis</option>
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179 <option value="Greys">Greys</option>
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180 <option value="Purples">Purples</option>
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181 <option value="Blues">Blues</option>
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182 <option value="Greens">Greens</option>
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183 <option value="Oranges">Oranges</option>
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184 <option value="Reds">Reds</option>
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185 <option value="YlOrBr">YlOrBr</option>
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186 <option value="YlOrRd">YlOrRd</option>
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187 <option value="OrRd">OrRd</option>
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188 <option value="PuRd">PuRd</option>
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189 <option value="RdPu">RdPu</option>
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190 <option value="BuPu">BuPu</option>
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191 <option value="GnBu">GnBu</option>
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192 <option value="PuBu">PuBu</option>
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193 <option value="YlGnBu">YlGnBu</option>
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194 <option value="PuBuGn">PuBuGn</option>
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195 <option value="BuGn">BuGn</option>
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196 <option value="YlGn">YlGn</option>
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197 </param>
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198 </when>
0
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199 </conditional>
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200 <param argument="--prefer_horizontal" type="float" min="0" max="1" value="0.9" optional="true" label="Ratio of times to try horizontal fitting as opposed to vertical"/>
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201 <param argument="--scale" type="float" value="1.0" optional="True" label="Scaling between computation and drawing"/>
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202 <param argument="--relative_scaling" type="float" min="0.0" max="1.0" value="0.0" optional="true" label="Scaling of words by frequency (0 - 1)"/>
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203 <param argument="--no_collocations" type="boolean" truevalue="--no_collocations" falsevalue="" value="True" label="Do not add collocations (bigrams) to word cloud"/>
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204 <param argument="--include_numbers" type="boolean" truevalue="--include_numbers" falsevalue="" value="False" label="Whether to include numbers as phrases or not"/>
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205 <param argument="--no_normalize_plurals" type="boolean" truevalue="--no_normalize_plurals" falsevalue="" label="Whether to remove trailing s from words"/>
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206 <param argument="--repeat" type="boolean" truevalue="--repeat" falsevalue="" label="Whether to repeat words and phrases until max_words or min_font_size is reached"/>
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207 <param argument="--random_state" type="integer" value="10" label="Random seed" />
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208 </inputs>
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209 <outputs>
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210 <data name="output" format="png" label="Word cloud image" from_work_dir="output.png"/>
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211 </outputs>
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212 <tests>
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213 <test expect_num_outputs="1">
2
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214 <param name="text" value="test.txt"/>
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215 <param name="font_step" value="2"/>
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216 <param name="min_word_length" value="2"/>
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217 <param name="width" value="200"/>
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218 <param name="height" value="100"/>
3
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219 <conditional name="color_choice">
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220 <param name="color_option" value="colormap"/>
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221 <param name="colormap" value="inferno"/>
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222 </conditional>
2
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223 <param name="scale" value="1.8"/>
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224 <param name="no_collocations" value="false"/>
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225 <conditional name="fonts">
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226 <param name="fonts_selector" value="none"/>
0
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227 </conditional>
2
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228 <output name="output" file="output0.png" ftype="png"/>
0
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229 </test>
2
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230
0
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231 <test expect_num_outputs="1">
2
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232 <param name="text" value="test.txt"/>
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233 <param name="stopwords" value="stopwords.txt"/>
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234 <conditional name="fonts">
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235 <param name="fonts_selector" value="cached"/>
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236 <param name="fonts_select" value="Test Font"/>
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237 </conditional>
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238 <output name="output" file="output1.png" ftype="png"/>
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239 </test>
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240
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241 <test expect_num_outputs="1">
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242 <param name="text" value="test.txt"/>
0
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243 <param name="stopwords" value="stopwords.txt"/>
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244 <conditional name="fonts">
2
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245 <param name="fonts_selector" value="history"/>
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246 <param name="fontfile" value="font.ttf"/>
0
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247 </conditional>
2
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248 <output name="output" file="output1.png" ftype="png"/>
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249 </test>
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250
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251 <test expect_num_outputs="1">
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252 <param name="text" value="test.txt"/>
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253 <param name="stopwords" value="stopwords.txt"/>
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254 <conditional name="background_options">
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255 <param name="mode" value="RGB"/>
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256 <param name="background_color" value="#9141ac"/>
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257 <conditional name="cloud_shape">
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258 <param name="cloud_shape_options" value="mask"/>
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259 <param name="mask" value="mask.png"/>
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260 <param name="contour_width" value="1.8"/>
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261 <param name="contour_color" value="#e01b24"/>
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262 </conditional>
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263 </conditional>
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264 <output name="output" file="output2.png" ftype="png"/>
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265 </test>
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266
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267 <test expect_num_outputs="1">
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268 <param name="text" value="test.txt"/>
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269 <param name="stopwords" value="stopwords.txt"/>
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270 <param name="include_numbers" value="true"/>
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271 <param name="no_normalize_plurals" value="false"/>
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272 <param name="repeat" value="false"/>
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273 <param name="random_state" value="10"/>
0
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274 <conditional name="color_choice">
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275 <param name="color_option" value="color"/>
2
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276 <param name="color" value="#99c1f1"/>
0
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277 </conditional>
2
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278 <conditional name="background_options">
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279 <param name="mode" value="RGBA"/>
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280 <conditional name="cloud_shape">
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281 <param name="cloud_shape_options" value="rectangle"/>
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282 </conditional>
0
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283 </conditional>
2
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284 <output name="output" file="output3.png" ftype="png"/>
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285 </test>
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286
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287 <test expect_num_outputs="1">
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288 <param name="text" value="test.txt"/>
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289 <param name="stopwords" value="stopwords.txt"/>
0
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290 <conditional name="color_choice">
2
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291 <param name="color_option" value="colormask"/>
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292 <param name="colormask" value="mask.png"/>
0
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293 </conditional>
2
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294 <output name="output" file="output4.png" ftype="png"/>
0
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295 </test>
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296 </tests>
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297 <help><![CDATA[
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298 A word cloud is a visual representation (image) of word data. In other words, it is a collection, or cluster, of words depicted in different sizes.
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299 The bigger and bolder the word appears, the more often it's mentioned within a given text and the more important it is.
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300 ]]></help>
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301 <citations>
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302 <citation type="bibtex">
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303 @misc{amueller2018wordcloud,
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304 title={Word Clouds with Python},
1
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305 author={Mueller, Andreas Christian},
0
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306 year={2018},
1
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307 url={https://github.com/amueller/word_cloud}
0
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308 }
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309 </citation>
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310 </citations>
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311 </tool>