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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:10:23 -0400
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0
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_plot" name="csvtk-plot" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> histogram, line/scatter plot, or boxplot based on column</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_cmd" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ###################
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11 ## Start Command ##
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12 ###################
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13 csvtk plot
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14
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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15 #if $plot_type.plot == "histogram"
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16 hist
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17 #elif $plot_type.plot == "boxplot"
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18 box
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19 #elif $plot_type.plot == "line"
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20 line
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21 #end if
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23 --num-cpus "\${GALAXY_SLOTS:-1}"
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24
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25 ## Add additional flags as specified ##
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26 #######################################
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27 $global_param.illegal_rows
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28 $global_param.empty_rows
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29 $global_param.header
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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30 $global_param.lazy_quotes
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31
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32 ## Set Tabular input/output flag if first input is tabular ##
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33 #############################################################
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34 #if $in_1.is_of_type("tabular"):
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35 -t -T
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36 #end if
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37
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38 ## Set input files ##
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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39 #####################
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40 $in_1
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41
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42 ## Specific Plot Parameters ##
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43 ##############################
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44 #if $plot_type.plot == "histogram"
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45 -f '$plot_type.column_text.in_text'
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46 --color-index $plot_type.colour
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47
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48 #elif $plot_type.plot == "boxplot"
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49 -f '$plot_type.column_text.in_text'
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50 $plot_type.horizontal
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51
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52 #if $plot_type.group_field.select_group != "none"
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53 -g '$plot_type.group_field.in_text'
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54 #end if
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55
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56 #if $plot_type.box_width
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57 --box-width '$plot_type.box_width'
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58 #end if
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59
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60 #elif $plot_type.plot == "line"
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61 $plot_type.scatter
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62 -x '$plot_type.column_text.in_text_x'
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63 -y '$plot_type.column_text.in_text_y'
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64
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65 #if $plot_type.group_field.select_group != "none"
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66 -g '$plot_type.group_field.in_text'
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67 #end if
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68
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69 $plot_type.label_location
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70
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71 #end if
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72
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73 ## General Plot Parameters ##
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74 #############################
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75
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76 #if $plot_parameters.figure_height
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77 --height '$plot_parameters.figure_height'
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78 #end if
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79
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80 #if $plot_parameters.figure_width
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81 --width '$plot_parameters.figure_width'
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82 #end if
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83
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84 #if $plot_parameters.tick_width
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85 --tick-width '$plot_parameters.tick_width'
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86 #end if
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87
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88 #if $plot_parameters.title
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89 --title '$plot_parameters.title'
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90 #end if
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91
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92 #if $plot_parameters.x_label
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93 --xlab '$plot_parameters.x_label'
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94 #end if
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95
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96 #if $plot_parameters.min_x
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97 --x-min '$plot_parameters.min_x'
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98 #end if
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99
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100 #if $plot_parameters.max_x
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101 --x-max '$plot_parameters.max_x'
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102 #end if
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103
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104 #if $plot_parameters.y_label
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105 --ylab '$plot_parameters.y_label'
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106 #end if
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107
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108 #if $plot_parameters.min_y
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109 --y-min '$plot_parameters.min_y'
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110 #end if
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111
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112 #if $plot_parameters.max_y
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113 --y-max '$plot_parameters.max_y'
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114 #end if
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115
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116 ## To output ##
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117 ###############
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118 > plot.png
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119
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120 ]]></command>
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121 <inputs>
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122 <expand macro="singular_input"/>
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123 <conditional name="plot_type">
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124 <param name="plot" type="select" label="Select plot type">
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125 <option value="histogram">Histogram</option>
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126 <option value="boxplot">Boxplot</option>
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127 <option value="line">Line/Scatter</option>
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128 </param>
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129 <when value="histogram">
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130 <expand macro="plot_field" />
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131 <param name="colour" type="integer"
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132 min="1" max="7"
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133 value="1"
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134 argument="--color-index"
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135 label="Select colour scheme"
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136 help="Choose a number from 1-7"
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137 />
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138 </when>
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139 <when value="boxplot" >
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140 <expand macro="plot_field" />
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141 <expand macro="groups_input" />
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142 <param type="boolean" name="horizontal" label="Horizontal Box Plot" argument="--horiz"
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143 checked="false"
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144 falsevalue=""
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145 truevalue="--horiz"
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146 />
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147 <param name="box_width" type="float"
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148 label="Box Width (Optional)"
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149 argument="--box-width"
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150 optional="true"
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151 />
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152 </when>
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153 <when value="line">
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154 <param name="scatter" type="boolean" label="Scatter Plot" argument="--scatter"
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155 checked="false"
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156 falsevalue=""
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157 truevalue="--scatter"
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158 help="Plot only points, no lines"
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159 />
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160 <conditional name="column_text" >
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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161 <param type="select" name="select" label="Select input data columns for the X and Y axis based on:" >
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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162 <option value="string">Column Name</option>
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163 <option value="column">Column Number</option>
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164 </param>
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165 <when value="column">
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166 <param type="data_column" name="in_text_x"
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167 data_ref="in_1"
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168 multiple="false"
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169 label="X-axis data column"
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170 />
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171 <param type="data_column" name="in_text_y"
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172 data_ref="in_1"
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173 multiple="false"
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174 label="Y-axis data column"
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175 />
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176 </when>
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177 <when value="string">
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178 <param type="text" name="in_text_x"
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179 optional="false"
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180 label="X-axis data column"
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181 help="Can use column name or column number">
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182 <expand macro="text_sanitizer" />
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183 </param>
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184 <param type="text" name="in_text_y"
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185 optional="false"
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186 label="Y-axis data column"
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187 help="Can use column name or column number">
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188 </param>
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189 </when>
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190 </conditional>
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191 <expand macro="groups_input" />
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192 <param name="label_location" type="select" label="Label Location"
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193 help="Only displays legend if a groups column is set">
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194 <option value="--legend-left">Left edge of plot</option>
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195 <option value="--legend-top">Top edge of plot</option>
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196 </param>
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197 </when>
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198 </conditional>
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199 <expand macro="global_plot_parameters" />
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200 <expand macro="global_parameters" />
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201 </inputs>
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202 <outputs>
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203 <data format="png" from_work_dir="plot.png" name="out_plot" label="${in_1.name} ${plot_type.plot}" />
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204 </outputs>
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205 <tests>
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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206 <test>
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207 <param name="in_1" value="plot.csv" />
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208 <conditional name="plot_type">
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209 <param name="plot" value="histogram" />
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210 <conditional name="column_text">
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211 <param name="select" value="string" />
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212 <param name="in_text" value="2" />
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213 </conditional>
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214 <param name="colour" value="2" />
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215 </conditional>
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216 <output name="out_plot" value="plot.png" ftype="png" compare="sim_size" delta="20000" />
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217 </test>
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218 <test>
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219 <param name="in_1" value="plot.csv" />
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220 <conditional name="plot_type">
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221 <param name="plot" value="boxplot" />
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222 <conditional name="column_text">
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223 <param name="select" value="column" />
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224 <param name="in_text" value="2" />
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225 </conditional>
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226 <conditional name="group_field">
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227 <param name="select_group" value="string" />
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228 <param name="in_text" value="1" />
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229 </conditional>
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230 <param name="horizontal" value="true" />
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231 <param name="box_width" value="50.5" />
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232 </conditional>
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233 <output name="out_plot" value="plot_box.png" compare="sim_size" delta="20000" />
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234 </test>
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235 <test>
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236 <param name="in_1" value="plot.csv" />
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diff changeset
237 <conditional name="plot_type">
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238 <param name="plot" value="line" />
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239 <param name="scatter" value="true" />
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diff changeset
240 <conditional name="column_text">
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241 <param name="select" value="column" />
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242 <param name="in_text_x" value="2" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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243 <param name="in_text_y" value="3" />
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244 </conditional>
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
245 <conditional name="group_field">
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246 <param name="select_group" value="string" />
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247 <param name="in_text" value="1" />
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248 </conditional>
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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249 </conditional>
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250 <output name="out_plot" value="plot_scatter.png" compare="sim_size" delta="20000" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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251 </test>
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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252 <test>
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253 <param name="in_1" value="plot.csv" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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254 <conditional name="plot_type">
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255 <param name="plot" value="line" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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256 <param name="scatter" value="false" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
257 <conditional name="column_text">
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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258 <param name="select" value="column" />
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diff changeset
259 <param name="in_text_x" value="2" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
260 <param name="in_text_y" value="3" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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261 </conditional>
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
262 <conditional name="group_field">
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diff changeset
263 <param name="select_group" value="string" />
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264 <param name="in_text" value="1" />
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265 </conditional>
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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266 <param name="label_location" value="--legend-top" />
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267 </conditional>
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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268 <section name="plot_parameters">
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269 <param name="figure_height" value="10.1" />
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270 <param name="figure_width" value="6.6" />
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271 <param name="tick_width" value="2.1" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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272 <param name="title" value="Test" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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273 <param name="x_label" value="Potentially Broken" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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274 <param name="min_x" value="1.1" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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275 <param name="max_x" value="109.1" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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276 <param name="y_label" value="How High Can We Go?" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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277 <param name="min_y" value="-10.4" />
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diff changeset
278 <param name="max_y" value="141.9" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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279 </section>
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280 <output name="out_plot" value="line_all_param.png" compare="sim_size" delta="20000" />
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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281 </test>
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282 </tests>
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283 <help><![CDATA[
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284
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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285 Csvtk - Plot Help
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286 -----------------
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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287
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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288 Info
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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289 ####
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290
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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291 Use Csvtk-Plot to plot histograms, line plots / scatter plots, or boxplots.
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292
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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293 Specify a column or a couple of columns from an input CSV/TSV dataset to generate wanted plots fast.
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294
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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295 .. class:: warningmark
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296
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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297 Single quotes are not allowed in text inputs!
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298
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299 @HELP_INPUT_DATA@
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300
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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301
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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302 @HELP_END_STATEMENT@
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303
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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304
f370d221c284 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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305 ]]></help>
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306 <expand macro="citations" />
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307 </tool>