Mercurial > repos > nml > csvtk_collapse

annotate collapse.xml @ 0:7ff05a1ffdd7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:18:56 -0400
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rev   line source
0
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1 <tool id="csvtk_collapse" name="csvtk-collapse" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> one field with selected fields as keys</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
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14 csvtk collapse --num-cpus "\${GALAXY_SLOTS:-1}"
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15
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16 ## Add additional flags as specified ##
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17 #######################################
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18 $ignore_case
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19 $global_param.illegal_rows
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20 $global_param.empty_rows
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21 $global_param.header
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22 $global_param.lazy_quotes
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23
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24 ## Set Tabular input/output flag if input is tabular ##
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25 #######################################################
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26 #if $in_1.is_of_type("tabular"):
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27 -t -T
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28 #end if
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29
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30 ## Set Input ##
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31 ###############
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32 '$in_1'
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33
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34 ## Specify fields for collapse ##
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35 #################################
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36 -F -f '$column_text.in_text'
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37
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38 ## other ##
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39 ###########
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40 -v '$value_column.in_text'
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41 -s '$separator'
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42
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43 ## To output ##
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44 ###############
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45 > collapsed
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46
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47 ]]></command>
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48 <inputs>
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49 <expand macro="singular_input" />
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50 <expand macro="fields_input" />
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51 <conditional name="value_column" >
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52 <param type="select" name="select" label="Select value column to collapse based on" argument="-v">
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53 <option value="string">Column Name</option>
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54 <option value="column">Column Number</option>
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55 </param>
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56 <when value="column">
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57 <param type="data_column" name="in_text"
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58 data_ref="in_1"
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59 multiple="false"
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60 label="Input column number"
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61 help="Select column to collapse on"
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62 />
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63 </when>
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64 <when value="string">
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65 <param type="text" name="in_text"
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66 optional="false"
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67 label="Input column name"
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68 help="Specify column name or number (ex. 1 for first column) to collapse on">
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69 <expand macro="text_sanitizer" />
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70 </param>
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71 </when>
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72 </conditional>
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73 <param name="separator" type="text" value="; " argument="-s"
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74 optional="false"
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75 label="Separator string"
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76 help="Input string of characters that will separate collapsed columns. The ' character is not allowed">
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77 <expand macro="text_sanitizer" />
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78 </param>
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79 <expand macro="ignore_case" />
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80 <expand macro="global_parameters" />
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81 </inputs>
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82 <outputs>
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83 <data format_source="in_1" name="collapse" from_work_dir="collapsed" label="${in_1.name} with ${value_column.in_text} collapsed by ${column_text.in_text}" />
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="in_1" value="blood_type.tsv" />
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88 <conditional name="column_text">
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89 <param name="select" value="string" />
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90 <param name="in_text" value="2" />
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91 </conditional>
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92 <conditional name="value_column">
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93 <param name="select" value="string" />
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94 <param name="in_text" value="1" />
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95 </conditional>
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96 <param name="separator" value="; " />
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97 <output name="collapse" file="collapsed.tsv" ftype="tabular" />
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98 </test>
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99 <test>
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100 <param name="in_1" value="illegal.csv" />
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101 <conditional name="column_text">
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102 <param name="select" value="string" />
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103 <param name="in_text" value="4" />
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104 </conditional>
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105 <conditional name="value_column">
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106 <param name="select" value="string" />
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107 <param name="in_text" value="1" />
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108 </conditional>
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109 <param name="separator" value="; " />
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110 <section name="global_param">
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111 <param name="illegal_rows" value="true" />
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112 </section>
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113 <output name="collapse" file="illegal_collapse.csv" />
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114 </test>
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115 </tests>
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116 <help><![CDATA[
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117
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118 Csvtk - Collapse Help
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119 ---------------------
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120
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121 Info
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122 ####
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123
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124 Csvtk collapse combines one field with selected fields as keys for what to combine
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125
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126 .. class:: warningmark
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127
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128 Single quotes are not allowed in text inputs!
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129
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130 @HELP_INPUT_DATA@
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131
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132
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133 Usage
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134 #####
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135
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136 To run csvtk-collapse, all you need is a valid (as defined above) CSV or TSV file with a column you want to use
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137 to collapse on based on any number of key column(s).
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138
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139 **Example collapse with one key column**
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140
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141 Input table:
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142
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143 +--------+--------+----------+
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144 | Name | Colour | Food |
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145 +========+========+==========+
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146 | Eric | Blue | Apples |
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147 +--------+--------+----------+
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148 | Darian | Blue | Pancakes |
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149 +--------+--------+----------+
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150 | Daniel | Red | Apples |
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151 +--------+--------+----------+
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152 | Emily | Blue | Apples |
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153 +--------+--------+----------+
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154
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155 Now if you wanted to find out who has the same favourite colour, you would specify the key column as "Colour" (-F -f)
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156 and the value column as "Name" (-v) to generate the following table:
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157
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158 +--------+---------------------+
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159 | Colour | Name |
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160 +========+=====================+
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161 | Red | Daniel |
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162 +--------+---------------------+
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163 | Blue | Eric; Darian; Emily |
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164 +--------+---------------------+
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165
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166 --------
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167
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168 **Example collapse with two key columns**
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169
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170 Same input table, now our key columns are "Colour" and "Food" which could be input as "2,3" (-F -f)
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171 and the same value column which would generate the following table:
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172
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173 +--------+----------+-------------+
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174 | Colour | Food | Name |
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175 +========+==========+=============+
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176 | Blue | Pancakes | Darian |
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177 +--------+----------+-------------+
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178 | Red | Apples | Daniel |
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179 +--------+----------+-------------+
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180 | Blue | Apples | Eric; Emily |
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181 +--------+----------+-------------+
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182
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183 ----
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184
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185 @HELP_COLUMNS@
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186
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187
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188 @HELP_END_STATEMENT@
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189
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190
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191 ]]></help>
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192 <expand macro="citations" />
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193 </tool>