Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.xml @ 12:9f398c5117d2 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 1ce7fafc21b8753e295caa8b7eda709ba1d18544"
author siwaa
date Tue, 17 Oct 2023 11:21:36 +0000
parents 423950cd59cb
children 3db1f57029a7
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1 <tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.6">
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2 <description>to run generate Stics Inputs for REDELAC</description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:b0f76897e1ece4a91ecfc71617fec5ebd04e2bd4</container>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 <![CDATA[
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8 #if $additional:
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9 additional=${additional} &&
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10 #else
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11 additional=noAdditionalPlantOrConfig &&
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12 #end if
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13 #if str( $IterUsmX.IterUsmX ) == 'usmx_one_after_other':
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14 parallel=${$IterUsmX.parallel} &&
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15 #else
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16 parallel=parallel &&
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17 #end if
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18 bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX.IterUsmX} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace}
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
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23 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>
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24 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
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25 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
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26 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
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27 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
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28 <param name="additional" type="data" optional="true" format="zip" label="[optional] Select a zipped archive with folder plant (and or) config (zip file)"/>
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29 <conditional name="IterUsmX">
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30 <param name="IterUsmX" type="boolean" checked="true" truevalue="usmx_one_after_other" falsevalue="usmx_at_once"/>
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31 <when value="usmx_one_after_other">
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32 <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
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33 </when>
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34 <when value="usmx_at_once">
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data format="zip" name="GeneratedWorkspace"
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40 label="GeneratedWorkspace$">
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41 </data>
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42 </outputs>
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43 <tests>
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44 <test>
9
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45 <param name="parallel" value="false" ftype="boolean" />
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46 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
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47 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
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48 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
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49 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
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50 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
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51 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
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52 <output name="GeneratedWorkspace" ftype="zip" >
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53 <assert_contents>
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54 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
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55 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
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56 </has_archive_member>
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57 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
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58 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
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59 </has_archive_member>
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60 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
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61 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
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62 </has_archive_member>
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63 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
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64 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
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65 </has_archive_member>
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66 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
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67 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
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68 </has_archive_member>
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69 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
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70 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
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71 </has_archive_member>
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72 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
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73 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
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74 </has_archive_member>
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75 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
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76 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
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77 </has_archive_member>
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78 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
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79 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
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80 </has_archive_member>
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81 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
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82 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
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83 </has_archive_member>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <test>
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88 <param name="parallel" value="true" ftype="boolean" />
8
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89 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
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90 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
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91 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
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92 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
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93 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
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94 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
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95 <output name="GeneratedWorkspace" ftype="zip" >
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96 <assert_contents>
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97 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
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98 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
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99 </has_archive_member>
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100 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
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101 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
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102 </has_archive_member>
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103 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
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104 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
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105 </has_archive_member>
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106 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
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107 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
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108 </has_archive_member>
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109 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
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110 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
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111 </has_archive_member>
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112 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
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113 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
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114 </has_archive_member>
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115 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
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116 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
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117 </has_archive_member>
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118 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
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119 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
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120 </has_archive_member>
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121 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
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122 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
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123 </has_archive_member>
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124 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
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125 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
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126 </has_archive_member>
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127 </assert_contents>
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128 </output>
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129 </test>
0
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130 </tests>
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131 <help>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
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132 *The usage of this tool is restricted to the user of the stics_authorized group.*
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133
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134 *To be granted, apply to the Project Stics Team and then request to SIWAA*
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135
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136 Documentation
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137 -------------
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
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138 A tool to generate Stics Inputs according to a plan for REDELAC
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139
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140 Credits
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141 -------
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142 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
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143 - Stics Site: https://www6.paca.inra.fr/stics_eng
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144 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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145 - Copyright: INRAE
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146 </help>
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147 </tool>