Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.xml @ 9:2a6d7d053ba7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
author siwaa
date Mon, 25 Sep 2023 16:25:51 +0000
parents 0625e6a639ea
children f707c2fb725b
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1 <tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.4">
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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:b782e0b7ce3af7e7a14a87ea750145ed1c2595a0</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 str( $IterUsmX.IterUsmX ) == 'usmx_one_after_other':
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9 parallel=${$IterUsmX.parallel} &&
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10 #else
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11 parallel=parallel &&
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12 #end if
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13 bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX.IterUsmX} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} ${GeneratedWorkspace}
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
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18 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>
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19 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
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20 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
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21 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
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22 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
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23 <param name="Tag" type="text" value="" label="Outputs tag"/>
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24 <conditional name="IterUsmX">
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25 <param name="IterUsmX" type="boolean" checked="true" truevalue="usmx_one_after_other" falsevalue="usmx_at_once"/>
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26 <when value="usmx_one_after_other">
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27 <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
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28 </when>
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29 <when value="usmx_at_once">
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30 </when>
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31 </conditional>
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32 </inputs>
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33 <outputs>
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34 <data format="zip" name="GeneratedWorkspace"
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35 label="GeneratedWorkspace${Tag}">
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36 </data>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="parallel" value="false" ftype="boolean" />
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41 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
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42 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
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43 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
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44 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
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45 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
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46 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
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47 <output name="GeneratedWorkspace" ftype="zip" >
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48 <assert_contents>
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49 <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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50 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
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51 </has_archive_member>
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52 <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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53 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
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54 </has_archive_member>
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55 <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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56 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
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57 </has_archive_member>
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58 <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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59 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
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60 </has_archive_member>
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61 <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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62 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
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63 </has_archive_member>
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64 <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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65 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
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66 </has_archive_member>
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67 <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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68 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
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69 </has_archive_member>
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70 <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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71 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
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72 </has_archive_member>
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73 <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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74 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
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75 </has_archive_member>
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76 <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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77 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
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78 </has_archive_member>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <test>
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83 <param name="parallel" value="true" ftype="boolean" />
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84 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
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85 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
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86 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
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87 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
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88 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
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89 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
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90 <output name="GeneratedWorkspace" ftype="zip" >
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91 <assert_contents>
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92 <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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93 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
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94 </has_archive_member>
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95 <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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96 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
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97 </has_archive_member>
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98 <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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99 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
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100 </has_archive_member>
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101 <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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102 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
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103 </has_archive_member>
0625e6a639ea "planemo upload for repository https://forgemia.inra.fr/redelac commit 2574be7ccd1fe343e6a8b0e4535e5db43008945f"
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104 <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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105 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
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106 </has_archive_member>
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107 <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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108 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
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109 </has_archive_member>
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110 <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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111 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
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112 </has_archive_member>
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113 <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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114 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
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115 </has_archive_member>
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116 <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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117 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
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118 </has_archive_member>
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119 <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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120 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
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121 </has_archive_member>
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122 </assert_contents>
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123 </output>
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124 </test>
0
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125 </tests>
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126 <help>
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127 *The usage of this tool is restricted to the user of the stics_authorized group.*
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128
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129 *To be granted, apply to the Project Stics Team and then request to SIWAA*
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130
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131 Documentation
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132 -------------
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133 A tool to generate Stics Inputs according to a plan for REDELAC
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134
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135 Credits
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136 -------
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137 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
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138 - Stics Site: https://www6.paca.inra.fr/stics_eng
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139 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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140 - Copyright: INRAE
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141 </help>
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142 </tool>