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comparison redelacSticsInputGenerator.xml @ 14:812bb8097dac draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit d16b9ecdb4dd51b69a6aaa4ab298b82455fe0267"
author siwaa
date Tue, 12 Dec 2023 10:38:20 +0000
parents 3db1f57029a7
children 413cec4dfe5f
comparison
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13:3db1f57029a7 14:812bb8097dac
1 <tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.7"> 1 <tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.8">
2 <description>to run generate Stics Inputs for REDELAC</description> 2 <description>to run generate Stics Inputs for REDELAC</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:0faa63e7838a2b86369026bf2e628842d7af9863</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:fc777963cf7921da512ee8b091f4cebcfd1fbe19</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"> 6 <command detect_errors="aggressive">
7 <![CDATA[ 7 <![CDATA[
8 #if $additional: 8 #if $additional:
9 additional=${additional} && 9 additional=${additional} &&
10 #else 10 #else
11 additional=noAdditionalPlantOrConfig && 11 additional=noAdditionalPlantOrConfig &&
12 #end if 12 #end if
13 #if str( $IterUsmX.IterUsmX ) == 'usmx_one_after_other': 13 #if $REDELAC.optim == 'optim':
14 parallel=${$IterUsmX.parallel} && 14 parallel=${$REDELAC.parallel} &&
15 #else 15 #else
16 parallel=parallel && 16 parallel=sequential &&
17 #end if 17 #end if
18 bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX.IterUsmX} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress} 18 bash $__tool_directory__/redelacSticsInputGenerator.bash ${REDELAC.optim} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress}
19 ]]> 19 ]]>
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/> 22 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
23 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/> 23 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>
24 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/> 24 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
25 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/> 25 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
26 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/> 26 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
27 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/> 27 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
28 <param name="additional" type="data" optional="true" format="zip" label="[optional] Select a zipped archive with folder plant (and or) config (zip file)"/> 28 <param name="additional" type="data" optional="true" format="zip" label="[optional] Select a zipped archive with folder plant (and or) config (zip file)"/>
29 <conditional name="IterUsmX"> 29 <conditional name="REDELAC">
30 <param name="IterUsmX" type="boolean" checked="true" truevalue="usmx_one_after_other" falsevalue="usmx_at_once"/> 30 <param name="optim" type="boolean" checked="true" truevalue="optim" falsevalue="noptim" label="To speed up the xml2txt conversion process by generating file only once"/>
31 <when value="usmx_one_after_other"> 31 <when value="optim">
32 <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/> 32 <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential" label="To parallelize the xml2txt conversion process" />
33 </when> 33 </when>
34 <when value="usmx_at_once"> 34 <when value="noptim">
35 </when> 35 </when>
36 </conditional> 36 </conditional>
37 <param name="compress" type="boolean" checked="true" truevalue="-6" falsevalue="-0"/> 37 <param name="compress" type="boolean" checked="true" truevalue="-6" falsevalue="-0" label="To compress or not the output(compressing does slow down the job)"/>
38 </inputs> 38 </inputs>
39 <outputs> 39 <outputs>
40 <data format="zip" name="GeneratedWorkspace" 40 <data format="zip" name="GeneratedWorkspace"
41 label="GeneratedWorkspace$"> 41 label="GeneratedWorkspace$">
42 </data> 42 </data>
43 </outputs> 43 </outputs>
44 <tests> 44 <tests>
45 <test> 45 <test>
46 <param name="optim" value="false" ftype="boolean" />
47 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
48 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
49 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
50 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
51 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
52 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
53 <output name="GeneratedWorkspace" ftype="zip" >
54 <assert_contents>
55 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
56 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
57 </has_archive_member>
58 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
59 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
60 </has_archive_member>
61 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
62 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
63 </has_archive_member>
64 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
65 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
66 </has_archive_member>
67 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
68 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
69 </has_archive_member>
70 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
71 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
72 </has_archive_member>
73 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
74 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
75 </has_archive_member>
76 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
77 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
78 </has_archive_member>
79 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
80 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
81 </has_archive_member>
82 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
83 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
84 </has_archive_member>
85 </assert_contents>
86 </output>
87 </test>
88 <test>
46 <param name="parallel" value="false" ftype="boolean" /> 89 <param name="parallel" value="false" ftype="boolean" />
47 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" /> 90 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
48 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" /> 91 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
49 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" /> 92 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
50 <param name="Tec" value="input/TecSheet.csv" ftype="csv" /> 93 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
172 </assert_contents> 215 </assert_contents>
173 </output> 216 </output>
174 </test> 217 </test>
175 </tests> 218 </tests>
176 <help> 219 <help>
177 *The usage of this tool is restricted to the user of the stics_authorized group.* 220 *The usage of this tool is restricted to the user of the redelac_authorized group.*
178 221
179 *To be granted, apply to the Project Stics Team and then request to SIWAA* 222 *To be granted, apply to the REDELAC Project Team and then request to SIWAA*
180 223
181 Documentation 224 Documentation
182 ------------- 225 -------------
183 A tool to generate Stics Inputs according to a plan for REDELAC 226 A tool to generate Stics Inputs according to a plan for REDELAC
184 227