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comparison redelacSticsTool.xml @ 0:7f8f474a7bd7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
author siwaa
date Tue, 06 Feb 2024 09:21:00 +0000
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children ed9c49c6c6e1
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-1:000000000000 0:7f8f474a7bd7
1 <tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.0">
2 <description>to run Stics for REDELAC</description>
3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:1cadd3c67d29b07acb658836292f286e62922c5b</container>
5 </requirements>
6 <command detect_errors="aggressive">
7 <![CDATA[
8 #if $additional:
9 additional=${additional} &&
10 #else
11 additional=noAdditionalPlantOrConfig &&
12 #end if
13 #if $REDELAC.optim == 'optim':
14 parallel=${$REDELAC.parallel} &&
15 #else
16 parallel=sequential &&
17 #end if
18 bash $__tool_directory__/redelacSticsTool.bash ${REDELAC.optim} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress} ${outputsOnly} ${Scenario} ${SimulationResults} ${SuccessionPlan}
19 ]]>
20 </command>
21 <inputs>
22 <param name="Scenario" type="text" value="scenarioName" label="Scenario Name"/>
23 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
24 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>
25 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
26 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
27 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
28 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
29 <param name="additional" type="data" optional="true" format="zip" label="[optional] Select a zipped archive with folder plant (and or) config (zip file)"/>
30 <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
31 <conditional name="REDELAC">
32 <param name="optim" type="boolean" checked="true" truevalue="optim" falsevalue="noptim" label="To speed up the xml2txt conversion process by generating file only once"/>
33 <when value="optim">
34 <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential" label="To parallelize the xml2txt conversion process" />
35 </when>
36 <when value="noptim">
37 </when>
38 </conditional>
39 <param name="outputsOnly" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="To get results only"/>
40 <param name="compress" type="boolean" checked="true" truevalue="-6" falsevalue="-0" label="To compress or not the output(compressing does slow down the job)"/>
41 </inputs>
42 <outputs>
43 <data format="zip" name="SimulationResults"
44 label="SticsOnResults">
45 </data>
46 <data format="zip" name="GeneratedWorkspace"
47 label="GeneratedWorkspace$">
48 <filter>outputsOnly == 'yes'</filter>
49 </data>
50 </outputs>
51 <tests>
52 <test>
53 <param name="optim" value="false" ftype="boolean" />
54 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
55 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
56 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
57 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
58 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
59 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
60 <output name="GeneratedWorkspace" ftype="zip" >
61 <assert_contents>
62 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
63 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
64 </has_archive_member>
65 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
66 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
67 </has_archive_member>
68 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
69 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
70 </has_archive_member>
71 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
72 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
73 </has_archive_member>
74 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
75 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
76 </has_archive_member>
77 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
78 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
79 </has_archive_member>
80 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
81 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
82 </has_archive_member>
83 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
84 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
85 </has_archive_member>
86 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
87 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
88 </has_archive_member>
89 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
90 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
91 </has_archive_member>
92 </assert_contents>
93 </output>
94 </test>
95 <test>
96 <param name="parallel" value="false" ftype="boolean" />
97 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
98 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
99 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
100 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
101 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
102 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
103 <output name="GeneratedWorkspace" ftype="zip" >
104 <assert_contents>
105 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
106 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
107 </has_archive_member>
108 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
109 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
110 </has_archive_member>
111 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
112 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
113 </has_archive_member>
114 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
115 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
116 </has_archive_member>
117 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
118 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
119 </has_archive_member>
120 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
121 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
122 </has_archive_member>
123 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
124 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
125 </has_archive_member>
126 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
127 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
128 </has_archive_member>
129 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
130 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
131 </has_archive_member>
132 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
133 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
134 </has_archive_member>
135 </assert_contents>
136 </output>
137 </test>
138 <test>
139 <param name="parallel" value="true" ftype="boolean" />
140 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
141 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
142 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
143 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
144 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
145 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
146 <output name="GeneratedWorkspace" ftype="zip" >
147 <assert_contents>
148 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
149 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
150 </has_archive_member>
151 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
152 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
153 </has_archive_member>
154 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
155 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
156 </has_archive_member>
157 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
158 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
159 </has_archive_member>
160 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
161 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
162 </has_archive_member>
163 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
164 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
165 </has_archive_member>
166 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
167 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
168 </has_archive_member>
169 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
170 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
171 </has_archive_member>
172 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
173 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
174 </has_archive_member>
175 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
176 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
177 </has_archive_member>
178 </assert_contents>
179 </output>
180 </test>
181 <test>
182 <param name="compress" value="false" ftype="boolean" />
183 <param name="parallel" value="true" ftype="boolean" />
184 <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
185 <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />
186 <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
187 <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
188 <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
189 <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
190 <output name="GeneratedWorkspace" ftype="zip" >
191 <assert_contents>
192 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
193 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
194 </has_archive_member>
195 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
196 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
197 </has_archive_member>
198 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
199 <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
200 </has_archive_member>
201 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
202 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
203 </has_archive_member>
204 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
205 <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
206 </has_archive_member>
207 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
208 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
209 </has_archive_member>
210 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
211 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
212 </has_archive_member>
213 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
214 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
215 </has_archive_member>
216 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
217 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
218 </has_archive_member>
219 <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
220 <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
221 </has_archive_member>
222 </assert_contents>
223 </output>
224 </test>
225 </tests>
226 <help>
227 *The usage of this tool is restricted to the user of the redelac_authorized group.*
228
229 *To be granted, apply to the REDELAC Project Team and then request to SIWAA*
230
231 Documentation
232 -------------
233 A tool to generate Stics Inputs according to a plan for REDELAC
234
235 Credits
236 -------
237 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
238 - Stics Site: https://www6.paca.inra.fr/stics_eng
239 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
240 - Copyright: INRAE
241 </help>
242 </tool>