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annotate runsim.xml @ 7:39eb9b8f63e6 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
author siwaa
date Mon, 05 Sep 2022 07:54:50 +0000
parents
children eff04f7eec9f
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39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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1 <tool id="CarboSeqRunSim" name="CarboSeqRunSim" version="1.0.0">
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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2 <description>To run the simulator</description>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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3 <requirements>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.0.0</container>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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5 </requirements>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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6 <command detect_errors="exit_code"><![CDATA[
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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7 bash -e -c "mkdir -p data/client.files &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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8 cp ${meteo_data} data/client.files/meteo.csv &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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9 cp ${crop_data} data/client.files/crop.csv &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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10 cp ${soil_data} data/client.files/soil.csv &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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11 mkdir -p data/mapping.files &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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12 cp ${crop_mapping} data/mapping.files/crop.mapping.csv &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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13 cp ${property_mapping} data/mapping.files/property.mapping.csv &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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14 mkdir output &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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15 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
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16 cp /usr/local/src/myscripts/usercases/run-sim/run.r . &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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17 Rscript run.r &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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18 cp output/SimulationSOCResults.RData ${run_output}"
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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19 ]]>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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20 </command>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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21 <inputs>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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22 <param name="meteo_data" type="data" format="csv" label="meteo data (csv file)"/>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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23 <param name="crop_data" type="data" format="csv" label="crop data (csv file)"/>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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24 <param name="soil_data" type="data" format="csv" label="soil data (csv file)"/>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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25 <param name="crop_mapping" type="data" format="csv" label="crop mapping (csv file)"/>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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26 <param name="property_mapping" type="data" format="csv" label="property mapping (csv file)"/>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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27 </inputs>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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28 <outputs>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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29 <data format='rdata' name="run_output" label="Simulation SOC Results"/>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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30 </outputs>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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31 <tests>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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32 <test>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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33 <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" />
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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34 <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" />
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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35 <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" />
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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36 <param name="crop_mapping" value="inputs/mapping.files/crop.mapping.csv" ftype="csv" />
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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37 <param name="property_mapping" value="inputs/mapping.files/property.mapping.csv" ftype="csv"/>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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38 <output name="run_output">
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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39 <assert_contents>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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40 <has_size value="5462" delta="100" />
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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41 </assert_contents>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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42 </output>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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43 </test>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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44 </tests>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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45 <help>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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46 the CarboSeqPrepareSim tool
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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47 ===========================
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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48
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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49 credits
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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50 -------
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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51
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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52 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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53 - Tool Maintainer: Eric Casellas eric.casellas@inrae.fr
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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54 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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55 - Copyright: INRAE
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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56 </help>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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57 </tool>