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annotate runsim.xml @ 10:f60bb19f7880 draft default tip

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/37cec685ade2bbd92376a2a1716ace3b9beab6f9 commit 37cec685ade2bbd92376a2a1716ace3b9beab6f9-dirty"
author siwaa
date Mon, 21 Nov 2022 16:00:30 +0000
parents eff04f7eec9f
children
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10
f60bb19f7880 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/37cec685ade2bbd92376a2a1716ace3b9beab6f9 commit 37cec685ade2bbd92376a2a1716ace3b9beab6f9-dirty"
siwaa
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1 <tool id="CarboSeqRunSim" name="CarboSeqRunSim" version="1.2.0">
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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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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>
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f60bb19f7880 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/37cec685ade2bbd92376a2a1716ace3b9beab6f9 commit 37cec685ade2bbd92376a2a1716ace3b9beab6f9-dirty"
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4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.2.0</container>
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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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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[
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eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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7 bash -e -c "mkdir inputs &&
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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8 cp ${meteo_data} inputs/meteo.csv &&
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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9 cp ${crop_data} inputs/crop.csv &&
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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10 cp ${soil_data} inputs/soil.csv &&
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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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11 mkdir output &&
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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12 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
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eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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13 export CSVMAPPER_INPUT_DIR=\$(realpath -s inputs) &&
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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14 #if $id_pairs
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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15 export CSOPRALIBS_ID_IDSUCC_CSV_FILE=${id_pairs} &&
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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16 #end if
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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17 export CSOPRALIBS_SIM_PARAMS_IMPLEMENTATION=${simulator} &&
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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18 Rscript /usr/local/src/myscripts/usercases/run-sim/run.r &&
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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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19 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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20 ]]>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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21 </command>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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22 <inputs>
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eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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23 <param name="simulator" type="select" label="Simulator">
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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24 <option value="rothC" selected="true">rothC</option>
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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25 <option value="soilr">soilr</option>
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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26 </param>
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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27 <param name="meteo_data" type="data" format="csv" label="Meteo data (csv file)"/>
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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28 <param name="crop_data" type="data" format="csv" label="Crop data (csv file)"/>
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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29 <param name="soil_data" type="data" format="csv" label="Soil data (csv file)"/>
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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30 <param name="id_pairs" type="data" optional="true" format="csv" label="Id pairs (csv file)"/>
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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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31 </inputs>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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32 <outputs>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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33 <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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34 </outputs>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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35 <tests>
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eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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36 <test>
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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37 <param name="simulator" value="rothC" />
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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38 <param name="id_pairs" value="outputs/id-idSucc-pairs.csv" ftype="csv"/>
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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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39 <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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40 <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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41 <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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42 <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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43 <assert_contents>
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f60bb19f7880 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/37cec685ade2bbd92376a2a1716ace3b9beab6f9 commit 37cec685ade2bbd92376a2a1716ace3b9beab6f9-dirty"
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44 <has_size value="4741" delta="100" />
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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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45 </assert_contents>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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46 </output>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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47 </test>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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48 </tests>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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49 <help>
8
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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50 the CarboSeq run-sim tool
eff04f7eec9f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
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51 ==========================
7
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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52
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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53 credits
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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54 -------
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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55
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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56 - 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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57 - 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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58 - Copyright: INRAE
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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59 </help>
39eb9b8f63e6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
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60 </tool>