Mercurial > repos > siwaa > carboseq
annotate findidpairs.xml @ 10:f60bb19f7880 draft default tip
"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 | b75e5e1a0646 |
| children |
| rev | line source |
|---|---|
|
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="CarboSeqFindIdPairs" name="CarboSeqFindIdPairs" version="1.2.0"> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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2 <description>To get IdPairs</description> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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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"
siwaa
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4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.2.0</container> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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5 </requirements> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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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"
siwaa
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7 bash -e -c "mkdir inputs && |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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8 cp ${meteo_data} inputs/meteo.csv && |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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9 cp ${crop_data} inputs/crop.csv && |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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10 cp ${soil_data} inputs/soil.csv && |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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11 mkdir output && |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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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"
siwaa
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13 export CSVMAPPER_INPUT_DIR=\$(realpath -s inputs) && |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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14 Rscript /usr/local/src/myscripts/usercases/find-idPairs/run.r && |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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15 cp output/id-idSucc-pairs.csv ${findpairs_output}" |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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16 ]]> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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17 </command> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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18 <inputs> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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19 <param name="meteo_data" type="data" format="csv" label="Meteo data (csv file)"/> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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20 <param name="crop_data" type="data" format="csv" label="Crop data (csv file)"/> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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21 <param name="soil_data" type="data" format="csv" label="Soil data (csv file)"/> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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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"
siwaa
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23 <outputs> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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24 <data format='csv' name="findpairs_output" label="IdPairs"/> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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25 </outputs> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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26 <tests> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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27 <test> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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28 <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" /> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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29 <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" /> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
parents:
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30 <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" /> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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31 <output name="findpairs_output" file="outputs/id-idSucc-pairs.csv" /> |
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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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32 </test> |
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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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33 </tests> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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34 <help> |
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eff04f7eec9f
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
siwaa
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35 the CarboSeq find-idpairs tool |
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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 ============================== |
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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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37 |
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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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38 credits |
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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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39 ------- |
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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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40 |
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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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41 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr |
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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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42 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq |
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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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43 - Copyright: INRAE |
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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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44 </help> |
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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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45 </tool> |