Mercurial > repos > siwaa > carboseq_s

annotate carboseqSimulator.xml @ 17:56b0bf51585a draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/806f38d2aa86cb93ec97c29004b0b8cc5bc28033/toos/CarboSeqSimulator commit 806f38d2aa86cb93ec97c29004b0b8cc5bc28033-dirty"
author siwaa
date Thu, 19 Dec 2024 08:20:55 +0000
parents 5ed871d666b4
children ce2b35fc669b
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56b0bf51585a "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/806f38d2aa86cb93ec97c29004b0b8cc5bc28033/toos/CarboSeqSimulator commit 806f38d2aa86cb93ec97c29004b0b8cc5bc28033-dirty"
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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.19">
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2 <description>To run the CarboSeq simulator</description>
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3 <requirements>
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2af4b1e46d90 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/0376c8590ba7b401f91db9be50a49e03cf5044fb/toos/CarboSeqSimulator commit 0376c8590ba7b401f91db9be50a49e03cf5044fb-dirty"
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4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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7 (env | grep DOCKER_IMAGE) &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
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9ad79c2d8e0b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/75b22cbc75bbd0c301eabef3a734ca47468bb47e/toos/CarboSeqSimulator commit 75b22cbc75bbd0c301eabef3a734ca47468bb47e-dirty"
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9 export "TMPDIR=\$(realpath -s tmp)" &&
9ad79c2d8e0b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/75b22cbc75bbd0c301eabef3a734ca47468bb47e/toos/CarboSeqSimulator commit 75b22cbc75bbd0c301eabef3a734ca47468bb47e-dirty"
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10 bash -e -c "
9ad79c2d8e0b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/75b22cbc75bbd0c301eabef3a734ca47468bb47e/toos/CarboSeqSimulator commit 75b22cbc75bbd0c301eabef3a734ca47468bb47e-dirty"
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11 echo \$TMPDIR &&
9ad79c2d8e0b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/75b22cbc75bbd0c301eabef3a734ca47468bb47e/toos/CarboSeqSimulator commit 75b22cbc75bbd0c301eabef3a734ca47468bb47e-dirty"
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12 mkdir tmp &&
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7e43dc776bda "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/6d8408bc51a9a3e037181e8ca08212a5c96f2321/toos/CarboSeqSimulator commit 6d8408bc51a9a3e037181e8ca08212a5c96f2321-dirty"
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13 mkdir output &&
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14 unzip -d input ${input} &&
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15 cp /usr/local/src/myscripts/semantifier.jar . &&
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16 cp /usr/local/src/myscripts/start_server.sh . &&
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17 cp -r /usr/local/src/myscripts/config_mappers . &&
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18 cp -r /usr/local/src/myscripts/data . &&
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19 cp /usr/local/src/myscripts/scenarios/run-sim-perf/run.r . &&
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56b0bf51585a "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/806f38d2aa86cb93ec97c29004b0b8cc5bc28033/toos/CarboSeqSimulator commit 806f38d2aa86cb93ec97c29004b0b8cc5bc28033-dirty"
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20 set -a && . /usr/local/src/myscripts/.env && set +a &&
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5ed871d666b4 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/be8c2ab794a3722ee6edc3c9f7e73ccc45806f31/toos/CarboSeqSimulator commit be8c2ab794a3722ee6edc3c9f7e73ccc45806f31-dirty"
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21 Rscript ./run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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22 cp output/* ${output}"
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
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27 <param name="semantifier" type="select" label="Choose the semantifier mode:">
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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28 <option value="modeltoolbox_sem_local" selected="true">local</option>
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29 <option value="modeltoolbox_sem_remote">remote</option>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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30 </param>
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31 </inputs>
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32 <outputs>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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33 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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34 </outputs>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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35 <tests>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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36 <test>
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37 <param name="input" value="input/inputFiles.zip" ftype="zip" />
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38 <param name="semantifier" value="modeltoolbox_sem_local" />
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39 <output name="output" ftype="rdata" >
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40 <assert_contents>
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41 <has_size value="595" negate="false" />
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42 <has_size value="0" negate="true" />
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43 </assert_contents>
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44 </output>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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45 </test>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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46 <test>
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47 <param name="input" value="input/inputFiles.zip" ftype="zip" />
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48 <param name="semantifier" value="modeltoolbox_sem_remote" />
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49 <output name="output" ftype="rdata" >
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50 <assert_contents>
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51 <has_size value="595" negate="false" />
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52 <has_size value="0" negate="true" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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57 <help>
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58 the CarboSeq CarboseqSimulator tool
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59 ===================================
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60
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61 credits
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62 -------
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63 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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64 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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65 - Copyright: INRAE
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66 </help>
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67 </tool>