Mercurial > repos > siwaa > carboseq_s

annotate carboseqSimulator.xml @ 12:7e43dc776bda draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/6d8408bc51a9a3e037181e8ca08212a5c96f2321/toos/CarboSeqSimulator commit 6d8408bc51a9a3e037181e8ca08212a5c96f2321-dirty"
author siwaa
date Thu, 19 Sep 2024 15:58:11 +0000
parents 097985b1b7c6
children 9ad79c2d8e0b
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097985b1b7c6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/f3192a3a79e9265b088c9c126972718cfb375643/toos/CarboSeqSimulator commit f3192a3a79e9265b088c9c126972718cfb375643-dirty"
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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.16">
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2 <description>To run the CarboSeq simulator</description>
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097985b1b7c6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/f3192a3a79e9265b088c9c126972718cfb375643/toos/CarboSeqSimulator commit f3192a3a79e9265b088c9c126972718cfb375643-dirty"
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3 <environment_variables>
097985b1b7c6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/f3192a3a79e9265b088c9c126972718cfb375643/toos/CarboSeqSimulator commit f3192a3a79e9265b088c9c126972718cfb375643-dirty"
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4 <environment_variable name="TMPDIR">\$(realpath -s tmp)</environment_variable>
097985b1b7c6 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/f3192a3a79e9265b088c9c126972718cfb375643/toos/CarboSeqSimulator commit f3192a3a79e9265b088c9c126972718cfb375643-dirty"
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5 </environment_variables>
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6 <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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7 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
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8 </requirements>
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9 <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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10 (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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11 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
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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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12 bash -e -c "mkdir tmp &&
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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f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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15 cp /usr/local/src/myscripts/semantifier.jar . &&
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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16 cp /usr/local/src/myscripts/start_server.sh . &&
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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17 cp -r /usr/local/src/myscripts/config_mappers . &&
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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18 cp -r /usr/local/src/myscripts/data . &&
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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19 Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${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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20 cp output/* ${output}"
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
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25 <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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26 <option value="modeltoolbox_sem_local" selected="true">local</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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27 <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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28 </param>
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29 </inputs>
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30 <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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31 <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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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 <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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34 <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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35 <param name="input" value="input/40Sites.zip" ftype="zip" />
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 <param name="semantifier" value="modeltoolbox_sem_local" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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37 <output name="output" ftype="rdata" >
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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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38 <assert_contents>
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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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39 <has_size value="1202" negate="false" />
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40 <has_size value="0" negate="true" />
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41 </assert_contents>
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42 </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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43 </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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44 <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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45 <param name="input" value="input/40Sites.zip" ftype="zip" />
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 <param name="semantifier" value="modeltoolbox_sem_remote" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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47 <output name="output" ftype="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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48 <assert_contents>
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49 <has_size value="1202" negate="false" />
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f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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50 <has_size value="0" negate="true" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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51 </assert_contents>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
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52 </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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53 </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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54 </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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55 <help>
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56 the CarboSeq CarboseqSimulator tool
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57 ===================================
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58
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59 credits
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60 -------
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61 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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62 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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63 - Copyright: INRAE
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64 </help>
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65 </tool>