Mercurial > repos > sblanck > mpagenomics
annotate selectionExtracted.xml @ 5:4f753bb8681e draft
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
| author | sblanck |
|---|---|
| date | Tue, 20 Apr 2021 13:11:24 +0000 |
| parents | 3fcbb8030fcc |
| children | 7076911e5c64 |
| rev | line source |
|---|---|
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5
4f753bb8681e
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
sblanck
parents:
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1 <tool id="markersSelection" name="Markers selection" version="1.3.0"> |
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4
3fcbb8030fcc
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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2 <requirements> |
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3fcbb8030fcc
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
sblanck
parents:
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3 <container type="docker">sblanck/mpagenomicsdependencies</container> |
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3fcbb8030fcc
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
sblanck
parents:
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4 </requirements> |
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0
4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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5 <description> of previously extracted signal</description> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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6 <command> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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7 <![CDATA[ |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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8 Rscript |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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9 ${__tool_directory__}/selectionExtracted.R |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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10 --input '$input' |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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11 --response '$response' |
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3fcbb8030fcc
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
sblanck
parents:
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12 --new_file_path '$output.extra_files_path' |
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0
4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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13 --folds '$folds' |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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14 --loss '$loss' |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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15 --outputlog '$outputlog' |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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16 --output '$output' |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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17 --log '$log' |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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18 ]]> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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19 </command> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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20 <inputs> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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21 <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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22 <param name="response" type="data" format="csv" label="Data response" help="Data response csv file. See below for more information on file format" /> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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23 <param name="folds" type="integer" min="1" value="10" label ="Number of folds for cross validation" help="Integer between 1 and number of file in the .cel file dataset"/> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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24 <param name="loss" type="select" multiple="false" label="Response type"> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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25 <option value="linear">Linear</option> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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26 <option value="logistic">Logistic</option> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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27 </param> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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28 |
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5
4f753bb8681e
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
sblanck
parents:
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29 <!--param name="outputgraph" type="select" label="Output figures"> |
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0
4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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30 <option value="TRUE">Yes</option> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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31 <option value="FALSE">No</option> |
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5
4f753bb8681e
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
sblanck
parents:
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32 </param--> |
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0
4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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33 <param name="outputlog" type="select" label="Output log"> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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34 <option value="TRUE">Yes</option> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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35 <option value="FALSE">No</option> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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36 </param> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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37 </inputs> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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38 <outputs> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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39 <data format="tabular" name="output" label="selection of ${input.name}" /> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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40 <data format="log" name="log" label="log of selection of ${input.name}" > |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
parents:
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41 <filter>outputlog == "TRUE"</filter> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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42 </data> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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43 </outputs> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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44 <stdio> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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45 <exit_code range="1:" level="fatal" description="See logs for more details" /> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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46 </stdio> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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47 <help> |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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48 **What it does** |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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parents:
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49 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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50 This tool selects some relevant markers according to a response using penalized regressions. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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51 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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52 Input: |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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53 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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54 *A tabular text file containing 3 fixed columns and 1 column per sample:* |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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55 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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56 - chr: Chromosome. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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57 - position: Genomic position (in bp). |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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58 - probeNames: Names of the probes. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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59 - One column per sample which contain the copy number signal for each sample. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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60 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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61 Output: |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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62 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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63 *A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNP):* |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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64 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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65 - chr: Chromosome containing the selected SNP. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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66 - position: Position of the selected SNP. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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67 - index: Index of the selected SNP. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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68 - names: Name of the selected SNP. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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69 - coefficient: Regression coefficient of the selected SNP. |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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70 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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71 ----- |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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72 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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73 **Data Response csv file** |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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74 |
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4d539083cf7f
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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75 Data response csv file format: |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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76 |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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77 - The first column contains the names of the different files of the dataset. |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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78 |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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79 - The second column is the response associated with each file. |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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80 |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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81 - Column names of these two columns are respectively files and response. |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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82 |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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83 - Columns are separated by a comma |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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84 |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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85 - *Extensions of the files (.CEL for example) should be removed* |
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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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86 |
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87 |
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88 |
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89 **Example** |
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90 |
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91 Let 3 .cel files in the studied dataset :: |
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92 |
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93 patient1.cel |
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94 patient2.cel |
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95 patient3.cel |
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96 |
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97 The csv file should look like this :: |
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98 |
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99 files,response |
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100 patient1,1.92145 |
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101 patient2,2.12481 |
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102 patient3,1.23545 |
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103 |
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104 |
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105 ----- |
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106 |
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107 **Citation** |
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108 |
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109 If you use this tool please cite : |
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110 |
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111 `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ |
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112 |
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113 </help> |
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114 </tool> |