Mercurial > repos > sblanck > mpagenomics

annotate selection.xml @ 0:4d539083cf7f draft

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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
author sblanck
date Tue, 12 May 2020 10:40:36 -0400
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4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
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1 <tool id="selection" name="Markers selection" force_history_refresh="True" version="0.1.0">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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2 <command>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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3 <![CDATA[
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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4 Rscript
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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5 ${__tool_directory__}/selection.R
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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6 --input '$input'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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7 --response '$response'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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8 --chrom '$chromosome'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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9 --new_file_path '$__new_file_path__'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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10 --settingsSignal '$settingsSNP.signal'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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11 #if $settingsSNP.signal == "CN":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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12 --settingsSnp '$settingsSNP.snp'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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13 #end if
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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14 #if $settingsSNP.signal == "fracB":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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15 --settingsSnp 'none'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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16 #end if
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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17 --settingsType '$settings.settingsType'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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18 #if $settings.settingsType == "tumor":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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19 --settingsType '$tumorcsv'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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20 #end if
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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21 #if $settings.settingsType == "standard":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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22 --settingsType 'none'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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23 #end if
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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24 --folds '$folds'
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25 --settingsLoss '$settingsLoss.loss'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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26 --outputgraph '$outputgraph'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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27 --output '$output'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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28 --pdffigures '$pdffigures'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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29 --outputlog '$outputlog'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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30 --log '$log'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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31 --userId '$__user_id__'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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32 #if $settingsLoss.loss == "linear":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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33 --settingsPackage '$settingsLoss.package'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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34 #end if
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35 #if $settingsLoss.loss == "logistic":
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36 --settingsPackage'HDPenReg'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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37 #end if
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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38 ]]>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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39 </command>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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40 <inputs>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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41 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
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42
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43 <param name="response" type="data" format="csv" label="Data response" help="Data response csv file. See below for more information on file format" />
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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44
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45 <param name="chromosome" type="select" size="6" multiple="true" label="Chromosomes">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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46 <option value="1">chr 1</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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47 <option value="2">chr 2</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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48 <option value="3">chr 3</option>
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49 <option value="4">chr 4</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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50 <option value="5">chr 5</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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51 <option value="6">chr 6</option>
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52 <option value="7">chr 7</option>
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53 <option value="8">chr 8</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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54 <option value="9">chr 9</option>
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55 <option value="10">chr 10</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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56 <option value="11">chr 11</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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57 <option value="12">chr 12</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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58 <option value="13">chr 13</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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59 <option value="14">chr 14</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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60 <option value="15">chr 15</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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61 <option value="16">chr 16</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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62 <option value="17">chr 17</option>
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63 <option value="18">chr 18</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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64 <option value="19">chr 19</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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65 <option value="20">chr 20</option>
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66 <option value="21">chr 21</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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67 <option value="22">chr 22</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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68 <option value="23">chr 23</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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69 <option value="24">chr 24</option>
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70 <option value="25">chr 25</option>
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71 </param>
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72 <conditional name="settingsSNP">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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73 <param name="signal" type="select" multiple="false" label="Signal you want to work on">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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74 <option value="CN">CN</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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75 <option value="fracB">fracB</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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76 </param>
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77 <when value="fracB"/>
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78 <when value="CN">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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79 <param name="snp" type="select" label="Select Probes">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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80 <option value="FALSE">CN and SNP probes</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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81 <option value="TRUE">Only SNP probes</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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82 </param>
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83 </when>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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84 </conditional>
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85 <conditional name="settings">
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86 <param name="settingsType" type="select" label="Reference" help="">
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87 <option value="standard">Study without reference</option>
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88 <option value="tumor">Normal-tumor study</option>
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89 </param>
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90 <when value="standard" />
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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91 <when value="tumor">
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92 <param name="tumorcsv" type="data" format="csv" label="tumor boost csv file" help="Normal-tumor csv file. See below for more information."/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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93 </when>
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94 </conditional>
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95
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96 <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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97 <conditional name="settingsLoss">
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98 <param name="loss" type="select" multiple="false" label="Response type">
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99 <option value="linear">Linear</option>
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100 <option value="logistic">Logistic</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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101 </param>
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102 <when value="logistic" />
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103 <when value="linear">
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104 <param name="package" type="select" multiple="false" label="Method" help="Either “HDPenReg” or “spikeslab”. Used package in linear case">
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105 <option value="HDPenReg">HDPenReg</option>
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106 <option value="spikeslab">spikeslab</option>
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107 </param>
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108 </when>
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109 </conditional>
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110 <param name="outputgraph" type="select" multiple="false" label="Plot figures">
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111 <option value="TRUE">Yes</option>
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112 <option value="FALSE">No</option>
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113 </param>
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114 <param name="outputlog" type="select" label="Output log">
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115 <option value="TRUE">Yes</option>
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116 <option value="FALSE">No</option>
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117 </param>
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118
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119 </inputs>
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120 <outputs>
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121 <data format="tabular" name="output" label="selection of ${input.name}" />
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122 <data format="pdf" name="pdffigures" label="figures of SNPs selection of ${input.name}">
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123 <filter>outputgraph == "TRUE"</filter>
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124 <filter>(settingsLoss['package'] != 'spikeslab')</filter>
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125 </data>
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126 <data format="log" name="log" label="log of SNPs selection of ${input.name}">
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127 <filter>outputlog == "TRUE"</filter>
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128 </data>
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129 </outputs>
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130 <stdio>
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131 <exit_code range="1:" level="fatal" description="See logs for more details" />
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132 </stdio>
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133 <help>
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134 .. class:: warningmark
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135
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136 Data normalization must be run with the Data Normalization tool prior to SNPs selection. Otherwise, the standalone version can be used to perform marker selection from matrices containing data normalized with tools different from the one proposed in this instance.
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137
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138 -----
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139
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140 **What it does**
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141
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142 This tool selects some relevant markers according to a response using penalized regressions.
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143
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144 Output:
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145
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146 A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNPs):
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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147
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148 - chr: Chromosome containing the selected SNP.
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149 - position: Position of the selected SNP.
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150 - index: Index of the selected SNP.
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151 - names: Name of the selected SNP.
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152 - coefficient: Regression coefficient of the selected SNP.
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153
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154 -----
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155
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156 **Data Response csv file**
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157
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158 Data response csv file format:
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159
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160 - The first column contains the names of the different files of the data-set.
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161
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162 - The second column contains the response associated with each file.
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163
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164 - Column names of these two columns are respectively files and response.
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165
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166 - Columns are separated by a comma
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167
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168 - *Extensions of the files (.CEL for example) should be removed*
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169
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170
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171
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172 **Example**
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173
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174 Let 3 .cel files in the studied dataset ::
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175
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176 patient1.cel
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177 patient2.cel
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178 patient3.cel
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179
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180 The csv file should look like this ::
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181
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182 files,response
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183 patient1,1.92145
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184 patient2,2.12481
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185 patient3,1.23545
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186
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187
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188 -----
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189
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190 **Normal-tumor study**
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191
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192 In cases where normal (control) samples match to tumor samples, they are taken as references to extract copy number profile. In this case, a normal-tumor csv file must be provided :
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193
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194 - The first column contains the names of the files corresponding to normal samples of the dataset.
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195
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196 - The second column contains the names of the tumor samples files.
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197
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198 - Column names of these two columns are respectively normal and tumor.
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199
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200 - Columns are separated by a comma.
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201
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202 - *Extensions of the files (.CEL for example) should be removed*
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203
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204
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205 **Example**
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206
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207 Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel file.) ::
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208
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209 patient1_normal.cel
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210 patient1_tumor.cel
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211 patient2_normal.cel
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212 patient2_tumor.cel
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213 patient3_normal.cel
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214 patient3_tumor.cel
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215
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216
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217 The csv file should look like this ::
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219 normal,tumor
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220 patient1_normal,patient1_tumor
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221 patient2_normal,patient2_tumor
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222 patient3_normal,patient3_tumor
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223
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224 -----
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225
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227
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228 **Citation**
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229
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230 If you use this tool please cite :
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231
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232 `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint &lt;http://fr.arxiv.org/abs/1401.5035&gt;`_
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233
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234 </help>
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235 </tool>