Mercurial > repos > sblanck > mpagenomics_wrappers

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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
author sblanck
date Tue, 12 May 2020 13:40:07 +0000
parents af4f63f27c77
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af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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1 <tool id="preprocess" name="Data Normalization" force_history_refresh="True" version="1.1.0">
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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2 <requirements>
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3 <!--requirement type="set_environment">R_SCRIPT_PATH</requirement-->
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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4 <requirement type="package" version="1.1.2">mpagenomics</requirement>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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5 </requirements>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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6 <!--command interpreter="python"-->
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7 <command>
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8 <![CDATA[
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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9 Rscript
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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10 ${__tool_directory__}/preprocess.R
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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11 --summary '$summary'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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12 --new_file_path '$__new_file_path__'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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13 --inputcdffull_name '$inputcdffull.name'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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14 --inputufl_name '$inputufl.name'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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15 --inputugp_name '$inputugp.name'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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16 --inputacs_name '$inputacs.name'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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17 --inputcdffull '$inputcdffull'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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18 --inputufl '$inputufl'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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19 --inputugp '$inputugp'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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20 --inputacs '$inputacs'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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21 --dataSetName '$datasetName'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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22 #if $settings.settingsType == "tumor":
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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23 --tumorcsv '$tumorcsv'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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24 #end if
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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25 #if $settings.settingsType == "standard":
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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26 --tumorcsv 'none'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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27 #end if
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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28 --settingsType '$settings.settingsType'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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29 --outputgraph '$outputgraph'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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30 --zipfigures '$zipfigures'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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31 --outputlog '$outputlog'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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32 --log '$log'
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33 --user_id '$__user_id__'
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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34 --input "#for $input in $inputs# $input;$input.name, #end for#"
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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35 ]]>
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36
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37 </command>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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38 <inputs>
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39 <param name="datasetName" type="text" label="Dataset Name"/>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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40 <param name="inputs" type="data" format="cel" multiple="True" label="Cel files dataset" help="Cel files dataset previously uploaded with the Multiple File Datasets tool."/>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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41 <param name="inputcdffull" type="data" format="cdf" label="cdf file" help=".cdf file name must comply with the following format : &lt; chiptype &gt;,&lt; tag &gt;.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf)." />
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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42 <param name="inputufl" type="data" format="ufl" label="ufl file" help=".ufl file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl)."/>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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43 <param name="inputugp" type="data" format="ugp" label="ugp file" help=".ugp file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp)."/>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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44 <param name="inputacs" type="data" format="acs" label="acs file" help=".acs file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs)."/>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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45 <conditional name="settings">
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46 <param name="settingsType" type="select" label="Reference">
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47 <option value="standard">Study without reference</option>
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48 <option value="tumor">Normal-tumor study with TumorBoost</option>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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49 </param>
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50 <when value="standard" />
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51 <when value="tumor">
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52 <param name="tumorcsv" type="data" format="csv" label="TumorBoost csv file" help="Normal-tumor csv file. See below for more information."/>
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53 </when>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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54 </conditional>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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55 <!--param name="outputgraph" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output figures" /-->
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56 <!--param name="outputlog" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output log" /-->
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57 <param name="outputgraph" type="select" label="Output figures">
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58 <option value="TRUE">Yes</option>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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59 <option value="FALSE">No</option>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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60 </param>
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61 <param name="outputlog" type="select" label="Output log">
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62 <option value="TRUE">Yes</option>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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63 <option value="FALSE">No</option>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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64 </param>
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65 <!--param name="chipType" type="text" label="chipType" /-->
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66 <!--param name="workspace" type="text" label="Workspace"/-->
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67 </inputs>
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68
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69 <outputs>
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70 <!-- Would like to make this hidden or not appear all together, but
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71 variable outputs require a primary dataset. If hidden refresh
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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72 doesn't occur.
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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73 -->
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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74 <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" />
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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75 <data format="zip" name="zipfigures" label="figures of normalization of ${datasetName}">
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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76 <filter>outputgraph == "TRUE"</filter>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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77 </data>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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78 <data format="log" name="log" label="log of normalization ${datasetName}">
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79 <filter>outputlog == "TRUE"</filter>
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80 </data>
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81 </outputs>
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82
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83 <stdio>
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84 <exit_code range="1:" level="fatal" description="See logs for more details" />
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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85 </stdio>
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86
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87 <help>
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88
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89 **What it does**
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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90
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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91 This preprocessing step consists in a correction of biological and technical biaises due to the experiment. Raw data from Affymetrix arrays are provided in different CEL files. These data must be normalized before statistical analysis.
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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92 The pre-processing is proposed as a wrapper of aroma.* packages (using CRMAv2 and TumorBoost when appropriate). Note that this implies that the pre-processing step is only available for Affymetrix arrays.
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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93
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94 -----
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95
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96 **Chip file naming conventions**
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97
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98 Chip filenames must strictly follow the following rules :
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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99
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100 - *.cdf* filename must comply with the following format : &lt; chiptype &gt;,&lt; tag &gt;.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf). Note the use of a comma (not a point) between &lt;chiptype&gt; and the tag "Full".
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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101
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102 - *.ufl* filename must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl).
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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103
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104 - *.ugp* filename must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp).
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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105
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106 - *.acs* file name must start with &lt; chiptype &gt;,&lt; tag &gt; (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs).
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107
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108 -----
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109
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110 **Normal-tumor study with TumorBoost**
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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111
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112 In cases where normal (control) samples match to tumor samples, normalization can be improved using TumorBoost. In this case, a normal-tumor csv file must be provided :
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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113
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114 - The first column contains the names of the files corresponding to normal samples of the dataset.
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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115
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116 - The second column contains the names of the tumor samples files.
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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117
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118 - Column names of these two columns are respectively normal and tumor.
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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119
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120 - Columns are separated by a comma.
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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121
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122 - *Extensions of the files (.CEL for example) should be removed*
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123
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124
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125
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126 **Example**
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127
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128 Let 6 .cel files in the dataset studied (3 patients, each of them being represented by a couple of normal and tumor cel files.) ::
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129
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130 patient1_normal.cel
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131 patient1_tumor.cel
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132 patient2_normal.cel
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133 patient2_tumor.cel
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134 patient3_normal.cel
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135 patient3_tumor.cel
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136
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137
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138 The csv file should look like this ::
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139
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140 normal,tumor
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141 patient1_normal,patient1_tumor
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142 patient2_normal,patient2_tumor
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143 patient3_normal,patient3_tumor
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144
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145
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146 -----
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147
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148 **Citation**
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149
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150 When using this tool, please cite :
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151
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152 `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;`_
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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153
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154 As CRMAv2 normalization is used, please also cite `H. Bengtsson, P. Wirapati, and T. P. Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 &amp; 6. Bioinformatics, 5(17):2149–2156, 2009. &lt;http://bioinformatics.oxfordjournals.org/content/25/17/2149.short&gt;`_
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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156 When using TumorBoost to improve normalization in a normal-tumor study, please cite `H. Bengtsson, P. Neuvial, and T. P. Speed. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics, 11, 2010 &lt;http://www.biomedcentral.com/1471-2105/11/245&gt;`_
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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158 </help>
af4f63f27c77 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f
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159 </tool>