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
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1 <tool id="markersSelection" name="Markers selection" version="1.3.0">
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2 <requirements>
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3 <container type="docker">sblanck/mpagenomicsdependencies</container>
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4 </requirements>
0
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5 <description> of previously extracted signal</description>
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6 <command>
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7 <![CDATA[
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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8 Rscript
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9 ${__tool_directory__}/selectionExtracted.R
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10 --input '$input'
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11 --response '$response'
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12 --new_file_path '$output.extra_files_path'
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13 --folds '$folds'
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14 --loss '$loss'
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15 --outputlog '$outputlog'
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16 --output '$output'
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17 --log '$log'
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18 ]]>
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19 </command>
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20 <inputs>
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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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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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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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24 <param name="loss" type="select" multiple="false" label="Response type">
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25 <option value="linear">Linear</option>
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26 <option value="logistic">Logistic</option>
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27 </param>
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28
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29 <!--param name="outputgraph" type="select" label="Output figures">
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30 <option value="TRUE">Yes</option>
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31 <option value="FALSE">No</option>
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32 </param-->
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33 <param name="outputlog" type="select" label="Output log">
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34 <option value="TRUE">Yes</option>
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35 <option value="FALSE">No</option>
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36 </param>
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37 </inputs>
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38 <outputs>
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39 <data format="tabular" name="output" label="selection of ${input.name}" />
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40 <data format="log" name="log" label="log of selection of ${input.name}" >
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41 <filter>outputlog == "TRUE"</filter>
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42 </data>
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43 </outputs>
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44 <stdio>
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45 <exit_code range="1:" level="fatal" description="See logs for more details" />
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46 </stdio>
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47 <help>
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48 **What it does**
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49
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50 This tool selects some relevant markers according to a response using penalized regressions.
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51
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52 Input:
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53
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54 *A tabular text file containing 3 fixed columns and 1 column per sample:*
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55
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56 - chr: Chromosome.
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57 - position: Genomic position (in bp).
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58 - probeNames: Names of the probes.
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59 - One column per sample which contain the copy number signal for each sample.
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60
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61 Output:
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62
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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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64
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65 - chr: Chromosome containing the selected SNP.
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66 - position: Position of the selected SNP.
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67 - index: Index of the selected SNP.
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68 - names: Name of the selected SNP.
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69 - coefficient: Regression coefficient of the selected SNP.
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70
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71 -----
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72
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73 **Data Response csv file**
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75 Data response csv file format:
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76
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77 - The first column contains the names of the different files of the dataset.
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78
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79 - The second column is the response associated with each file.
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81 - Column names of these two columns are respectively files and response.
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83 - Columns are separated by a comma
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84
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85 - *Extensions of the files (.CEL for example) should be removed*
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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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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 &lt;http://fr.arxiv.org/abs/1401.5035&gt;`_
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112
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113 </help>
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114 </tool>