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1 <tool id="markersSelection" name="Markers selection" force_history_refresh="True" version="0.1.0">
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2 <requirement type="package" version="1.1.2">mpagenomics</requirement>
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3 <command interpreter="python">
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4 markersSelection.py '$input' '$response' '$__new_file_path__' '$folds' '$loss' '$outputlog' '$output' '$log'
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
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8 <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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9 <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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10 <param name="loss" type="select" multiple="false" label="Response type">
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11 <option value="linear">Linear</option>
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12 <option value="logistic">Logistic</option>
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13 </param>
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14
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15 <param name="outputgraph" type="select" label="Output figures">
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16 <option value="TRUE">Yes</option>
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17 <option value="FALSE">No</option>
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18 </param>
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19 <param name="outputlog" type="select" label="Output log">
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20 <option value="TRUE">Yes</option>
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21 <option value="FALSE">No</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data format="txt" name="output" label="selection of ${input.name}" />
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26 <data format="log" name="log" label="log of selection of ${input.name}" >
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27 <filter>outputlog == "TRUE"</filter>
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28 </data>
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29 </outputs>
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30 <stdio>
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31 <exit_code range="1:" level="fatal" description="See logs for more details" />
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32 </stdio>
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33 <help>
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34 **What it does**
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35
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36 This tool selects some relevant markers according to a response using penalized regressions.
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37
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38 Input:
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39
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40 *A tabular text file containing 3 fixed columns and 1 column per sample:*
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41
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42 - chr: Chromosome.
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43 - position: Genomic position (in bp).
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44 - probeNames: Names of the probes.
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45 - One column per sample which contain the copy number signal for each sample.
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46
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47 Output:
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48
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49 *A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNP):*
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50
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51 - chr: Chromosome containing the selected SNP.
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52 - position: Position of the selected SNP.
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53 - index: Index of the selected SNP.
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54 - names: Name of the selected SNP.
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55 - coefficient: Regression coefficient of the selected SNP.
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56
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57 -----
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58
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59 **Data Response csv file**
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60
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61 Data response csv file format:
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62
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63 - The first column contains the names of the different files of the dataset.
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64
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65 - The second column is the response associated with each file.
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66
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67 - Column names of these two columns are respectively files and response.
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68
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69 - Columns are separated by a comma
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70
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71 - *Extensions of the files (.CEL for example) should be removed*
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72
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73
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74
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75 **Example**
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76
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77 Let 3 .cel files in the studied dataset ::
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78
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79 patient1.cel
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80 patient2.cel
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81 patient3.cel
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82
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83 The csv file should look like this ::
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84
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85 files,response
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86 patient1,1.92145
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87 patient2,2.12481
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88 patient3,1.23545
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89
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90
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91 -----
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92
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93 **Citation**
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94
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95 If you use this tool please cite :
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96
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97 `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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98
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99 </help>
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100 </tool>
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