Mercurial > repos > sblanck > mpagenomics_wrappers

annotate selectionExtracted.xml @ 8:d5ed62b4d3ac draft default tip

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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
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8
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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1 <tool id="markersSelection" name="Markers selection" force_history_refresh="True" version="0.1.0">
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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2 <description> of previously extracted signal</description>
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3 <command>
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4 <![CDATA[
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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5 Rscript
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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6 ${__tool_directory__}/selectionExtracted.R
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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7 --input '$input'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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8 --response '$response'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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9 --new_file_path '$__new_file_path__'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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10 --folds '$folds'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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11 --loss '$loss'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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12 --outputlog '$outputlog'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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13 --output '$output'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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14 --log '$log'
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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19 <param name="response" type="data" format="csv" label="Data response" help="Data response csv file. See below for more information on file format" />
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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20 <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"/>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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21 <param name="loss" type="select" multiple="false" label="Response type">
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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22 <option value="linear">Linear</option>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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23 <option value="logistic">Logistic</option>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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24 </param>
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25
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26 <param name="outputgraph" type="select" label="Output figures">
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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27 <option value="TRUE">Yes</option>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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28 <option value="FALSE">No</option>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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29 </param>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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30 <param name="outputlog" type="select" label="Output log">
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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31 <option value="TRUE">Yes</option>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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32 <option value="FALSE">No</option>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data format="tabular" name="output" label="selection of ${input.name}" />
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37 <data format="log" name="log" label="log of selection of ${input.name}" >
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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38 <filter>outputlog == "TRUE"</filter>
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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39 </data>
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40 </outputs>
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41 <stdio>
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42 <exit_code range="1:" level="fatal" description="See logs for more details" />
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43 </stdio>
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44 <help>
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45 **What it does**
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46
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47 This tool selects some relevant markers according to a response using penalized regressions.
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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48
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49 Input:
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50
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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51 *A tabular text file containing 3 fixed columns and 1 column per sample:*
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52
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53 - chr: Chromosome.
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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54 - position: Genomic position (in bp).
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55 - probeNames: Names of the probes.
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56 - One column per sample which contain the copy number signal for each sample.
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57
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58 Output:
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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59
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60 *A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNP):*
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61
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62 - chr: Chromosome containing the selected SNP.
d5ed62b4d3ac planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233
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63 - position: Position of the selected SNP.
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64 - index: Index of the selected SNP.
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65 - names: Name of the selected SNP.
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66 - coefficient: Regression coefficient of the selected SNP.
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67
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68 -----
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69
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70 **Data Response csv file**
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71
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72 Data response csv file format:
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73
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74 - The first column contains the names of the different files of the dataset.
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75
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76 - The second column is the response associated with each file.
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77
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78 - Column names of these two columns are respectively files and response.
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79
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80 - Columns are separated by a comma
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82 - *Extensions of the files (.CEL for example) should be removed*
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85
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86 **Example**
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87
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88 Let 3 .cel files in the studied dataset ::
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89
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90 patient1.cel
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91 patient2.cel
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92 patient3.cel
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93
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94 The csv file should look like this ::
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95
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96 files,response
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97 patient1,1.92145
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98 patient2,2.12481
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99 patient3,1.23545
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101
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102 -----
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103
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104 **Citation**
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105
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106 If you use this tool please cite :
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107
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108 `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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109
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110 </help>
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111 </tool>