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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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1 <tool id="markersSelection" name="Markers selection" force_history_refresh="True" version="0.1.0">
2 <description> of previously extracted signal</description>
3 <command>
4 <![CDATA[
5 Rscript
6 ${__tool_directory__}/selectionExtracted.R
7 --input '$input'
8 --response '$response'
9 --new_file_path '$__new_file_path__'
10 --folds '$folds'
11 --loss '$loss'
12 --outputlog '$outputlog'
13 --output '$output'
14 --log '$log'
15 ]]>
16 </command>
17 <inputs>
18 <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
19 <param name="response" type="data" format="csv" label="Data response" help="Data response csv file. See below for more information on file format" />
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"/>
21 <param name="loss" type="select" multiple="false" label="Response type">
22 <option value="linear">Linear</option>
23 <option value="logistic">Logistic</option>
24 </param>
25
26 <param name="outputgraph" type="select" label="Output figures">
27 <option value="TRUE">Yes</option>
28 <option value="FALSE">No</option>
29 </param>
30 <param name="outputlog" type="select" label="Output log">
31 <option value="TRUE">Yes</option>
32 <option value="FALSE">No</option>
33 </param>
34 </inputs>
35 <outputs>
36 <data format="tabular" name="output" label="selection of ${input.name}" />
37 <data format="log" name="log" label="log of selection of ${input.name}" >
38 <filter>outputlog == "TRUE"</filter>
39 </data>
40 </outputs>
41 <stdio>
42 <exit_code range="1:" level="fatal" description="See logs for more details" />
43 </stdio>
44 <help>
45 **What it does**
46
47 This tool selects some relevant markers according to a response using penalized regressions.
48
49 Input:
50
51 *A tabular text file containing 3 fixed columns and 1 column per sample:*
52
53 - chr: Chromosome.
54 - position: Genomic position (in bp).
55 - probeNames: Names of the probes.
56 - One column per sample which contain the copy number signal for each sample.
57
58 Output:
59
60 *A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNP):*
61
62 - chr: Chromosome containing the selected SNP.
63 - position: Position of the selected SNP.
64 - index: Index of the selected SNP.
65 - names: Name of the selected SNP.
66 - coefficient: Regression coefficient of the selected SNP.
67
68 -----
69
70 **Data Response csv file**
71
72 Data response csv file format:
73
74 - The first column contains the names of the different files of the dataset.
75
76 - The second column is the response associated with each file.
77
78 - Column names of these two columns are respectively files and response.
79
80 - Columns are separated by a comma
81
82 - *Extensions of the files (.CEL for example) should be removed*
83
84
85
86 **Example**
87
88 Let 3 .cel files in the studied dataset ::
89
90 patient1.cel
91 patient2.cel
92 patient3.cel
93
94 The csv file should look like this ::
95
96 files,response
97 patient1,1.92145
98 patient2,2.12481
99 patient3,1.23545
100
101
102 -----
103
104 **Citation**
105
106 If you use this tool please cite :
107
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;`_
109
110 </help>
111 </tool>