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comparison segmentation.xml @ 0:4d539083cf7f draft

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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="segmentation" name="Segmentation and calling" force_history_refresh="True" version="1.1.0">
2 <description>of a previously normalized signal</description>
3 <requirement type="package" version="1.1.2">mpagenomics</requirement>
4 <command>
5 <![CDATA[
6 Rscript
7 ${__tool_directory__}/segmentation.R
8 #if $signalType.signal == "CN":
9 --nbcall '$signalType.nbcall'
10 --cellularity '$signalType.cellularity'
11 #else
12 --nbcall '3'
13 --cellularity '1.0'
14 #end if
15 --input '$input'
16 --new_file_path '$__new_file_path__'
17 --outputlog '$outputlog'
18 --output '$output'
19 --log '$log'
20 --outputgraph '$outputgraph'
21 --graph '$graph'
22 --method '$method'
23 --signalType '$signalType.signal'
24 --user_id '$__user_id__'
25 ]]>
26
27 </command>
28 <inputs>
29 <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
30
31 <param name="method" type="select" label="Segmentation method" help="">
32 <option value="cghseg">cghseg</option>
33 <option value="PELT">PELT</option>
34 </param>
35
36 <conditional name="signalType">
37 <param name="signal" type="select" multiple="false" label="Signal type">
38 <option value="CN">CN</option>
39 <option value="fracB">fracB</option>
40 </param>
41 <when value="fracB"/>
42 <when value="CN">
43
44 <param name="nbcall" type="select" label="Number of calling classes" help="The number of levels to be used for calling. Either 3 (loss, normal, gain), 4 (including amplifications), 5 (including double deletions) ">
45 <option value="3">3</option>
46 <option value="4">4</option>
47 <option value="5">5</option>
48 </param>
49 <param name="cellularity" type="float" size="5" value="1" min="0" max="1" label="Cellularity" help="Ratio of tumor cells in the sample. Real value between 0 and 1"/>
50 </when>
51 </conditional>
52 <param name="outputgraph" type="select" label="Output figures">
53 <option value="TRUE">Yes</option>
54 <option value="FALSE">No</option>
55 </param>
56 <param name="outputlog" type="select" label="Output log">
57 <option value="TRUE">Yes</option>
58 <option value="FALSE">No</option>
59 </param>
60 </inputs>
61 <outputs>
62 <data format="scr" name="output" label="segmentation of ${input.name}" />
63 <data format="log" name="log" label="log of segmentation of ${input.name}">
64 <filter>outputlog == "TRUE"</filter>
65 </data>
66 <data format="pdf" name="graph" label="graph of segmentation of ${input.name}">
67 <filter>outputgraph == "TRUE"</filter>
68 </data>
69 </outputs>
70 <stdio>
71 <exit_code range="1:" level="fatal" description="See logs for more details" />
72 </stdio>
73 <help>
74
75 **What it does**
76 This tool segments normalized profiles provided by the user and labels segments found in the copy-number profiles.
77
78 Input format:
79
80 *A tabular text file containing 3 fixed columns and 1 column per sample:*
81
82 - chr: Chromosome.
83 - position: Genomic position (in bp)
84 - probeName: Probes names.
85 - One column per sample which contains the copy number profile for each sample
86
87 Output format:
88
89 *A tabular text file containing 7 columns which describe all the segments (1 line per segment):*
90
91 - sampleNames: Column names corresponding to samples in the input file.
92 - chrom: Chromosome of the segment.
93 - chromStart: Starting position (in bp) of the segment. This position is not included in the segment.
94 - chromEnd: Ending position (in bp) of the segment. This position is included in the segment.
95 - probes: Number of probes in the segment.
96 - means: Mean of the segment.
97 - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”).
98
99 -----
100
101 **Citation**
102 If you use this tool please cite :
103
104 `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;`_
105
106 If segmentation is performed with PELT, please also cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. &lt;http://arxiv.org/abs/1101.1438&gt;`_
107
108 If segmentation is performed by cghseg, please cite `Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. &lt;http://www.ncbi.nlm.nih.gov/pubmed/15705208&gt;`_ ,
109 and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. &lt;http://arxiv.org/abs/1004.0887&gt;`_
110
111 When using the labels of the segments, please cite CGHCall `M. A. van de Wiel, K. I. Kim, S. J. Vosse, W. N. van Wieringen, S. M. Wilting, and B. Ylstra. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics, 23(7):892–894, 2007. &lt;http://bioinformatics.oxfordjournals.org/content/23/7/892.abstract&gt;`_
112
113 </help>
114 </tool>