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annotate 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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4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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1 <tool id="segmentation" name="Segmentation and calling" force_history_refresh="True" version="1.1.0">
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2 <description>of a previously normalized signal</description>
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3 <requirement type="package" version="1.1.2">mpagenomics</requirement>
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4 <command>
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5 <![CDATA[
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6 Rscript
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7 ${__tool_directory__}/segmentation.R
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8 #if $signalType.signal == "CN":
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9 --nbcall '$signalType.nbcall'
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10 --cellularity '$signalType.cellularity'
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11 #else
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12 --nbcall '3'
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13 --cellularity '1.0'
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14 #end if
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15 --input '$input'
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16 --new_file_path '$__new_file_path__'
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17 --outputlog '$outputlog'
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18 --output '$output'
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19 --log '$log'
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20 --outputgraph '$outputgraph'
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21 --graph '$graph'
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22 --method '$method'
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23 --signalType '$signalType.signal'
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24 --user_id '$__user_id__'
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25 ]]>
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26
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27 </command>
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28 <inputs>
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29 <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
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30
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31 <param name="method" type="select" label="Segmentation method" help="">
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32 <option value="cghseg">cghseg</option>
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33 <option value="PELT">PELT</option>
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34 </param>
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35
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36 <conditional name="signalType">
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37 <param name="signal" type="select" multiple="false" label="Signal type">
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38 <option value="CN">CN</option>
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39 <option value="fracB">fracB</option>
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40 </param>
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41 <when value="fracB"/>
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42 <when value="CN">
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43
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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) ">
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45 <option value="3">3</option>
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46 <option value="4">4</option>
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47 <option value="5">5</option>
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48 </param>
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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"/>
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50 </when>
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51 </conditional>
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52 <param name="outputgraph" type="select" label="Output figures">
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53 <option value="TRUE">Yes</option>
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54 <option value="FALSE">No</option>
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55 </param>
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56 <param name="outputlog" type="select" label="Output log">
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57 <option value="TRUE">Yes</option>
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58 <option value="FALSE">No</option>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data format="scr" name="output" label="segmentation of ${input.name}" />
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63 <data format="log" name="log" label="log of segmentation of ${input.name}">
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64 <filter>outputlog == "TRUE"</filter>
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65 </data>
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66 <data format="pdf" name="graph" label="graph of segmentation of ${input.name}">
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67 <filter>outputgraph == "TRUE"</filter>
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68 </data>
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69 </outputs>
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70 <stdio>
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71 <exit_code range="1:" level="fatal" description="See logs for more details" />
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72 </stdio>
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73 <help>
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74
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75 **What it does**
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76 This tool segments normalized profiles provided by the user and labels segments found in the copy-number profiles.
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77
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78 Input format:
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79
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80 *A tabular text file containing 3 fixed columns and 1 column per sample:*
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81
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82 - chr: Chromosome.
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83 - position: Genomic position (in bp)
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84 - probeName: Probes names.
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85 - One column per sample which contains the copy number profile for each sample
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86
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87 Output format:
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88
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89 *A tabular text file containing 7 columns which describe all the segments (1 line per segment):*
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90
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91 - sampleNames: Column names corresponding to samples in the input file.
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92 - chrom: Chromosome of the segment.
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93 - chromStart: Starting position (in bp) of the segment. This position is not included in the segment.
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94 - chromEnd: Ending position (in bp) of the segment. This position is included in the segment.
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95 - probes: Number of probes in the segment.
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96 - means: Mean of the segment.
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97 - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”).
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98
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99 -----
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100
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101 **Citation**
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102 If you use this tool please cite :
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103
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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;`_
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105
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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;`_
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107
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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;`_ ,
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109 and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. &lt;http://arxiv.org/abs/1004.0887&gt;`_
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110
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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;`_
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112
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113 </help>
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114 </tool>