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annotate small_rna_maps.xml @ 1:40972a8dfab9 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit ad60e6655aabe30246043d95f14646b2527c9255
author artbio
date Mon, 24 Jul 2017 12:31:04 -0400
parents 6d48150495e3
children 507383cce5a8
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40972a8dfab9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit ad60e6655aabe30246043d95f14646b2527c9255
artbio
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1 <tool id="small_rna_maps" name="small_rna_maps" version="0.9.1">
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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7 <requirement type="package" version="0.6_28=r3.3.1_0">r-latticeextra</requirement>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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8 <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Tool exception" />
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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12 </stdio>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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13 <command detect_errors="exit_code"><![CDATA[
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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14 #for $file in $input
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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15 samtools index '$file' &&
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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16 #end for
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17 python '$__tool_directory__'/small_rna_maps.py
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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18 --input
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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19 #for $file in $input
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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20 '$file'
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21 #end for
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22 --sample_name
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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23 #for $sample in $input
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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24 '$sample.name'
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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25 #end for
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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26 #if $extra_plot == 'Sizes':
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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27 --sizes '$output_sizes'
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28 #end if
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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29 --output '$output_tab' &&
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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30 Rscript '$__tool_directory__'/small_rna_maps.r --output_tab '$output_tab'
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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31 --output_pdf '$output_pdf'
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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32 #if $extra_plot != 'Sizes':
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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33 --extra_plot '$extra_plot'
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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34 #else
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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35 --sizes $output_sizes
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36 #end if
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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37 ]]></command>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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38 <inputs>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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39 <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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40 <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map">
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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41 <option value="Coverage">Coverage</option>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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42 <option value="Mean">Mean Sizes</option>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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43 <option value="Median">Median Sizes</option>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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44 <option value="Sizes">Size Distributions</option>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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45 </param>
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46 </inputs>
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47
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48 <outputs>
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49 <data format="tabular" name="output_tab" label="Map dataframe" />
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50 <data format="tabular" name="output_sizes" label="Size dataframe" >
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51 <filter>extra_plot == "Sizes"</filter>
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52 </data>
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53 <data format="pdf" name="output_pdf" label="PDF file" />
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54
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
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60 <param name="extra_plot" value="Mean" />
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61 <output file="output.tab" name="output_tab" />
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62 <output file="mean.pdf" name="output_pdf" />
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63 </test>
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64 <test>
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65 <param name="input" value="input1.bam,input1.bam" ftype="bam"/>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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66 <param name="extra_plot" value="Mean" />
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67 <output file="doubled.tab" name="output_tab" />
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68 <output file="doubled_mean.pdf" name="output_pdf" />
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69 </test>
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70 <test>
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71 <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
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72 <param name="extra_plot" value="Median" />
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73 <output file="output.tab" name="output_tab" />
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74 <output file="median.pdf" name="output_pdf" />
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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75 </test>
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76 <test>
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77 <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
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78 <param name="extra_plot" value="Coverage" />
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79 <output file="output.tab" name="output_tab" />
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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80 <output file="coverage.pdf" name="output_pdf" />
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81 </test>
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82 <test>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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83 <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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84 <param name="extra_plot" value="Sizes" />
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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85 <output file="output.tab" name="output_tab" />
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86 <output file="sizes.tab" name="output_sizes" />
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87 <output file="sizes.pdf" name="output_pdf" />
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88 </test>
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89 </tests>
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90
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91
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92 <help>
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93
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94 **What it does**
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95
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96 Generate read count maps from alignment BAM files, using pysam and lattice.
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97
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98 In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted.
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99
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100 **Inputs**
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101
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102 bam alignment files that *must* be
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103
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104 - single-read
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105 - sorted
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106 - mapping to the same reference
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107
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108 **Output**
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109
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110 A pdf file generated by the R package lattice
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111
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112 One or two dataframes used to plot data
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113
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114 </help>
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115
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116 <citations>
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117 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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118 <citation type="bibtex">@Book{,
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119 title = {Lattice: Multivariate Data Visualization with R},
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120 author = {Deepayan Sarkar},
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121 publisher = {Springer},
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122 address = {New York},
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123 year = {2008},
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124 note = {ISBN 978-0-387-75968-5},
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125 url = {http://lmdvr.r-forge.r-project.org},
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126 }</citation>
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127 </citations>
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128 </tool>
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129