annotate mircounts.xml @ 9:2a08a6eb471c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
author artbio
date Wed, 25 Apr 2018 12:48:27 -0400
parents 3f62272192f9
children de227b7307cf
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2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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1 <tool id="mircounts" name="miRcounts" version="1.2.6">
0
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2 <description> Counts miRNA alignments from small RNA sequence data</description>
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3 <requirements>
2
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4 <requirement type="package" version="1.18">gnu-wget</requirement>
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5 <requirement type="package" version="1.2.0">bowtie</requirement>
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6 <requirement type="package" version="1.6.0">samtools</requirement>
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7 <requirement type="package" version="0.11.2.2">pysam</requirement>
0
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8 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
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9 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
7
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12 wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey
0
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13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
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14 wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz &&
0
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15 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey &&
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16 #if $cutadapt.cutoption == "yes":
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17 python '$__tool_directory__'/yac.py --input $cutadapt.input
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18 --output clipped_input.fastq
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19 --output_format fastq
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20 --adapter_to_clip $cutadapt.clip_source.clip_sequence
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21 --min $cutadapt.min
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22 --max $cutadapt.max
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23 --Nmode $cutadapt.Nmode &&
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24 #else
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25 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
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26 #end if
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27 bowtie-build hairpin.fa hairpin >/dev/null &&
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28 bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' 2>&1 &&
0
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29 samtools index $output &&
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30 python '$__tool_directory__'/mircounts.py -pm --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe;
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31 #if $plotting.plottingOption == 'yes':
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32 Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
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33 #end if
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34 ]]></command>
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35 <inputs>
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36 <conditional name="cutadapt">
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37 <param label="Remove adapter sequence before aligning" name="cutoption" type="select">
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38 <option value="no">no</option>
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39 <option selected="True" value="yes">yes</option>
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40 </param>
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41 <when value="yes">
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42 <param format="fastq,fastqsanger" label="Source file" name="input" type="data" />
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43 <param label="min size" name="min" size="4" type="integer" value="15" help="Minimum size of accepted clipped reads" />
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44 <param label="max size" name="max" size="4" type="integer" value="36" help="Maximum size of accepted clipped reads"/>
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45 <param label="Accept reads containing N?" name="Nmode" type="select">
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46 <option selected="True" value="accept">accept</option>
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47 <option value="reject">reject</option>
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48 </param>
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49 <conditional name="clip_source">
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50 <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select">
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51 <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option>
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52 <option value="user">Use custom sequence</option>
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53 </param>
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54 <when value="prebuilt">
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55 <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select">
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56 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
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57 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
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58 <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option>
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59 <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option>
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60 </param>
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61 </when>
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62 <when value="user">
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63 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
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64 </when>
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65 </conditional>
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66 </when>
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67 <when value="no">
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68 <param label="Select fastq files to align" name="clipped_input" type="data" format="fastq,fastqsanger" help="Note that sequences reads must be clipped from their adapter" />
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69 </when>
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70 </conditional>
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71 <param name="genomeKey" type="select" label="Choose Organism">
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72 <options from_data_table="miRbase_GenomeKeys">
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73 <column name="name" index="1"/>
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74 <column name="value" index="0"/>
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75 </options>
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76 </param>
4
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77 <param name="mirbase_version" type="select" label="Choose miRbase version">
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78 <option selected="true" value="22">22</option>
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79 <option value="21">21</option>
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80 <option value="20">20</option>
4
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81 <option value="19">19</option>
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82 </param>
0
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83 <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select">
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84 <option value="0">0</option>
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artbio
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85 <option selected="true" value="1">1</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
86 <option value="2">2</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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87 <option value="3">3</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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88 </param>
6
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artbio
parents: 5
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89 <param help="Output mature Mir counts" label="Output mature Mir counts"
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90 name="output_mir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" />
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91 <param help="Output pre-Mir counts" label="Output pre-Mir counts"
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artbio
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92 name="output_premir_counts" type="boolean" falsevalue="0" checked="true" truevalue="1" />
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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93 <conditional name="plotting">
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artbio
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94 <param label="Additional miRNA charts" name="plottingOption" type="select">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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95 <option value="no">no</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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96 <option value="yes" selected="True">yes</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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97 </param>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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98 <when value="yes">
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artbio
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99 <param label="Display Coverage with absolute number of reads or relatively to the total number of read matching the gene or mir" name="display" type="select">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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100 <option selected="True" value="relative">Relative Coverage</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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101 <option value="absolute">Absolute Coverage</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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102 </param>
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103 </when>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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104 <when value="no">
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105 </when>
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106 </conditional>
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107 </inputs>
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108 <outputs>
6
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109 <data format="bam" label="BAM alignment" name="output" hidden="true" />
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110 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3" hidden="true" />
4
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111 <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file">
6
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112 <filter>output_premir_counts == True</filter>
4
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113 <actions>
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114 <action name="column_names" type="metadata" default="Gene,Counts" />
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115 </actions>
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116 </data>
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117 <data format="tabular" label="Mir Counts" name="mir_count_file">
6
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118 <filter>output_mir_counts == True</filter>
4
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artbio
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119 <actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
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120 <action name="column_names" type="metadata" default="Gene,Counts" />
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artbio
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121 </actions>
da1aa7de2b19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
artbio
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122 </data>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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123 <data format="tabular" label="Coverage Table" name="coverage_dataframe">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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124 <filter>plotting['plottingOption'] == "yes"</filter>
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125 </data>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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126 <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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127 <filter>plotting['plottingOption'] == "yes"</filter>
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128 </data>
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129 </outputs>
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130 <tests>
9
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131 <test>
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artbio
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diff changeset
132 <param name="cutoption" value="yes" />
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artbio
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diff changeset
133 <param name="min" value="15"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
134 <param name="max" value="25"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
135 <param name="Nmode" value="reject"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
136 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
137 <param name="v" value="0"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
138 <param name="genomeKey" value="dme"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
139 <param name="mirbase_version" value="22"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
140 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
141 <param name="plottingOption" value="no"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
142 <param name="output_premir_counts" value="True"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
143 <param name="output_mir_counts" value="True"/>
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artbio
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144 <output name="output" file="unclipped.out.22.bam" ftype="bam"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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145 <output name="gff3" file="translated_dme.22.gff3" ftype="gff3" lines_diff="22"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
146 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff changeset
147 <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/>
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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148 </test>
0
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149 <test>
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artbio
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150 <param name="cutoption" value="yes" />
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artbio
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151 <param name="min" value="15"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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152 <param name="max" value="25"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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153 <param name="Nmode" value="reject"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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154 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
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artbio
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155 <param name="v" value="0"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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156 <param name="genomeKey" value="dme"/>
8
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artbio
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diff changeset
157 <param name="mirbase_version" value="21"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
158 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
159 <param name="plottingOption" value="no"/>
6
543472c9e272 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 756ee14320d2f72e17b2336e340e28ec847c6577
artbio
parents: 5
diff changeset
160 <param name="output_premir_counts" value="True"/>
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artbio
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diff changeset
161 <param name="output_mir_counts" value="True"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
162 <output name="output" file="unclipped.out.bam" ftype="bam"/>
5
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artbio
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diff changeset
163 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
164 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
165 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
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166 </test>
9
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diff changeset
167 <test>
0
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artbio
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diff changeset
168 <param name="cutoption" value="yes" />
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artbio
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diff changeset
169 <param name="min" value="15"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
170 <param name="max" value="25"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
171 <param name="Nmode" value="reject"/>
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artbio
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172 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
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173 <param name="v" value="0"/>
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174 <param name="genomeKey" value="dme"/>
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175 <param name="mirbase_version" value="21"/>
0
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176 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
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177 <param name="plottingOption" value="yes"/>
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178 <param name="display" value="relative"/>
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179 <param name="output_premir_counts" value="True"/>
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180 <param name="output_mir_counts" value="True"/>
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181 <output name="output" file="unclipped.out.bam" ftype="bam"/>
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182 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
0
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183 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
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184 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
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185 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/>
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186 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/>
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187 </test>
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188 <test>
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189 <param name="cutoption" value="no" />
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190 <param name="v" value="1"/>
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191 <param name="genomeKey" value="dme"/>
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192 <param name="mirbase_version" value="21"/>
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193 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/>
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194 <param name="plottingOption" value="yes"/>
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195 <param name="display" value="absolute"/>
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196 <param name="output_premir_counts" value="True"/>
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197 <param name="output_mir_counts" value="True"/>
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198 <output name="output" file="clipped.out.bam" ftype="bam"/>
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199 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
0
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200 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/>
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201 <output name="mir_count_file" file="mirs_clipped_count.tab"/>
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202 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/>
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203 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/>
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204 </test>
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205 </tests>
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206 <help>
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207
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208 **What it does**
1
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209
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210 + Clips adapter (optional)
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211 + Aligns small RNA reads to miRNA mirBase_ reference using bowtie
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212 + Computes pre-mir and mir counts using the pysam python package
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213 + Plots pre-mir read coverages using R lattice package (optional)
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214
0
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215 This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments.
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216
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217 .. _mirBase: ftp://mirbase.org/pub/mirbase/
0
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218
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219 ------
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220
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221
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222 **Inputs**
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223
1
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224 1. A fastq file of reads that may or may not be clipped from their adapter sequence. The tool includes a clipping option if needed.
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225 2. Select the appropriate organism which reads originate from.
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226 3. Choose whether you wish or not to plot the pre-mir coverages. The coverage can be expressed in absolute number of reads covering the real coordinates of the pre-mir sequences, or, as a fraction of the maximum coverage (set to 1) covering the coordinates of pre-mirs expressed as a fraction of the length of the pre-mirs.
0
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227
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228
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229 ------
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230
1
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231 Absolute :
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232
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233 + .. image:: premirs_absolute.png
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234
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235 Relative :
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236
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237 + .. image:: premirs_relative.png
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238
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239 -------
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240
0
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241 **Outputs**
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242
1
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243 1. A BAM alignment of input reads
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244 2. A GFF3 file generated by the tool to compute mature mir counts
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245 3. A table of pre-mir counts
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246 4. A table of mature mir counts
0
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247
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248 Optional:
1
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249
0
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250 5. A table of pre-mir coverage
1
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251 6. A PDF file with covererage plots
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252
0
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253
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254 </help>
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255 <citations>
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256 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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257 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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258 <citation type="bibtex">@Book{,
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259 title = {Lattice: Multivariate Data Visualization with R},
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260 author = {Deepayan Sarkar},
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261 publisher = {Springer},
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262 address = {New York},
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263 year = {2008},
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264 note = {ISBN 978-0-387-75968-5},
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265 url = {http://lmdvr.r-forge.r-project.org},
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266 }</citation>
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267 </citations>
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268 </tool>