annotate mircounts.xml @ 1:cadc0f2c6b29 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
author artbio
date Tue, 25 Jul 2017 09:40:25 -0400
parents da29af78a960
children f59c643b00fc
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cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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1 <tool id="mircounts" name="miRcounts" version="0.9.1">
0
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2 <description> Counts miRNA alignments from small RNA sequence data</description>
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3 <requirements>
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4 <requirement type="package" version="1.2">bowtie</requirement>
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5 <requirement type="package" version="1.4.1">samtools</requirement>
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6 <requirement type="package" version="0.11.2.1">pysam</requirement>
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7 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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8 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ## To be refactored with guidelines in https://github.com/ARTbio/tools-artbio/issues/140
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12 wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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14 wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz &&
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15 sh '$__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
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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19 --output_format fastq
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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20 --adapter_to_clip $cutadapt.clip_source.clip_sequence
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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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 &&
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28 bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq 2>/dev/null | samtools sort -O bam -o '$output' &&
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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29 samtools index $output &&
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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30 python '$__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">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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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>
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77 <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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78 <option value="0">0</option>
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79 <option selected="true" value="1">1</option>
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80 <option value="2">2</option>
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81 <option value="3">3</option>
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82 </param>
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83 <conditional name="plotting">
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84 <param label="Additional miRNA charts" name="plottingOption" type="select">
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diff changeset
85 <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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86 <option value="yes" selected="True">yes</option>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
87 </param>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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88 <when value="yes">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
89 <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
parents:
diff changeset
90 <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
parents:
diff changeset
91 <option value="absolute">Absolute Coverage</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
92 </param>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
93 </when>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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94 <when value="no">
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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95 </when>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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96 </conditional>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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97 </inputs>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
98 <outputs>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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99 <data format="bam" label="BAM alignment" name="output" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
100 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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101 <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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102 <data format="tabular" label="Mir Counts" name="mir_count_file" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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103 <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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104 <filter>plotting['plottingOption'] == "yes"</filter>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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105 </data>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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106 <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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107 <filter>plotting['plottingOption'] == "yes"</filter>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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108 </data>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
109 </outputs>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
110 <tests>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
111 <test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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112 <param name="cutoption" value="yes" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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113 <param name="min" value="15"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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114 <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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115 <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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116 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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117 <param name="v" value="0"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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118 <param name="genomeKey" value="dme"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
119 <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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120 <param name="plottingOption" value="no"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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121 <output name="output" file="unclipped.out.bam" ftype="bam"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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122 <output name="gff3" file="translated_dme.gff3" ftype="gff3"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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123 <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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124 <output name="mir_count_file" file="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
125 </test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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126 <test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
127 <param name="cutoption" value="yes" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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128 <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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129 <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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130 <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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131 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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132 <param name="v" value="0"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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133 <param name="genomeKey" value="dme"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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134 <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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135 <param name="plottingOption" value="yes"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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136 <param name="display" value="relative"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
137 <output name="output" file="unclipped.out.bam" ftype="bam"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
138 <output name="gff3" file="translated_dme.gff3" ftype="gff3"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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139 <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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140 <output name="mir_count_file" file="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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141 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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142 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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143 </test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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144 <test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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145 <param name="cutoption" value="no" />
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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146 <param name="v" value="1"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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147 <param name="genomeKey" value="dme"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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148 <param name="clipped_input" value="input.clipped.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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149 <param name="plottingOption" value="yes"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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150 <param name="display" value="absolute"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
151 <output name="output" file="clipped.out.bam" ftype="bam"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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152 <output name="gff3" file="translated_dme.gff3" ftype="gff3"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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153 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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154 <output name="mir_count_file" file="mirs_clipped_count.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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155 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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156 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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157 </test>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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158 </tests>
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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159 <help>
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160
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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161 **What it does**
1
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
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162
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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163 + Clips adapter (optional)
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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164 + Aligns small RNA reads to miRNA mirBase_ reference using bowtie
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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165 + Computes pre-mir and mir counts using the pysam python package
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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166 + Plots pre-mir read coverages using R lattice package (optional)
cadc0f2c6b29 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
artbio
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167
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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168 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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169
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artbio
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170 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/
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171
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artbio
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172 ------
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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173
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174
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175 **Inputs**
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176
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177 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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178 2. Select the appropriate organism which reads originate from.
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179 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.
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180
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181
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182 ------
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183
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184 Absolute :
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185
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186 + .. image:: premirs_absolute.png
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187
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188 Relative :
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189
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190 + .. image:: premirs_relative.png
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191
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192 -------
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193
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194 **Outputs**
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195
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196 1. A BAM alignment of input reads
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197 2. A GFF3 file generated by the tool to compute mature mir counts
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198 3. A table of pre-mir counts
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199 4. A table of mature mir counts
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200
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201 Optional:
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202
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203 5. A table of pre-mir coverage
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204 6. A PDF file with covererage plots
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205
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206
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207 </help>
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208 <citations>
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209 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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210 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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211 <citation type="bibtex">@Book{,
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212 title = {Lattice: Multivariate Data Visualization with R},
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213 author = {Deepayan Sarkar},
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214 publisher = {Springer},
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215 address = {New York},
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216 year = {2008},
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217 note = {ISBN 978-0-387-75968-5},
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218 url = {http://lmdvr.r-forge.r-project.org},
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219 }</citation>
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220 </citations>
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221 </tool>