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annotate repenrich.xml @ 0:f6f0f1e5e940 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
author artbio
date Wed, 02 Aug 2017 05:17:29 -0400
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children 51b4590a972d
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f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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1 <tool id="repenrich" name="RepEnrich" version="1.4.0">
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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2 <description>Repeat Element Profiling</description>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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3 <requirements>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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4 <requirement type="package" version="1.2.0">bowtie</requirement>
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5 <requirement type="package" version="0.1.19">samtools</requirement>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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6 <requirement type="package" version="2.20.1">bedtools</requirement>
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7 <requirement type="package" version="1.69">biopython</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Tool exception" />
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11 </stdio>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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12 <command detect_errors="exit_code"><![CDATA[
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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13 #import re
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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14 #set input_base = 'Sample'
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15 #set baseReference = 'Genome'
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16 ln -f -s '$genome' '${baseReference}.fa' &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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17 ln -f -s '$input_fastq' '${input_base}.fastq' &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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18 #if $seq_method.seq_method_list == "paired-end":
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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19 ln -f -s '$input2_fastq' '${input_base}_2.fastq' &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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20 #end if
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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21 bowtie-build '$genome' ${baseReference} &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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22 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
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23 #if $seq_method.seq_method_list == "single-read":
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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24 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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25 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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26 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
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27 echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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28 #else:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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29 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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30 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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31 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
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32 echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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33 #end if
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34 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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35 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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36 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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37 samtools index ${input_base}_unique.bam &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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38 rm ${input_base}_unique.sam &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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39 #if $seq_method.seq_method_list == "single-read":
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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40 python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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41 #else:
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42 python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap_1.fastq --fastqfile2 ${input_base}_multimap_2.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" --pairedend TRUE &&
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43 #end if
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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44 cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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45 cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular &&
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46 cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular
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47 ]]></command>
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48 <!-- basic error handling -->
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49 <inputs>
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50 <conditional name="seq_method">
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51 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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52 <option selected="True" value="single-read">Single-read sequencing</option>
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53 <option value="paired-end">Paired-end sequencing</option>
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54 </param>
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55 <when value="single-read">
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56 <param format="fastq,fastqsanger" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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57 </when>
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58 <when value="paired-end">
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59 <param format="fastq,fastqsanger" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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60 <param format="fastq,fastqsanger" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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61 </when>
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62 </conditional>
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63 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />
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64 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
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65 </inputs>
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66
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67 <outputs>
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68 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb">
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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69 </data>
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70 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular">
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71 </data>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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72 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular">
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73 </data>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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74 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular">
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75 </data>
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76 </outputs>
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77
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78 <tests>
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79 <test>
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80 <param name="seq_method_list" value="single-read"/>
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81 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/>
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82 <param name="genome" value="chrM.fa" ftype="fasta"/>
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83 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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84 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
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85 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
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86 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
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87 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
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88 </test>
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89 <test>
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90 <param name="seq_method_list" value="paired-end"/>
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91 <param name="input_fastq" value="Samp_L.fastq" ftype="fastq"/>
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92 <param name="input2_fastq" value="Samp_R.fastq" ftype="fastq"/>
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93 <param name="genome" value="chrM.fa" ftype="fasta"/>
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94 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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95 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
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96 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
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97 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
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98 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
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99 </test>
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100 </tests>
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101
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102 <help>
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103
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104 **What it does**
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105
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106 Reads are mapped to the genome using the Bowtie1 aligner. Reads mapping uniquely to the genome are assigned to subfamilies of repetitive elements based on their degree of overlap to RepeatMasker annotated genomic instances of each repetitive element subfamily. Reads mapping to multiple locations are separately mapped to repetitive element assemblies – referred to as repetitive element psuedogenomes – built from RepeatMasker annotated genomic instances of repetitive element subfamilies. RepEnrich then return tables of counts merged from both strategies, that can be further processed in statistical analysis for differential expression. For detailed information see the `original publication`_.
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107
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108 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583
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109
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110 **Inputs**
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111
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112 *Reference genome* : reference genome in fasta format
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113
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114 *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format.
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115
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116 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
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117
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118 This file looks like:
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119
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120 <![CDATA[
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121
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122 SW perc perc perc query position in query matching repeat position in repeat
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123
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124 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID
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125
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126 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486
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127
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128 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487
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129
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130 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488
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131
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132 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489
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133
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134 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490
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135
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136 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491
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137
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138 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492
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139
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140 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493
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141
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142 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494
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143
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144 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495
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145
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146 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496
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148 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497
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150 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498
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151
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152 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499
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154 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500
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155
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156 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501
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157
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158 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502
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159
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160 ]]>
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162 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons)
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163
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164 **Outputs**
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165
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166 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format, for further statistical tests differential expression analysis or graphics
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167
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168 **RepEnrich**
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169
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170 This Galaxy tool is a wrapper of the RepEnrich tool by steven_criscione@brown.edu et al. whose code and manual are available in `GitHub`_.
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171
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172 .. _GitHub: https://github.com/nskvir/RepEnrich
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173
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174 Python scripts RepEnrich.py and RepEnrich_setup.py have been adapted to python 3. Note that sorting of Fraction counts, Family fraction counts and Class fraction counts is different with this Galaxy wrapper or with RepEnrich as found in the `RepEnrich code repository`_. However, this different sorting does not affect subsequent statistical analyses
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175
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176 .. _RepEnrich code repository: https://github.com/nskvir/RepEnrich
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177
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178 **Execution time**
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179
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180 .. class:: warningmark
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181
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182 This tool includes steps to index the reference genome, index repeat sequences and align reads to these indexes. Therefore the run time may be **long to very long**.
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183
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184 .. class:: infomark
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185
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186 For more information on the tools, please visit our `code repository`_.
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187
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188 If you would like to give us feedback or you run into any trouble, please send an email to artbio.ibps@gmail.com
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189
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190 This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_.
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191
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192 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/
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193 .. _ARTbio team: http://artbio.fr
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194 .. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics
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195
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196 </help>
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197
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198 <citations>
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199 <citation type="doi">10.1186/1471-2164-15-583</citation>
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200 </citations>
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201 </tool>