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1 <tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE" version="1.0.0">
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2 <description> Simple utility to summarize final annotations from RepeatExplorer CLUSTER_TABLE</description>
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18
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3 <requirements>
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4 <requirement type="package">r-optparse</requirement>
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5 </requirements>
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6
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7 <command interpreter="Rscript" detect_errors="exit_code" >
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8 $__tool_directory__/summarize_cluster_table.R
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9 --cluster_table=$cluster_table
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10 --output=$output
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11
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12 </command>
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13
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14 <inputs>
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15 <param format="txt" type="data" name="cluster_table" label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv" help="CLUSTER_TABLE.csv must contains completed Final_annotation column" />
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16 </inputs>
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17
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18 <outputs>
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19 <data format="tabular" name="output" label="Summary of repeat proportions from ${cluster_table.hid}"/>
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18
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20 </outputs>
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21 <help>
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22 **The tool calculates genome proportions of identified repeats based on cluster annotations in CLUSTER_TABLE.csv**
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23
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24 The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv. Contamination and organelle clusters are discarded from quantification. Table header with information about numbers of analyzed reads should remain unchanged - see example below.
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18
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25
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26 Example of CLUSTER_TABLE.csv: ::
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27
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28 Number_of_reads_in_clusters 1185180
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29 Number_of_clusters 62148
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30 Number_of_superclusters 62031
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31 Number_of_singlets 314820
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32 Number_of_analyzed_reads 1500000
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33 Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation Final_annotation
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34 10 4 11967 11967 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE Other All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE
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35 137 5 2094 2094 All/repeat Other All/repeat
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36 112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA
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37 16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence) All/repeat/satellite
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38 125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid
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39 124 40 2645 2645 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana Putative LTR elements All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana
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40
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41 </help>
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42 </tool>
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