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1 <tool id="RMsearch" name="RepeatMasker custom search" version="1.0.3">
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2
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3 <description>Scan clustering results using RepeatMasker against custom database of repeats</description>
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4 <requirements>
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5 <requirement type="package" version="4.0.7" >repeatmasker</requirement>
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6 <requirement type="package">r-r2html</requirement>
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7 <requirement type="package">r-getopt</requirement>
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8 </requirements>
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9
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10 <command interpreter="python3">
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11 RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html
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12 </command>
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13
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14 <inputs>
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15 <param format="zip" type="data" name="input_zip" label="RepeatExplorer output data archive" help="Zip archive obtained from previouse Graph-based sequence clustering"/>
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16 <param name="RMdatabase" format="fasta" type="data" label="Library of repeats" help="Library of repeats as DNA sequences in fasta format. The recommended format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
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17 </inputs>
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18
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19 <outputs>
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20 <data format="html" name="output_html" label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} " />
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21 </outputs>
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22
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23 <help>
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24 **What it does**
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25
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26 Use this tool if you want to scan previous clustering result with custom database of repeats using repeatmasker.
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27
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28 </help>
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29 </tool>
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