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1 <tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3">
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0
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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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13
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5 <requirement type="package" version="4.0.7">repeatmasker</requirement>
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6 <requirement type="package" version="3.6">python</requirement>
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7 <requirement type="package" version="2.3.2">r-r2html</requirement>
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8 <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement>
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0
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9 </requirements>
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10
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11 <command>
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12
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13 python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html;
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0
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15 </command>
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16
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17 <inputs>
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18 <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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19 <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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20 </inputs>
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21
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22 <outputs>
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23 <data format="html" name="output_html" label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} " />
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24 </outputs>
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25
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26 <help>
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27 **What it does**
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28
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29 Use this tool if you want to scan previous clustering result with custom database of repeats using repeatmasker.
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30
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31 </help>
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32 </tool>
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33
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