annotate RM_custom_search.xml @ 34:91996b991991 draft default tip

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<tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3.3">

    <description>Scan clustering results using RepeatMasker against custom database of
        repeats
    </description>
    <requirements>
        <requirement type="package" version="4.0.7">repeatmasker</requirement>
        <requirement type="package" version="3.6">python</requirement>
        <requirement type="package" version="2.3.2">r-r2html</requirement>
        <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="RM_custom_search.py"/>
        <include type="literal" path="parallel.py"/>
        <include type="literal" path="rmsk_summary_table_multiple.r"/>
        <include type="literal" path="RM_html_report.R"/>
    </required_files>


    <command>

        python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g
        $__root_dir__ -r $output_html;

    </command>

    <inputs>
        <param format="zip" type="data" name="input_zip"
               label="RepeatExplorer output data archive"
               help="Zip archive obtained from previouse Graph-based sequence clustering"/>
        <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'"/>
    </inputs>

    <outputs>
        <data format="html" name="output_html"
              label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} "/>
    </outputs>

    <help>
        **What it does**

        Use this tool if you want to scan previous clustering result with custom database
        of repeats using repeatmasker.

    </help>
</tool>