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planemo upload for repository commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 04:12:06 -0500
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<tool id="rnaz_annotate" name="Annotate RNAz" version="2.1">
        <requirement type="package" version="2.1">rnaz</requirement>
        <requirement type="package" version="3.6.7">python</requirement>
        <requirement type="package" version="0.8.0">pybedtools</requirement>
    <command detect_errors="exit_code"><![CDATA[
    python3 '$__tool_directory__/'
    --bed '$bed'
    --input '$input'
    --bedout '$output1'
    --rnazout '$output2'
        <param format="txt" name="input" type="data" label="RNAz output to annotate" />
        <param type="data" name="bed" format="bed" label="Bed file with annotation" />
        <data name="output1" format="bed" />
        <data name="output2" format="txt" />
            <param name="input" value="unknown.rnaz.clustered"/>
            <param name="bed" value="Annotation.bed"/>
            <output name="output1" file="unknown.rnaz.clustered.annotated.bed"/>
            <output name="output2" file="unknown.rnaz.clustered.annotated.rnaz"/>
            <param name="input" value="tRNA.rnaz.clustered"/>
            <param name="bed" value="Annotation.bed"/>
            <output name="output1" file="tRNA.rnaz.clustered.annotated.bed"/>
            <output name="output2" file="tRNA.rnaz.clustered.annotated.rnaz"/>

    Annotated rnaz hits with an annotation BED file, 
    replaces and
    Best used after clustering of RNAz hits.

    usage: [-h] [-b BED] [-i INPUT] [-o BEDOUT] [-r RNAZOUT]

    Intersect RNAz output with Annotation from BED

    optional arguments:
    -h, --help            show this help message and exit
    -b BED, --bed BED     Annotation BED file
    -i INPUT, --input INPUT (RNAz output)
    -o BEDOUT, --bedout BEDOUT (Annotated BED output)
    -r RNAZOUT, --rnazout RNAZOUT (Annotated rnaz-format output)

        <citation type="doi">10.1142/9789814295291_0009</citation>