annotate rnazAnnotate.xml @ 0:e123d5c6f489 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty

<tool id="rnaz_annotate" name="Annotate RNAz" version="2.1">
    <requirements>
        <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>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    python3 '$__tool_directory__/AnnotateRNAz.py'
    --bed '$bed'
    --input '$input'
    --bedout '$output1'
    --rnazout '$output2'
    ]]></command>
    <inputs>
        <param format="txt" name="input" type="data" label="RNAz output to annotate" />
        <param type="data" name="bed" format="bed" label="Bed file with annotation" />
    </inputs>
    <outputs>
        <data name="output1" format="bed" />
        <data name="output2" format="txt" />
    </outputs>
    <tests>
        <test>
            <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"/>
        </test>
        <test>
            <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"/>
        </test>
    </tests>
    <help><![CDATA[

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

    usage: AnnotateRNAz.py [-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)
    ]]>
    </help>

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

</tool>