view rnazCluster.xml @ 0:dd08d42985fb draft default tip

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

<tool id="rnaz_cluster" name="RNAz Cluster" version="2.1">
    <requirements>
        <requirement type="package" version="2.1">rnaz</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    rnazCluster.pl
    --cutoff $cutoff
    $window_or_loci
    #if $header:
        $header
    #end if
    '$input'
    > '$output'
    ]]></command>
    <inputs>
        <param type="data" name="input" format="text" />
        <param argument="--cutoff" type="float" value="0.5" label="Only consider hits with RNAz class probality P>cutoff" />
        <param name="window_or_loci" type="select" label="Print information for window or loci">
            <option value="--windows">Print information for windows only</option>
            <option value="--loci">Print information for loci only</option>
        </param>
        <param argument="--header" type="boolean" checked="true" truevalue="--header" falsevalue="" label="Print a header explaining the fields of the output" />
    </inputs>
    <outputs>
        <data name="output" format="data"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="unknown.rnaz"/>
            <param name="cutoff" value="0"/>
            <output name="output" file="unknown.rnaz.clustered"/>
        </test>
        <test>
            <param name="input" value="tRNA.rnaz"/>
            <param name="window_or_loci" value="loci"/>
            <output name="output" file="tRNA.rnaz.clustered"/>
        </test>
    </tests>
    <help><![CDATA[

    Clusters RNAz windows back into overlapping loci.

    Usage: rnazCluster.pl [options] [file]

    Options: -c X, --cutoff=X Only consider hits with RNAz class
    probablility P > X (Default:0.5)

    -w, --windows -l, --loci Set these flags to print information for
    windows and/or loci in the output. By default, both single windows
    and combined loci are printed.

    -d, --header Print a header explaining the fields of the output
    (see below for a detailed description of the fields).

    ]]></help>

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