comparison cluster.xml @ 0:eb31dd5dc3ed draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty

0:eb31dd5dc3ed

<tool id="cluster" name="cluster" version="@VERSION@">
    <description>Cluster an existing contact map into genome bins</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        bin3C cluster
        $clobber
        --max-image $max_image
        --min-extent $min_extent
        --min-reflen $min_reflen
        --min-signal $min_signal
        -s 201987356473
        $no_report
        $no_spades
        $no_plot
        $no_fasta
        $only_large
        $fasta
        $contact_map out
    ]]></command>
    
    <inputs>
        <param name="contact_map" type="data" format="gz" label="Contact map" help="This file is generated from mkmap command" />
        <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" label="Clobber existing files" />
        <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/>
        <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
        <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>
        <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/>
        <param name="no_report" type="boolean" truevalue="--no-report" falsevalue="" checked="false" label="Do not generate a cluster report" />
        <param name="no_spades" type="boolean" truevalue="--no-spades" falsevalue="" checked="false" label="Assembly was not done using SPAdes" />
        <param name="no_plot" type="boolean" truevalue="--no-plot" falsevalue="" checked="false" label="Do not generate a clustered heatmap" />
        <param name="no_fasta" type="boolean" truevalue="--no-fasta" falsevalue="" checked="false" label="Do not generate cluster FASTA files" />
        <param name="only_large" type="boolean" truevalue="--only-large" falsevalue="" checked="false" label="Only write FASTA for clusters longer than min_extent" />
        <param name="fasta" type="data" format="fasta" label="Alternative source FASTA location from that supplied during mkmap" />
    </inputs>

    <outputs>
        <data name="output" label="${tool.name} on ${on_string} Output">
            <discover_datasets pattern="__designation_and_ext__" directory="out" />
        </data>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[

    Documentation can be found at `<https://github.com/cerebis/bin3C>`_.

    ]]></help>
<expand macro="citations" />
</tool>