view mkmap.xml @ 0:eb31dd5dc3ed draft

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

<tool id="mkmap" name="mkmap" version="@VERSION@">
    <description>Create a new contact map from assembly sequences and Hi-C bam file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        bin3C mkmap
        $clobber
        --max-image $max_image
        --min-extent $min_extent
        --min-reflen $min_reflen
        --min-signal $min_signal
        $eta
        #if bin_size != 0
            --bin-size $bin_size
        #end if
        #if min_insert != 0
            --min-insert $min_insert
        #end if
        --min-mapq $min_mapq
        --strong $strong
        #if neb_name != ""
            --enzyme $neb_name
        #end if
        $ref $bam out
    ]]></command>
    
    <inputs>
        <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" />
        <param name="bam" type="data" format="bam" label="Input bam file in query order" />
        <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" checked="false" 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="eta" type="boolean" truevalue="--eta" falsevalue="" checked="false" label="Re-count bam alignments to provide an ETA" />
        <param name="bin_size" type="integer" min="0" value="0" label="Size of bins for windows extent maps" />
        <param name="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" />
        <param name="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" />
        <param name="strong" type="integer" min="1" value="10" label="Accepted alignments must being N matches" />
        <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for
                        multiple enzymes" />
    </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>