view mkmap.xml @ 29:57e22d15fed9 draft default tip

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-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[
        samtools sort -@ \${GALAXY_SLOTS:-1} -o sorted.bam -n $bam &&
        bin3C mkmap
        --min-extent $min_extent
        --min-reflen $min_reflen
        --min-signal $min_signal
        #if str($bin_size) != "0":
            --bin-size $bin_size
        #end if
        --min-insert $min_insert
        --min-mapq $min_mapq
        $eta
        --strong $strong
        #if str($neb_name) != "":
            #for $enzyme in str($neb_name).split(',')
                -e $enzyme
            #end for 
        #end if
        $ref sorted.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="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">
            <help><![CDATA[Use , (comma) to separate multiple enzymes e.g enzyme1,enzyme2]]> </help>
        </param>
    </inputs>

    <outputs>
        <data name="contact_map" format="binary" label="${tool.name} on ${on_string} Contact map" from_work_dir="out/contact_map.p.gz"/>
        <data name="log" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/>
    </outputs>

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

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

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