annotate qc3c_bam.xml @ 0:64d1f6186527 draft default tip

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/qc3c commit bd5512047445d9a39a198b7cffeba78fe7b9d140-dirty

<tool id="qc3c_bam" name="qc3c_bam" version="@VERSION@">
    <description>qc3C Alignment-based analysis</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        qc3C bam
        -p $sample_rate
        -s $seed
        --write_report
        $verbose
        -t \${GALAXY_SLOTS:-1}
        --output-path './out'
        -m $mean_insert
        -q $min_mapq
        #if str($neb_name) != "":
            #for $enzyme in str($neb_name).split(',')
                -e $enzyme
            #end for 
        #end if
        -b $bam
    ]]></command>
    
    <inputs>
        <param name="bam" type="data" format="bam" label="Input name-sorted bam file of Hi-C reads mapped to references" />
        <param name="sample_rate" type="float" min="0" value="0" label="Sample only a proportion of all read-pairs"/>
        <param name="seed" type="integer" min="1" value="20191902" label="Minimum cluster extent used in output"/>
        <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="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for
                        multiple enzymes" />
        <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Create a result report in JSONLines format" />
    </inputs>

    <outputs>
        <data name="report" format="json" label="{tool.name} on ${on_string} Report" from_work_dir="out/report.jsonl"/>
        <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/qc3C.log"/>
    </outputs>

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

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

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