annotate qc3c_kmer.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_kmer" name="qc3c_kmer" version="@VERSION@">
    <description>qc3C Kmer-based analysis</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        jellyfish count -m $kmer_size -s 2G -C -o kmers.jf $fastq &&

        qc3C kmer
        #if str($sample_rate) != "0":
            -p $sample_rate
        #end if
        -s $seed
        --write_report
        $verbose
        -t \${GALAXY_SLOTS:-1}
        --output-path './out'
        -m $mean_insert
        --output-table table.tsv
        -x $max_coverage
        -l kmers.jf
        #if str($neb_name) != "":
            #for $enzyme in str($neb_name).split(',')
                -e $enzyme
            #end for 
        #end if
        -r $fastq
    ]]></command>
    
    <inputs>
        <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FastQ format reads" />
        <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="Mean fragment length to use in estimating the unobserved junction rate" />
        <param name="max_coverage" type="integer" min="0" value="500" label="Ignore regions with more than this coverage" />
        <param name="kmer_size" type="integer" min="0" value="24" label="Kmer size" />
        <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for
                        multiple enzymes" />
        <param name="output_table" type="boolean" truevalue="true" falsevalue="" checked="false" label="Save the collected per-read statistics table to a file" />
        <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose output" />
    </inputs>

    <outputs>
        <data name="report" format="json" label="{tool.name} on ${on_string} Report" from_work_dir="out/report.jsonl"/>
        <data name="table" format="tabular" label="{tool.name} on ${on_string} Table" from_work_dir="out/table.tsv"/>
        <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>
</tool>