annotate tools/ilmn_pacbio/assembly_stats.xml @ 1:cdcb0ce84a1b

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<tool id="assembly_stats" name="Assembly Statistics" version="1.0.0">
    <description>Calculate common measures of assembly quality</description>
    <command interpreter="python">
        assembly_stats.py $input1 $output1 --minContigLength=${minLength}
    </command>
    <inputs>
        <param name="input1" format="fasta" type="data" label="Select FASTA file containing contigs"/>
        <param name="minLength" type="integer" value="0" label="Minimum length of contigs to consider"/>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="Assembly statistics for ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="3.fasta" ftype="fasta"/>
            <param name="minLength" value="100"/>
            <output name="output1" ftype="tabular" file="assembly_stats.tabular" />
        </test>
    </tests>
    <help>

**What it does**

Reports standard measures of *de novo* assembly quality such as number of contigs, sum of contigs, mean contig length, and N50.

**Parameter list**

Minimum length
    Only include contigs of this size or greater for calculating statistics.

**Output**

Num contigs
    Total number of contigs in the assembly

Sum of contig lengths
    Total sum of contig lengths

Maximum contig length
    Maximum of the contig lengths

Mean contig length
    Average contig length

N50
    Contig length at which 50% of the assembly is contained in contigs of this size or greater.

99%
    Number of contigs accounting for 99% of the observed assembly.

    </help>
</tool>