/tools/ilmn_pacbio/assembly_stats.xml

 1<tool id="assembly_stats" name="Assembly Statistics" version="1.0.0">
 2    <description>Calculate common measures of assembly quality</description>
 3    <command interpreter="python">
 4        assembly_stats.py $input1 $output1 --minContigLength=${minLength}
 5    </command>
 6    <inputs>
 7        <param name="input1" format="fasta" type="data" label="Select FASTA file containing contigs"/>
 8        <param name="minLength" type="integer" value="0" label="Minimum length of contigs to consider"/>
 9    </inputs>
10    <outputs>
11        <data name="output1" format="tabular" label="Assembly statistics for ${on_string}"/>
12    </outputs>
13    <tests>
14        <test>
15            <param name="input1" value="3.fasta" ftype="fasta"/>
16            <param name="minLength" value="100"/>
17            <output name="output1" ftype="tabular" file="assembly_stats.tabular" />
18        </test>
19    </tests>
20    <help>
21
22**What it does**
23
24Reports standard measures of *de novo* assembly quality such as number of contigs, sum of contigs, mean contig length, and N50.
25
26**Parameter list**
27
28Minimum length
29    Only include contigs of this size or greater for calculating statistics.
30
31**Output**
32
33Num contigs
34    Total number of contigs in the assembly
35
36Sum of contig lengths
37    Total sum of contig lengths
38
39Maximum contig length
40    Maximum of the contig lengths
41
42Mean contig length
43    Average contig length
44
45N50
46    Contig length at which 50% of the assembly is contained in contigs of this size or greater.
47
4899%
49    Number of contigs accounting for 99% of the observed assembly.
50
51    </help>
52</tool>
53
54