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55 lines
1.5 KiB
XML
55 lines
1.5 KiB
XML
<tool id="assembly_stats" name="Assembly Statistics" version="1.0.0">
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<description>Calculate common measures of assembly quality</description>
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<command interpreter="python">
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assembly_stats.py $input1 $output1 --minContigLength=${minLength}
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</command>
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<inputs>
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<param name="input1" format="fasta" type="data" label="Select FASTA file containing contigs"/>
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<param name="minLength" type="integer" value="0" label="Minimum length of contigs to consider"/>
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</inputs>
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<outputs>
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<data name="output1" format="tabular" label="Assembly statistics for ${on_string}"/>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="3.fasta" ftype="fasta"/>
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<param name="minLength" value="100"/>
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<output name="output1" ftype="tabular" file="assembly_stats.tabular" />
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</test>
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</tests>
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<help>
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**What it does**
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Reports standard measures of *de novo* assembly quality such as number of contigs, sum of contigs, mean contig length, and N50.
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**Parameter list**
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Minimum length
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Only include contigs of this size or greater for calculating statistics.
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**Output**
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Num contigs
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Total number of contigs in the assembly
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Sum of contig lengths
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Total sum of contig lengths
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Maximum contig length
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Maximum of the contig lengths
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Mean contig length
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Average contig length
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N50
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Contig length at which 50% of the assembly is contained in contigs of this size or greater.
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99%
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Number of contigs accounting for 99% of the observed assembly.
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</help>
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</tool>
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