Mercurial > repos > xuebing > sharplabtool
view tools/ilmn_pacbio/assembly_stats.xml @ 2:c2a356708570
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author | xuebing |
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date | Fri, 09 Mar 2012 19:45:42 -0500 |
parents | 9071e359b9a3 |
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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>