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1 <tool id="assembly_stats" name="Assembly Statistics" version="1.0.0">
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2 <description>Calculate common measures of assembly quality</description>
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3 <command interpreter="python">
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4 assembly_stats.py $input1 $output1 --minContigLength=${minLength}
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5 </command>
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6 <inputs>
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7 <param name="input1" format="fasta" type="data" label="Select FASTA file containing contigs"/>
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8 <param name="minLength" type="integer" value="0" label="Minimum length of contigs to consider"/>
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9 </inputs>
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10 <outputs>
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11 <data name="output1" format="tabular" label="Assembly statistics for ${on_string}"/>
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input1" value="3.fasta" ftype="fasta"/>
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16 <param name="minLength" value="100"/>
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17 <output name="output1" ftype="tabular" file="assembly_stats.tabular" />
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18 </test>
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19 </tests>
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20 <help>
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21
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22 **What it does**
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23
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24 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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25
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26 **Parameter list**
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27
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28 Minimum length
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29 Only include contigs of this size or greater for calculating statistics.
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30
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31 **Output**
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32
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33 Num contigs
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34 Total number of contigs in the assembly
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35
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36 Sum of contig lengths
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37 Total sum of contig lengths
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38
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39 Maximum contig length
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40 Maximum of the contig lengths
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41
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42 Mean contig length
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43 Average contig length
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44
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45 N50
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46 Contig length at which 50% of the assembly is contained in contigs of this size or greater.
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47
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48 99%
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49 Number of contigs accounting for 99% of the observed assembly.
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50
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51 </help>
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52 </tool>
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53
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54
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