|
0
|
1 <tool id="fasta-stats" name="Fasta Statistics" version="1.0.0">
|
|
|
2 <description>Display summary statistics for a fasta file.</description>
|
|
|
3 <command interpreter="perl">
|
|
|
4 fasta-stats.pl $dataset > $stats
|
|
|
5 </command>
|
|
|
6 <inputs>
|
|
|
7 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
|
|
|
8 </inputs>
|
|
|
9 <outputs>
|
|
|
10 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
|
|
|
11 </outputs>
|
|
|
12
|
|
|
13 <help>
|
|
|
14 **Fasta Stats**
|
|
|
15 Displays the summary statistics for a fasta file.
|
|
|
16
|
|
|
17 Written by Torsten Seemann - Victorian Bioinformatics Consortium
|
|
|
18
|
|
|
19 Wrapped by Simon Gladman - Victorian Bioinformatics Consortium
|
|
|
20
|
|
|
21 ------
|
|
|
22
|
|
|
23 Outputs in tabular form:
|
|
|
24 Lengths: n50, min, max, median and average
|
|
|
25
|
|
|
26 Number of base pairs: A, C, G, T, N, Total and Total_not_N
|
|
|
27
|
|
|
28 Number of sequences
|
|
|
29
|
|
|
30 GC content in %
|
|
|
31
|
|
|
32 ------
|
|
|
33
|
|
|
34 Inputs:
|
|
|
35
|
|
|
36 Fasta dataset
|
|
|
37 </help>
|
|
|
38 </tool>
|
