Mercurial > repos > simon-gladman > fasta_stats

comparison fasta-stats.xml @ 0:153f7a414921 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author simon-gladman
date Tue, 25 Jun 2013 01:51:03 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:153f7a414921
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>