Mercurial > repos > iuc > fasta_stats

comparison fasta-stats.xml @ 0:9c620a950d3a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
author iuc
date Thu, 22 Nov 2018 04:16:35 -0500
parents
children 16f1f3e2de42
comparison
equal deleted inserted replaced
-1:000000000000 0:9c620a950d3a
1 <tool id="fasta-stats" name="Fasta Statistics" version="1.0.1">
2 <description>Display summary statistics for a fasta file.</description>
3 <requirements>
4 <requirement type="package" version="5.26">perl</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 perl '${__tool_directory__}/fasta-stats.pl'
8 '$dataset'
9 > '$stats'
10 ]]>
11 </command>
12 <inputs>
13 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
14 </inputs>
15 <outputs>
16 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="dataset" value="test.fasta"/>
21 <output name="stats" file="test_out.txt"/>
22 </test>
23 </tests>
24 <help>
25 **Fasta Stats**
26 Displays the summary statistics for a fasta file.
27
28 ------
29
30 Outputs in tabular form:
31 Lengths: n50, min, max, median and average
32
33 Number of base pairs: A, C, G, T, N, Total and Total_not_N
34
35 Number of sequences
36
37 GC content in %
38
39 ------
40
41 Inputs:
42
43 Fasta dataset
44 </help>
45 <citations>
46 <citation type="bibtex">
47 @UNPUBLISHED{Seemann_Gladman2012,
48 author = {Torsten Seemann and Simon Gladman},
49 title = {Fasta Statistics: Display summary statistics for a fasta file.},
50 year = {2012},
51 url = {https://github.com/galaxyproject/tools-iuc},
52 }
53 </citation>
54 </citations>
55 </tool>