Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison phyloconversion/length_outliers.xml @ 0:5b9a38ec4a39 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5b9a38ec4a39
1 <tool id="length_outliers" name="length_outliers" version="1.0">
2 <description>Identifies sequences shorter than average in FASTA file</description>
3 <command interpreter="perl">
4 length_outliers.pl $infile $outfile1 $outfile2 $percent
5 </command>
6 <inputs>
7 <param name="infile" type="data" format="fasta" label="Input File" help="FASTA file to convert" />
8 <param name="percent" type="integer" value = "50" label="Percent" help="Sequences less than this percent of average are deleted" />
9 </inputs>
10 <outputs>
11 <data format="fasta" name="outfile1" label="Passed sequences${tool.name} on ${on_string}: Out file" />
12 <data format="fasta" name="outfile2" label="Short sequences ${tool.name} on ${on_string}: Out file" />
13 </outputs>
14 <help>
15 **What it does**
16
17 Deletes sequences from a fasta file that are shorter than a specified percentage of the average of all sequences.
18
19 ------
20
21 **Inputs**
22
23 FASTA
24
25 ------
26
27 **Outputs**
28
29 2 FASTA files: one with sequences that are long enough, the other with sequences that are too short.
30
31 ------
32
33 **Additional Information**
34
35 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
36 osiris_phylogenetics site at bitbucket.org
37
38 ------
39
40 **Citations**
41
42 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use
43 of this tool in a publication, please consider citing the following.
44
45 Current Osiris Citation is here
46
47 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
48 </help>
49 </tool>