Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

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