Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison phylostatistics/tree_species.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="tree_species" name="tree_species" version="1.0">
2 <description>Writes species not in a phylogeny to a text list.</description>
3 <command interpreter="perl">
4 tree_species.pl $infile $treefile > $outfile
5 </command>
6 <inputs>
7 <param format="txt" name="infile" type="data" label="Full text list of species."/>
8 <param format="txt" name="treefile" type="data" label="Tree to search. Newick format."/>
9 </inputs>
10 <outputs>
11 <data format="txt" name="outfile" label="${tool.name} on ${on_string}: stdout" />
12 </outputs>
13 <help>
14 **What it does**
15
16 This tool can be used to determine which species from a list are not present in a tree.
17 Searches, one at a time, for species (OTUs) that are present in a tree file. If not found, the species is written to the output file.
18
19 ------
20
21 **Inputs**
22
23 1. A text list of species to use to search.
24 2. A phylogeny file.
25
26 ------
27
28 **Outputs**
29
30 A text list of species (OTU) names.
31
32 -------
33
34 **Additional Information**
35
36 This is a very simple perl script that just searches a text file for the presence of each line in the other file.
37
38 -------
39
40 **Citations**
41
42 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.
43
44 Current Osiris Citation is here
45
46 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
47
48 </help>
49 </tool>