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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="remove_gbs_dupes" name="remove_gbs_dupes" version="1.0">
2 <description> Finds duplicates in genbankstrip output files </description>
3 <command interpreter="perl">
4 remove_gbs_dupes.pl $infile $okfile $dupefile $subsp $var
5 </command>
6 <inputs>
7 <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/>
8 <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/>
9 <param name='subsp' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing subsp'/>
10 <param name='var' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing _var_'/>
11 </inputs>
12 <outputs>
13 <data format="tabular" name="okfile" label="Unique phytab lines from ${on_string}" />
14 <data format="tabular" name="dupefile" label="Duplicated phytab lines from ${on_string}" />
15 </outputs>
16 <help>
17 **What it does**
18
19 Finds species names that end in _2 or _3 or ... _N which are duplicate genes in a species in genbankstrip, and it writes those lines to another file.
20
21 ------
22
23 **Inputs**
24
25 1. PHYTAB format input file.
26
27 ------
28
29 **Outputs**
30
31 Two PHYTAB format files. One contains only unique species. The other contains duplicates.
32
33 -------
34
35 **Citations**
36
37 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.
38
39 Current Osiris Citation is here
40
41 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
42
43 </help>
44 </tool>