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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="phytab_prune_with_list" name="Prune PHYTAB using list">
2 <description>Filters PHYTAB dataset by comparison to a text list</description>
3 <command interpreter="python">
4 prune_phytab_using_list.py $input1 $matchlist $tokeep > $output
5 </command>
6 <inputs>
7 <param name="input1" type="data" format="tabular" label="PHYTAB sequence file"/>
8 <param name="matchlist" type="data" format="txt" label="List to match to data file" />
9 <param name="tokeep" type="select" optional="false" label="keep|discard" help="Choose whether to keep or discard matches">
10 <option value="keep">Keep lines in output that match list</option>
11 <option value="discard">Remove lines in output that match list</option>
12 </param>
13 </inputs>
14 <outputs>
15 <data format="tabular" name="output" label="Phytab file ${tool.name} on ${on_string}" >
16 </data>
17 </outputs>
18 <help>
19
20 **What it does**
21
22 This tool filters a PHYTAB sequence file to remove undesired sequences based on a list provided.
23
24 -----
25
26 **Basic Example**
27
28 The input data must be in phytab column format (fields are tab-delimited). Column 1 is species name, C2 is genefamily, C3 unique sequence identifier, C4 is sequence::
29
30 species1 gene1 uniquenameA acgttagcgcgctatagc
31 species2 gene1 uniquenameB acgttag--cgctataaa
32 species3 gene1 uniquenameC acgttagcgcgctatagc
33 species4 gene1 uniquenameD acgttagcgcgctatagc
34 species1 gene2 uniquenameE --gttagtttgcta
35 species3 gene2 uniquenameF gtgttagtttgcta
36
37 Sequences from selected taxa, genes, or specific sequences provided on the List input will be excluded or retained (depending on the popup option selected) in the resulting PHYTAB output.
38 The format of the list may consist of
39
40 taxa only::
41
42 species1
43 species4
44
45 genes only::
46
47 geneA
48 geneB
49
50 specific genes from select taxa (tab-delimited)::
51
52 species1 geneA
53 species4 geneB
54
55 (This last sort of list is produced by the tool 'Long Branch Finder'.)
56
57 ------
58
59 **Additional Information**
60
61 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
62 osiris_phylogenetics site at bitbucket.org
63
64 ------
65
66 **Citations**
67
68 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.
69
70 Current Osiris Citation is here
71
72 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
73
74
75 </help>
76 </tool>