Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison alignment/gap-rem.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="gap-rem" name="Sequence Gap Remover" version="1.0">
2 <description>Removes gap in sequences</description>
3 <command interpreter="perl">seqfill.pl $file $question_mark $hyphen $N $usePart $pfile</command>
4 <inputs>
5 <param format="phylipnon" name="file" type="data" label="File" />
6 <param type ="boolean" name="usePart" checked="true" truevalue="true" falsevalue="false" label="Also use Partition File -- if unchecked, it will be ignored." />
7 <param format="txt" name="pfile" checked="true" type="data" label="Partition file" />
8 <param type="boolean" name="question_mark" checked="true" truevalue="true" falsevalue="false" label="'?' signifies gap" />
9 <param type="boolean" name="hyphen" checked="true" truevalue="true" falsevalue="false" label="'-' signifies gap" />
10 <param type="boolean" name="N" checked="true" truevalue="true" falsevalue="false" label="'N' signifies gap"/>
11 </inputs>
12
13 <outputs>
14 <data from_work_dir="out.phylipnon" format="phylipnon" name="out1" label="DATA ${tool.name}" />
15 <data from_work_dir="partOut.txt" format="txt" name="out2" label="PARTITION ${tool.name}" />
16 </outputs>
17
18 <help>
19 **What it does**
20 Sequence Gap Remover
21
22 Gaps across all species are introduced by phylocatenator when selecting pre-aligned datasets
23
24 Takes an input phylip file and removes any specified gap characters that exist in the same columns of containing sequences.
25
26 ------
27
28 **Inputs**
29
30 Phylip
31
32 ------
33
34 **Outputs**
35
36 Text file
37
38 ------
39
40 **Additional Information**
41
42 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
43 bitbucket.org
44
45 -------
46
47 **Citations**
48
49 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
50 citing the following.
51
52 Current Osiris Citation is here
53
54 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
55 </help>
56
57 </tool>