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comparison phyloconversion/uniprotfasta2phytab.xml @ 0:5b9a38ec4a39 draft default tip

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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="uniprotfasta2phytab" name="UNIPROTPHYTAB2FASTA" version="1.0">
2 <description>Converts FASTA file downloaded from uniprot with sequences from same species and gene family to PHYTAB
3 format</description>
4 <command interpreter="perl">
5 uniprotfasta2phytab.pl $infile $gene > $outfile
6 </command>
7 <inputs>
8 <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
9 <param name="gene" type="text" format="tabular" label="Name of gene family" help="" />
10 </inputs>
11 <outputs>
12 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
13 </outputs>
14 <help>
15 **What it does**
16
17 FASTA2PHYTAB takes an input FASTA file with sequences from the gene family, and extracts species name and
18 partition (gene family) name that will apply for all sequences. The output is a PHYTAB tabular format file.
19
20 ------
21
22 **Inputs**
23
24 A FASTA file downloaded from uniprot. This should have a header something like
25 >tr|B9UM22|B9UM22_MOUSE G protein-coupled receptor 81 OS=Mus musculus GN=Gpr81 PE=2 SV=1
26
27 ------
28
29 **Outputs**
30
31 PHYTAB file format: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
32
33 ------
34
35 **Additional Information**
36
37 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
38 osiris_phylogenetics site at bitbucket.org
39
40 ------
41
42 **Citations**
43
44 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a
45 publication, please consider citing the following.
46
47 Current Osiris Citation is here
48
49 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
50 </help>
51 </tool>