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