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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="addstring2fashead" name="AddString2FAShead" version="1.0">
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2 <description>Converts FASTA file with sequences from same species and gene family to PHYTAB format</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="perl">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 addstring2fashead.pl $infile $species > $outfile
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5 2>&amp;1
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6 </command>
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7 <inputs>
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8 <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
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9 <param name="species" type="text" format="tabular" label="Text string" help="" />
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10 </inputs>
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11 <outputs>
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12 <data format="tabular" name="outfile" label="${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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17 This tool adds a text string to the beginning of all headers of an input file in FASTA format. The FASTA
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18 input file should have sequences from the same species and gene family. The output is a PHYTAB 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 FASTA file of sequences from same species and gene family. FASTA format:
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25 http://www.ncbi.nlm.nih.gov/blast/blastcgihelp.shtml
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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. Description:
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32 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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33
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34 -------
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35
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36 **Additional Information**
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37
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38 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the 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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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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45 publication, please consider citing the following.
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46
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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>