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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="beautify_fasta" name="Beautify_FASTA" version="1.0">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description>Converts interleaved FASTA to non-interleaved</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 beautify_fasta.pl $infile $outfile $delpipes $convgi $delslash $renumber $space
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 </command>
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6 <inputs>
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7 <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 <param name='delpipes' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert Pipes' help='Convert pipe symbols in fasta sequence id to space.'/>
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9 <param name='convgi' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert gi|' help='Converts instances of gi| to gi_.'/>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 <param name='delslash' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert slash \ ' help='Converts instances of \ to _.'/>
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11 <param name='renumber' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Add a unique number' help='Sequentially add a unique number to beginning of each sequence.'/>
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12 <param name='space' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Add a unique number' help='Add a space after the unique number.'/>
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13 </inputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 <outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 <data format="fasta" name="outfile" label="${tool.name} on ${on_string}: Out file" />
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 </outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 <help>**What it does**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18
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19 Input an interleaved FASTA file. Beautify_FASTA converts interleaved FASTA to
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 non-interleaved (full sequence on one line). In addition, you can choose to
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 convert symbols from the FASTA ID. The FASTA ID is the descriptor from the >
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 to the first space. The FASTA description (first line after any space) is not changed.
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23
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24 ------
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25
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 **Inputs**
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27
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28 Interleaved FASTA file.
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29
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30 ------
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31
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32 **Outputs**
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33
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34 Non-interleaved FASTA file with optional modifications to the FASTA ID.
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35
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36 -------
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37
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 **Additional Information**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 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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41 osiris_phylogenetics site at bitbucket.org
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42
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43 ------
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44
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 **Citations**
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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 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 consider citing the following.
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49
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50 Current Osiris Citation is here
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51
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52 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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53
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54 </help>
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55 </tool>