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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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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="remove_gbs_dupes" name="remove_gbs_dupes" version="1.0">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description> Finds duplicates in genbankstrip output files </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 remove_gbs_dupes.pl $infile $okfile $dupefile $subsp $var
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5 </command>
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6 <inputs>
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7 <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/>
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9 <param name='subsp' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing subsp'/>
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10 <param name='var' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing _var_'/>
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="okfile" label="Unique phytab lines from ${on_string}" />
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14 <data format="tabular" name="dupefile" label="Duplicated phytab lines from ${on_string}" />
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15 </outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 **What it does**
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18
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19 Finds species names that end in _2 or _3 or ... _N which are duplicate genes in a species in genbankstrip, and it writes those lines to another file.
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20
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21 ------
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22
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23 **Inputs**
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24
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25 1. PHYTAB format input file.
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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 Two PHYTAB format files. One contains only unique species. The other contains duplicates.
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32
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33 -------
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34
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35 **Citations**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 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 citing the following.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 Current Osiris Citation is here
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40
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41 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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42
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43 </help>
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44 </tool>