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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="phytab_prune_with_list" name="Prune PHYTAB using list">
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2 <description>Filters PHYTAB dataset by comparison to a text list</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="python">
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4 prune_phytab_using_list.py $input1 $matchlist $tokeep > $output
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5 </command>
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6 <inputs>
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7 <param name="input1" type="data" format="tabular" label="PHYTAB sequence file"/>
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8 <param name="matchlist" type="data" format="txt" label="List to match to data file" />
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9 <param name="tokeep" type="select" optional="false" label="keep|discard" help="Choose whether to keep or discard matches">
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10 <option value="keep">Keep lines in output that match list</option>
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11 <option value="discard">Remove lines in output that match list</option>
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12 </param>
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13 </inputs>
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14 <outputs>
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15 <data format="tabular" name="output" label="Phytab file ${tool.name} on ${on_string}" >
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16 </data>
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17 </outputs>
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18 <help>
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19
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 **What it does**
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21
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22 This tool filters a PHYTAB sequence file to remove undesired sequences based on a list provided.
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23
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24 -----
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25
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26 **Basic Example**
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27
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28 The input data must be in phytab column format (fields are tab-delimited). Column 1 is species name, C2 is genefamily, C3 unique sequence identifier, C4 is sequence::
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29
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30 species1 gene1 uniquenameA acgttagcgcgctatagc
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31 species2 gene1 uniquenameB acgttag--cgctataaa
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32 species3 gene1 uniquenameC acgttagcgcgctatagc
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33 species4 gene1 uniquenameD acgttagcgcgctatagc
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34 species1 gene2 uniquenameE --gttagtttgcta
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35 species3 gene2 uniquenameF gtgttagtttgcta
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36
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37 Sequences from selected taxa, genes, or specific sequences provided on the List input will be excluded or retained (depending on the popup option selected) in the resulting PHYTAB output.
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38 The format of the list may consist of
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39
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40 taxa only::
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41
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42 species1
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43 species4
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44
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45 genes only::
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46
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47 geneA
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48 geneB
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49
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50 specific genes from select taxa (tab-delimited)::
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51
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52 species1 geneA
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53 species4 geneB
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54
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55 (This last sort of list is produced by the tool 'Long Branch Finder'.)
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56
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57 ------
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58
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59 **Additional Information**
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60
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61 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
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62 osiris_phylogenetics site at bitbucket.org
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63
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64 ------
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65
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66 **Citations**
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67
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68 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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69
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70 Current Osiris Citation is here
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71
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72 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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73
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74
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75 </help>
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76 </tool>