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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="get_sequences" name="Get_Sequences" version="1.0">
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2 <description>Create a file of selected sequences</description>
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3 <command interpreter="perl">get_seqs.pl
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4 $cosorted
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5 $paired
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6 $ignorecase
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7 -db $infile
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8 -table $input_table
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9 -col $id_column
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10 -selected $selected
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11 -unselected $unselected
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12 #for $i in $filters
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13 "${i.condition}:${i.column}:{i.value}"
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14 #end for
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15 </command>
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16 <inputs>
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17 <param name="infile" type="data" format="fasta,fastq,fastqsanger,fastqillumina,fastqsolexa" label="Sequence Database"/>
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18 <param name="input_table" type="data" format="tabular" label="File containing target IDs"/>
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19 <param name='id_column' type='data_column' data_ref='input_table' label='Column containing sequence IDs'/>
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20 <param name="cosorted" type="boolean" checked="true" truevalue='--cosorted' falsevalue='' label='Sequences appear in same order in both files' />
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21 <param name="paired" type="boolean" checked="true" truevalue="--paired" falsevalue="" label="Select both paired reads if one read matches" help="Requires Illumina-style read IDs (e.g. */1, */2)" />
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22 <param name='ignorecase' type='boolean' checked='false' truevalue='--ignorecase' falsevalue='' label='Ignore case differences between table and database IDs' />
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23 <param name='outselect' type='select' display='radio'>
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24 <option value='selected'>output selected sequences file only</option>
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25 <option value='unselected'>output other sequences file only</option>
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26 <option value='both'>generate both outfiles</option>
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27 </param>
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28 <repeat name='filters' title='Filter'>
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29 <param name='condition' type='select' display='radio' label='Condition'>
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30 <option value='s_eq'>text equals</option>
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31 <option value='s_ne'>text not equals</option>
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32 <option value='s_contains'>text contains</option>
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33 <option value='s_notcontains'>text does not contain</option>
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34 <option value='s_startswith'>text starts with</option>
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35 <option value='s_notstartswith'>text does not start with</option>
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36 <option value='s_endswith'>text ends with</option>
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37 <option value='s_notendswith'>text does not end with</option>
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38 <option value='n_eq'>number equals (==)</option>
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39 <option value='n_ne'>number not equals (!=)</option>
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40 <option value='n_gt'>number greater than (&gt;)</option>
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41 <option value='n_lt'>number less than (&lt;)</option>
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42 </param>
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43 <param name='column' type='data_column' data_ref='input_table' label='On column'/>
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44 <param name='value' type='text' label='Value'/>
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45 </repeat>
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46 </inputs>
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47 <outputs>
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48 <data name="selected" format="input" label="${tool.name} on $on_string: Selected sequences">
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49 <filter>outselect == "selected" or outselect == "both"</filter>
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50 </data>
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51 <data name="unselected" format="input" label="${tool.name} on $on_string: Unselected sequences">
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52 <filter>outselect == "unselected" or outselect == "both"</filter>
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53 </data>
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54 </outputs>
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55 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 **What it does**
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57
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58 Produces a file of selected sequences.
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59
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60 If the files are cosorted, a much faster algorithm is used. If it fails, it assumes the files were not cosorted and automatically tries again using the slower algorithm which does not require cosorted files.
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61
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62 One or more filters may be included to evaluate text or numeric data.
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63
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64 ------
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65
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66 **Inputs**
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67
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68 FASTA file of sequence database, text file of target IDs.
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69
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70 ------
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71
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72 **Outputs**
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73
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74 FASTA file. User may select to either output the selected sequences, the other sequences, or both files.
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75
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76 -------
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77
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78 **Additional Information**
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79
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80 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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81
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82 -------
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83
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84 **Citations**
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85
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86 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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87
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88 Current Osiris Citation is here
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89
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90 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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91 </help>
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92 </tool>