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3
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1 <tool id="tp_sorted_uniq" name="Unique" version="0.3">
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0
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2 <description>occurrences of each record</description>
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3 <requirements>
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4 <requirement type="package" version="8.21">gnu_coreutils</requirement>
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5 </requirements>
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6 <command interpreter='python'>
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1
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7 unsorted_uniq.py
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8 $ignore_case
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9 $is_numeric
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10 #if $adv_opts.adv_opts_selector=="advanced":
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11 $adv_opts.column_start
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12 $adv_opts.column_end
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13 #end if
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14 $outfile
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15 $infile
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16 </command>
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17 <inputs>
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18 <param name="infile" type="data" format="tabular,txt" label="File to scan for unique values" />
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19 <param name="ignore_case" type="boolean" label="ignore differences in case when comparing (-f)" truevalue="-f" falsevalue="false" checked="false"/>
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20 <param name="is_numeric" type="boolean" label="column only contains numeric values (-n)" truevalue="-n" falsevalue="false" checked="false" />
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21 <conditional name="adv_opts">
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22 <param name="adv_opts_selector" type="select" label="Advanced Options">
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23 <option value="basic" selected="True">Hide Advanced Options</option>
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24 <option value="advanced">Show Advanced Options</option>
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25 </param>
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26 <when value="basic" />
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27 <when value="advanced">
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28 <param name="column_start" label="Column start" type="data_column" data_ref="infile" help="Unique on specific column range"/>
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29 <param name="column_end" label="Column end" type="data_column" data_ref="infile" help="Unique on specific column range"/>
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30 </when>
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31 </conditional>
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32 </inputs>
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33 <outputs>
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34 <data format="infile" name="outfile" metadata_source="infile"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 </test>
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39 </tests>
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40 <help>
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41
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42 .. class:: infomark
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43
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44 **Syntax**
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45
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46 This tool returns all unique lines using the 'sort -u' command. It can be used with unsorted files.
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47 If you need additional options, like grouping or counting your unique results, please use the 'Unique lines from sorted file' tool.
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48
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49 -----
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50
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51 .. class:: infomark
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52
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53 The input file needs to be tab separated. Please convert your file if necessary.
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54
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55 -----
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56
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57 **Example**
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58
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59 - Input file::
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60
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61 chr1 10 100 gene1
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62 chr1 105 200 gene2
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63 chr1 10 100 gene1
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64 chr2 10 100 gene4
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65 chr2 1000 1900 gene5
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66 chr3 15 1656 gene6
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67 chr2 10 100 gene4
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68
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69 - Unique lines will result in::
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70
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71 chr1 10 100 gene1
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72 chr1 105 200 gene2
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73 chr2 10 100 gene4
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74 chr2 1000 1900 gene5
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75 chr3 15 1656 gene6
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76
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77
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78 </help>
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79 </tool>
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