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