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1 <tool id="Count1" name="Count">
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2 <description>occurrences of each record</description>
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3 <command interpreter="python">uniq.py -i $input -o $out_file1 -c "$column" -d $delim</command>
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4 <inputs>
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5 <param name="input" type="data" format="tabular" label="from dataset" help="Dataset missing? See TIP below"/>
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6 <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurrences of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
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7 <param name="delim" type="select" label="Delimited by">
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8 <option value="T">Tab</option>
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9 <option value="Sp">Whitespace</option>
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10 <option value="Dt">Dot</option>
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11 <option value="C">Comma</option>
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12 <option value="D">Dash</option>
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13 <option value="U">Underscore</option>
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14 <option value="P">Pipe</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="out_file1" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input" value="1.bed"/>
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23 <output name="out_file1" file="uniq_out.dat"/>
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24 <param name="column" value="1"/>
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25 <param name="delim" value="T"/>
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26 </test>
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27 </tests>
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28 <help>
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29
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30 .. class:: infomark
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31
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32 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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33
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34 -----
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35
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36 **Syntax**
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37
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38 This tool counts occurrences of unique values in selected column(s).
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39
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40 - If multiple columns are selected, counting is performed on each unique group of all values in the selected columns.
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41 - The first column of the resulting dataset will be the count of unique values in the selected column(s) and will be followed by each value.
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42
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43 -----
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44
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45 **Example**
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46
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47 - Input file::
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48
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49 chr1 10 100 gene1
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50 chr1 105 200 gene2
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51 chr1 205 300 gene3
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52 chr2 10 100 gene4
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53 chr2 1000 1900 gene5
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54 chr3 15 1656 gene6
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55 chr4 10 1765 gene7
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56 chr4 10 1765 gene8
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57
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58 - Counting unique values in column c1 will result in::
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59
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60 3 chr1
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61 2 chr2
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62 1 chr3
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63 2 chr4
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64
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65 - Counting unique values in the grouping of columns c2 and c3 will result in::
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66
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67 2 10 100
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68 2 10 1765
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69 1 1000 1900
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70 1 105 200
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71 1 15 1656
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72 1 205 300
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73
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74 </help>
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75 </tool>
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