[2] | 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 query" help="Query 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 query 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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