/tools/filters/uniq.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 75 lines · 60 code · 15 blank · 0 comment · 0 complexity · 43305040d5cfb5822d42d4fa3addbb07 MD5 · raw file
- <tool id="Count1" name="Count">
- <description>occurrences of each record</description>
- <command interpreter="python">uniq.py -i $input -o $out_file1 -c "$column" -d $delim</command>
- <inputs>
- <param name="input" type="data" format="tabular" label="from dataset" help="Dataset missing? See TIP below"/>
- <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" />
- <param name="delim" type="select" label="Delimited by">
- <option value="T">Tab</option>
- <option value="Sp">Whitespace</option>
- <option value="Dt">Dot</option>
- <option value="C">Comma</option>
- <option value="D">Dash</option>
- <option value="U">Underscore</option>
- <option value="P">Pipe</option>
- </param>
- </inputs>
- <outputs>
- <data format="tabular" name="out_file1" />
- </outputs>
- <tests>
- <test>
- <param name="input" value="1.bed"/>
- <output name="out_file1" file="uniq_out.dat"/>
- <param name="column" value="1"/>
- <param name="delim" value="T"/>
- </test>
- </tests>
- <help>
-
- .. class:: infomark
- **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
- -----
- **Syntax**
- This tool counts occurrences of unique values in selected column(s).
- - If multiple columns are selected, counting is performed on each unique group of all values in the selected columns.
- - 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.
- -----
- **Example**
- - Input file::
-
- chr1 10 100 gene1
- chr1 105 200 gene2
- chr1 205 300 gene3
- chr2 10 100 gene4
- chr2 1000 1900 gene5
- chr3 15 1656 gene6
- chr4 10 1765 gene7
- chr4 10 1765 gene8
- - Counting unique values in column c1 will result in::
- 3 chr1
- 2 chr2
- 1 chr3
- 2 chr4
- - Counting unique values in the grouping of columns c2 and c3 will result in::
- 2 10 100
- 2 10 1765
- 1 1000 1900
- 1 105 200
- 1 15 1656
- 1 205 300
- </help>
- </tool>