mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
mvdbeek
0c1334fea0
This tool currently fails with `sort: multi-character tab '$\\\\t'\n` (https://jenkins.galaxyproject.org/view/All/job/docker-main-tools/lastCompletedBuild/testReport/test.functional/test_toolbox_pytest/test_tool_Grouping1_test_1_/). This also removes test data that should be included in galaxy-test-data instead (xref https://github.com/galaxyproject/galaxy-test-data/pull/5), and adds a test file that was missing from https://github.com/galaxyproject/galaxy/pull/7205.
229 lines
8.4 KiB
XML
229 lines
8.4 KiB
XML
<tool id="Grouping1" name="Group" version="2.1.3">
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<description>data by a column and perform aggregate operation on other columns.</description>
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<requirements>
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<requirement type="package" version="1.15.4">numpy</requirement>
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<requirement type="package" version="8.31">coreutils</requirement>
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</requirements>
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<command detect_errors="exit_code">
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python '$__tool_directory__/grouping.py'
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'${out_file1}'
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'${input1}'
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'${groupcol}'
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'${ignorecase}'
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'${ignorelines}'
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#for $op in $operations
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'${op.optype},${op.opcol},${op.opround},${op.opdefault}'
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#end for
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</command>
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<inputs>
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<param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
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<param name="groupcol" label="Group by column" type="data_column" data_ref="input1" />
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<param name="ignorecase" type="boolean" truevalue="1" falsevalue="0">
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<label>Ignore case while grouping?</label>
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</param>
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<param name="ignorelines" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not grouped">
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<option value="62">></option>
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<option value="64">@</option>
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<option value="43">+</option>
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<option value="60"><</option>
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<option value="42">*</option>
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<option value="45">-</option>
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<option value="61">=</option>
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<option value="124">|</option>
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<option value="63">?</option>
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<option value="36">$</option>
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<option value="46">.</option>
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<option value="58">:</option>
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<option value="38">&</option>
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<option value="37">%</option>
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<option value="94">^</option>
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<option value="35">#</option>
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</param>
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<repeat name="operations" title="Operation">
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<param name="optype" type="select" label="Type">
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<option value="mean">Mean</option>
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<option value="median">Median</option>
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<option value="mode">Mode</option>
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<option value="max">Maximum</option>
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<option value="min">Minimum</option>
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<option value="sum">Sum</option>
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<option value="length">Count</option>
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<option value="unique">Count Distinct</option>
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<option value="cat">Concatenate</option>
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<option value="cat_uniq">Concatenate Distinct</option>
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<option value="random">Randomly pick</option>
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<option value="std">Standard deviation</option>
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</param>
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<param name="opcol" label="On column" type="data_column" data_ref="input1" />
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<param name="opround" type="select" label="Round result to nearest integer?">
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<option value="no">NO</option>
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<option value="yes">YES</option>
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</param>
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<param name="opdefault" type="float" optional="true" label="Replace non numeric data" help="leave empty for no replacements. Will replace, e.g., empty cells and text cells."/>
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</repeat>
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</inputs>
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<outputs>
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<data format="tabular" name="out_file1" />
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</outputs>
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<tests>
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<!-- Test valid data -->
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<test>
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<param name="input1" value="1.bed"/>
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<param name="groupcol" value="1"/>
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<param name="ignorecase" value="true"/>
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<repeat name="operations">
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<param name="optype" value="mean"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<output name="out_file1" file="groupby_out1.dat"/>
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</test>
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<!-- Test with an empty first field-->
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<test>
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<param name="input1" value="groupby_in_1.tabular"/>
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<param name="groupcol" value="1"/>
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<param name="ignorecase" value="true"/>
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<repeat name="operations">
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<param name="optype" value="cat_uniq"/>
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<param name="opcol" value="1"/>
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<param name="opround" value="no"/>
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</repeat>
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<output name="out_file1" file="groupby_out2.dat"/>
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</test>
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<test>
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<param name="input1" value="1.bed"/>
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<param name="groupcol" value="1"/>
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<param name="ignorecase" value="false"/>
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<repeat name="operations">
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<param name="optype" value="mean"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="median"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="mode"/>
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<param name="opcol" value="6"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="max"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="min"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="sum"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="length"/>
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<param name="opcol" value="1"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="unique"/>
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<param name="opcol" value="1"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="cat"/>
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<param name="opcol" value="1"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="cat_uniq"/>
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<param name="opcol" value="6"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="random"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<repeat name="operations">
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<param name="optype" value="std"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<output name="out_file1" file="groupby_out3.tabular" compare="sim_size"/>
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</test>
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<!-- test failure for non-numeric data -->
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<test expect_exit_code="1" expect_failure="true">
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<param name="input1" value="1.tabular"/>
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<param name="groupcol" value="1"/>
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<param name="ignorecase" value="true"/>
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<repeat name="operations">
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<param name="optype" value="mean"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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</repeat>
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<assert_stderr>
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<has_text text="non float value 'hap' found in colum 2"/>
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</assert_stderr>
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</test>
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<test>
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<param name="input1" value="groupby_in_1.tabular"/>
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<param name="groupcol" value="1"/>
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<param name="ignorecase" value="true"/>
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<repeat name="operations">
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<param name="optype" value="mean"/>
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<param name="opcol" value="2"/>
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<param name="opround" value="no"/>
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<param name="opdefault" value="0"/>
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</repeat>
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<output name="out_file1" file="groupby_out4.tabular"/>
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</test>
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</tests>
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<help>
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.. class:: infomark
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**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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-----
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**Syntax**
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This tool allows you to group the input dataset by a particular column and perform aggregate functions: Mean, Median, Mode, Sum, Max, Min, Count, Concatenate, and Randomly pick on any column(s).
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The Concatenate function will take, for each group, each item in the specified column and build a comma delimited list. Concatenate Unique will do the same but will build a list of unique items with no repetition.
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Count and Count Unique are equivalent to Concatenate and Concatenate Unique, but will only count the number of items and will return an integer.
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- If multiple modes are present, all are reported.
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-----
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**Example**
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- For the following input::
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chr22 1000 1003 TTT
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chr22 2000 2003 aaa
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chr10 2200 2203 TTT
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chr10 1200 1203 ttt
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chr22 1600 1603 AAA
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- **Grouping on column 4** while ignoring case, and performing operation **Count on column 1** will return::
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AAA 2
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TTT 3
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- **Grouping on column 4** while not ignoring case, and performing operation **Count on column 1** will return::
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aaa 1
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AAA 1
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ttt 1
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TTT 2
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</help>
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</tool>
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