mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
84 lines
2.7 KiB
XML
84 lines
2.7 KiB
XML
<tool id="Add_a_column1" name="Compute" version="1.1.0">
|
|
<description>an expression on every row</description>
|
|
<command interpreter="python">
|
|
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
|
|
</command>
|
|
<inputs>
|
|
<param name="cond" size="40" type="text" value="c3-c2" label="Add expression"/>
|
|
<param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
|
|
<param name="round" type="select" label="Round result?">
|
|
<option value="no">NO</option>
|
|
<option value="yes">YES</option>
|
|
</param>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="input" name="out_file1" metadata_source="input"/>
|
|
</outputs>
|
|
<tests>
|
|
<test>
|
|
<param name="cond" value="c3-c2"/>
|
|
<param name="input" value="1.bed"/>
|
|
<param name="round" value="no"/>
|
|
<output name="out_file1" file="column_maker_out1.interval"/>
|
|
</test>
|
|
<test>
|
|
<param name="cond" value="c4*1"/>
|
|
<param name="input" value="1.interval"/>
|
|
<param name="round" value="no"/>
|
|
<output name="out_file1" file="column_maker_out2.interval"/>
|
|
</test>
|
|
<test>
|
|
<param name="cond" value="c4*1"/>
|
|
<param name="input" value="1.interval"/>
|
|
<param name="round" value="yes"/>
|
|
<output name="out_file1" file="column_maker_out3.interval"/>
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
|
|
.. class:: infomark
|
|
|
|
**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
|
|
|
|
-----
|
|
|
|
**What it does**
|
|
|
|
This tool computes an expression for every row of a dataset and appends the result as a new column (field).
|
|
|
|
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
|
|
|
|
- **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position
|
|
|
|
-----
|
|
|
|
**Example**
|
|
|
|
If this is your input::
|
|
|
|
chr1 151077881 151077918 2 200 -
|
|
chr1 151081985 151082078 3 500 +
|
|
|
|
computing "c4*c5" will produce::
|
|
|
|
chr1 151077881 151077918 2 200 - 400.0
|
|
chr1 151081985 151082078 3 500 + 1500.0
|
|
|
|
if, at the same time, "Round result?" is set to **YES** results will look like this::
|
|
|
|
chr1 151077881 151077918 2 200 - 400
|
|
chr1 151081985 151082078 3 500 + 1500
|
|
|
|
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
|
|
|
|
chr1 151077881 151077918 2 200 - True
|
|
chr1 151081985 151082078 3 500 + True
|
|
|
|
or computing "type(c2)==type('') for Input will return::
|
|
|
|
chr1 151077881 151077918 2 200 - False
|
|
chr1 151081985 151082078 3 500 + False
|
|
|
|
</help>
|
|
</tool>
|