comparison column_maker.xml @ 0:4dadd821722f draft

Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:30:22 -0400
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children d3f10c90fc96
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-1:000000000000 0:4dadd821722f
1 <tool id="Add_a_column1" name="Compute" version="1.1.0">
2 <description>an expression on every row</description>
3 <command interpreter="python">
4 column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
5 </command>
6 <inputs>
7 <param name="cond" size="40" type="text" value="c3-c2" label="Add expression"/>
8 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
9 <param name="round" type="select" label="Round result?">
10 <option value="no">NO</option>
11 <option value="yes">YES</option>
12 </param>
13 </inputs>
14 <outputs>
15 <data format="input" name="out_file1" metadata_source="input"/>
16 </outputs>
17 <tests>
18 <test>
19 <param name="cond" value="c3-c2"/>
20 <param name="input" value="1.bed"/>
21 <param name="round" value="no"/>
22 <output name="out_file1" file="column_maker_out1.interval"/>
23 </test>
24 <test>
25 <param name="cond" value="c4*1"/>
26 <param name="input" value="1.interval"/>
27 <param name="round" value="no"/>
28 <output name="out_file1" file="column_maker_out2.interval"/>
29 </test>
30 <test>
31 <param name="cond" value="c4*1"/>
32 <param name="input" value="1.interval"/>
33 <param name="round" value="yes"/>
34 <output name="out_file1" file="column_maker_out3.interval"/>
35 </test>
36 </tests>
37 <help>
38
39 .. class:: infomark
40
41 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
42
43 -----
44
45 **What it does**
46
47 This tool computes an expression for every row of a dataset and appends the result as a new column (field).
48
49 - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
50
51 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position
52
53 -----
54
55 **Example**
56
57 If this is your input::
58
59 chr1 151077881 151077918 2 200 -
60 chr1 151081985 151082078 3 500 +
61
62 computing "c4*c5" will produce::
63
64 chr1 151077881 151077918 2 200 - 400.0
65 chr1 151081985 151082078 3 500 + 1500.0
66
67 if, at the same time, "Round result?" is set to **YES** results will look like this::
68
69 chr1 151077881 151077918 2 200 - 400
70 chr1 151081985 151082078 3 500 + 1500
71
72 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
73
74 chr1 151077881 151077918 2 200 - True
75 chr1 151081985 151082078 3 500 + True
76
77 or computing "type(c2)==type('') for Input will return::
78
79 chr1 151077881 151077918 2 200 - False
80 chr1 151081985 151082078 3 500 + False
81
82 </help>
83 </tool>