root/galaxy-central/tools/unix_tools/cut_tool.xml

リビジョン 3, 2.3 KB (コミッタ: kohda, 14 年 前)

Install Unix tools  http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html

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1<tool id="cshl_cut_tool" name="cut">
2  <description>columns from files</description>
3  <command interpreter="sh">
4        cut_wrapper.sh '$complement' '$cutwhat' '$list' '$input' '$output'
5  </command>
6
7  <inputs>
8        <param format="txt" name="input" type="data" label="file to cut" />
9               
10        <param name="complement" type="select" label="Operation">
11              <option value="">Keep</option>
12              <option value="--complement">Discard</option>
13        </param>
14
15        <param name="cutwhat" type="select" label="Cut by">
16              <option value="-f">fields</option>
17              <option value="-c">characters</option>
18        </param>
19
20        <param name="list" type="text" size="20" label="List of Fields/Characters/Bytes" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5" value = "" />
21  </inputs>
22
23  <tests>
24          <test>
25                  <param name="input" value="unix_cut_input1.txt" />
26                  <output name="output" file="unix_cut_output1.txt" />
27                  <param name="complement" value="Keep" />
28                  <param name="cutwhat" value="fields" />
29                  <param name="list"  value="1,3,4" />
30          </test>
31          <test>
32                  <param name="input" value="unix_cut_input1.txt" />
33                  <output name="output" file="unix_cut_output1.txt" />
34                  <param name="complement" value="Discard" />
35                  <param name="cutwhat" value="fields" />
36                  <param name="list"  value="2" />
37          </test>
38  </tests>
39
40  <outputs>
41    <data format="input" name="output" metadata_source="input"/>
42  </outputs>
43  <help>
44
45**What it does**
46
47This tool runs the **cut** unix command, which extract or delete columns from a file.
48
49-----
50
51Field List Example:
52
53**1,3,7** - Cut specific fields/characters.
54
55**3-**    - Cut from the third field/character to the end of the line.
56
57**2-5**   - Cut from the second to the fifth field/character.
58
59**-8**    - Cut from the first to the eight field/characters.
60
61
62
63
64Input Example::
65
66    fruit       color   price   weight
67    apple       red     1.4     0.5
68    orange      orange  1.5     0.3
69    banana      yellow  0.9     0.3
70
71
72Output Example ( **Keeping fields 1,3,4** )::
73
74    fruit       price   weight
75    apple       1.4     0.5
76    orange      1.5     0.3
77    banana      0.9     0.3
78
79Output Example ( **Discarding field 2** )::
80
81    fruit       price   weight
82    apple       1.4     0.5
83    orange      1.5     0.3
84    banana      0.9     0.3
85
86Output Example ( **Keeping 3 characters** )::
87
88    fru
89    app
90    ora
91    ban
92
93  </help>
94</tool>
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