root/galaxy-central/tools/filters/convert_characters.xml

リビジョン 2, 2.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="Convert characters1" name="Convert">
2  <description>delimiters to TAB</description>
3  <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
4  <inputs>
5    <param name="convert_from" type="select" label="Convert all">
6      <option value="s">Whitespaces</option>
7      <option value="T">Tabs</option>
8      <!--<option value="Sp">Spaces</option>-->
9      <option value="Dt">Dots</option>
10      <option value="C">Commas</option>
11      <option value="D">Dashes</option>
12      <option value="U">Underscores</option>
13      <option value="P">Pipes</option>
14      <option value="Co">Colons</option>
15    </param>
16    <param format="txt" name="input" type="data" label="in Query"/>
17  </inputs>
18  <outputs>
19    <data format="tabular" name="out_file1" />
20  </outputs>
21  <tests>
22    <test>
23      <param name="convert_from" value="s"/>
24      <param name="input" value="1.bed"/>
25      <output name="out_file1" file="eq-convert.dat"/>
26    </test>
27    <test>
28      <param name="convert_from" value="s"/>
29      <param name="input" value="a.txt"/>
30      <output name="out_file1" file="a.tab"/>
31    </test>
32  </tests>
33  <help>
34
35**What it does**
36
37Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.
38
39-----
40
41**Example**
42
43- Input file::
44
45    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
46    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
47    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
48    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
49
50- Converting all pipe delimiters of the above file to TABs will get::
51
52    chrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -
53    chrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -
54    chrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +
55    chrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +
56
57</help>
58</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。