comparison convert_characters.xml @ 0:64d46676a13e draft

Uploaded convert_characters tarball.
author devteam
date Tue, 04 Dec 2012 10:55:58 -0500
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-1:000000000000 0:64d46676a13e
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
37 Converts 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>