annotate convert_characters.xml @ 0:64d46676a13e draft

Uploaded convert_characters tarball.
author devteam
date Tue, 04 Dec 2012 10:55:58 -0500
parents
children b1cac85bdd7a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
1 <tool id="Convert characters1" name="Convert">
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
2 <description>delimiters to TAB</description>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
3 <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
4 <inputs>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
5 <param name="convert_from" type="select" label="Convert all">
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
6 <option value="s">Whitespaces</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
7 <option value="T">Tabs</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
8 <!--<option value="Sp">Spaces</option>-->
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
9 <option value="Dt">Dots</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
10 <option value="C">Commas</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
11 <option value="D">Dashes</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
12 <option value="U">Underscores</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
13 <option value="P">Pipes</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
14 <option value="Co">Colons</option>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
15 </param>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
16 <param format="txt" name="input" type="data" label="in Query"/>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
17 </inputs>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
18 <outputs>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
19 <data format="tabular" name="out_file1" />
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
20 </outputs>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
21 <tests>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
22 <test>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
23 <param name="convert_from" value="s"/>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
24 <param name="input" value="1.bed"/>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
25 <output name="out_file1" file="eq-convert.dat"/>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
26 </test>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
27 <test>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
28 <param name="convert_from" value="s"/>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
29 <param name="input" value="a.txt"/>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
30 <output name="out_file1" file="a.tab"/>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
31 </test>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
32 </tests>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
33 <help>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
34
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
35 **What it does**
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
36
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
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.
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
38
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
39 -----
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
40
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
41 **Example**
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
42
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
43 - Input file::
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
44
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
45 chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
46 chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
47 chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
48 chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
49
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
50 - Converting all pipe delimiters of the above file to TABs will get::
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
51
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
52 chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 -
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
53 chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 -
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
54 chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 +
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
55 chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 +
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
56
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
57 </help>
64d46676a13e Uploaded convert_characters tarball.
devteam
parents:
diff changeset
58 </tool>