annotate changeCase.xml @ 2:56c90926c8ef draft

planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 14:15:36 -0400
parents 3970d288ee1f
children ecf91530d461
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
56c90926c8ef planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 1
diff changeset
1 <tool id="ChangeCase" name="Change Case" version="1.0.0">
0
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
2 <description> of selected columns</description>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
3 <stdio>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
4 <exit_code range="1:" err_level="fatal" />
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
5 </stdio>
1
3970d288ee1f Updated command line format per dev team standards.
Dave B. <dave@bx.psu.edu>
parents: 0
diff changeset
6 <command interpreter="perl">changeCase.pl "${input}" "${cols}" "${delimiter}" "${casing}" "${out_file1}"</command>
0
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
7 <inputs>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
8 <param name="input" format="txt" type="data" label="From"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
9 <param name="cols" size="10" type="text" value="c1,c2" label="Change case of columns"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
10 <param name="delimiter" type="select" label="Delimited by">
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
11 <option value="TAB">Tab</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
12 <option value="SPACE">Whitespace</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
13 <option value="DOT">Dot</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
14 <option value="COMMA">Comma</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
15 <option value="DASH">Dash</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
16 <option value="UNDERSCORE">Underscore</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
17 <option value="PIPE">Pipe</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
18 </param>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
19 <param name="casing" type="select" label="To">
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
20 <option value="up">Upper case</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
21 <option value="lo">Lower case</option>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
22 </param>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
23 </inputs>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
24 <outputs>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
25 <data format="tabular" name="out_file1" />
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
26 </outputs>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
27 <tests>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
28 <test>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
29 <param name="input" value="1.txt" ftype="txt"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
30 <param name="cols" value="c1"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
31 <param name="delimiter" value="SPACE"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
32 <param name="casing" value="up"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
33 <output name="out_file1" file="changeCase_out1.tabular"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
34 </test>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
35 <test>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
36 <param name="input" value="1.bed" ftype="bed"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
37 <param name="cols" value="c1"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
38 <param name="delimiter" value="TAB"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
39 <param name="casing" value="up"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
40 <output name="out_file1" file="changeCase_out2.tabular"/>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
41 </test>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
42 </tests>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
43 <help>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
44
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
45 .. class:: warningmark
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
46
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
47 **This tool breaks column assignments.** To re-establish column assignments run the tool and click on the pencil icon in the resulting history item.
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
48
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
49 .. class:: warningmark
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
50
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
51 The format of the resulting dataset from this tool is always tabular.
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
52
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
53 -----
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
54
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
55 **What it does**
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
56
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
57 This tool selects specified columns from a dataset and converts the values of those columns to upper or lower case.
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
58
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
59 - Columns are specified as **c1**, **c2**, and so on.
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
60 - Columns can be specified in any order (e.g., **c2,c1,c6**)
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
61
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
62 -----
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
63
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
64 **Example**
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
65
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
66 Changing columns 1 and 3 ( delimited by Comma ) to upper case in::
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
67
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
68 apple,is,good
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
69 windows,is,bad
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
70
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
71 will result in::
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
72
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
73 APPLE is GOOD
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
74 WINDOWS is BAD
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
75
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
76 </help>
e6f966602870 Uploaded change_case tarball.
devteam
parents:
diff changeset
77 </tool>