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comparison catWrapper.xml @ 0:cf750d0edbd8 draft

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Imported from capsule None
author mvdbeek
date Tue, 03 Mar 2015 05:06:43 -0500
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1 <tool id="cat_multiple" name="Concatenate multiple datasets" version="0.1">
2 <description>tail-to-head</description>
3 <command interpreter="python">
4 catWrapper.py
5 $out_file1
6 #for $file in $input
7 $file
8 #end for
9 </command>
10 <inputs>
11 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
12 </inputs>
13 <outputs>
14 <data name="out_file1" format_source="input" metadata_source="input"/>
15 </outputs>
16 <tests>
17 <test>
18 <param name="input" value="1.bed,2.bed"/>
19 <output name="out_file1" file="cat_wrapper_out1.bed"/>
20 </test>
21 </tests>
22 <help>
23
24 .. class:: warningmark
25
26 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
27
28 -----
29
30 **What it does**
31
32 Concatenates datasets
33
34 -----
35
36 **Example**
37
38 Concatenating Dataset::
39
40 chrX 151087187 151087355 A 0 -
41 chrX 151572400 151572481 B 0 +
42
43 with Dataset1::
44
45 chr1 151242630 151242955 X 0 +
46 chr1 151271715 151271999 Y 0 +
47 chr1 151278832 151279227 Z 0 -
48
49 and with Dataset2::
50
51 chr2 100000030 200000955 P 0 +
52 chr2 100000015 200000999 Q 0 +
53
54 will result in the following::
55
56 chrX 151087187 151087355 A 0 -
57 chrX 151572400 151572481 B 0 +
58 chr1 151242630 151242955 X 0 +
59 chr1 151271715 151271999 Y 0 +
60 chr1 151278832 151279227 Z 0 -
61 chr2 100000030 200000955 P 0 +
62 chr2 100000015 200000999 Q 0 +
63
64 -----
65
66 Adapted from the concatenate tool that comes with galaxy.
67 </help>
68 </tool>