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comparison tools/filters/catWrapper.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cat1" name="Concatenate datasets">
2 <description>tail-to-head</description>
3 <command interpreter="python">
4 catWrapper.py
5 $out_file1
6 $input1
7 #for $q in $queries
8 ${q.input2}
9 #end for
10 </command>
11 <inputs>
12 <param name="input1" type="data" label="Concatenate Dataset"/>
13 <repeat name="queries" title="Dataset">
14 <param name="input2" type="data" label="Select" />
15 </repeat>
16 </inputs>
17 <outputs>
18 <data name="out_file1" format="input" metadata_source="input1"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="input1" value="1.bed"/>
23 <param name="input2" value="2.bed"/>
24 <output name="out_file1" file="cat_wrapper_out1.bed"/>
25 </test>
26 <!--TODO: if possible, enhance the underlying test code to handle this test
27 the problem is multiple params with the same name "input2"
28 <test>
29 <param name="input1" value="1.bed"/>
30 <param name="input2" value="2.bed"/>
31 <param name="input2" value="3.bed"/>
32 <output name="out_file1" file="cat_wrapper_out2.bed"/>
33 </test>
34 -->
35 </tests>
36 <help>
37
38 .. class:: warningmark
39
40 **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.
41
42 -----
43
44 **What it does**
45
46 Concatenates datasets
47
48 -----
49
50 **Example**
51
52 Concatenating Dataset::
53
54 chrX 151087187 151087355 A 0 -
55 chrX 151572400 151572481 B 0 +
56
57 with Dataset1::
58
59 chr1 151242630 151242955 X 0 +
60 chr1 151271715 151271999 Y 0 +
61 chr1 151278832 151279227 Z 0 -
62
63 and with Dataset2::
64
65 chr2 100000030 200000955 P 0 +
66 chr2 100000015 200000999 Q 0 +
67
68 will result in the following::
69
70 chrX 151087187 151087355 A 0 -
71 chrX 151572400 151572481 B 0 +
72 chr1 151242630 151242955 X 0 +
73 chr1 151271715 151271999 Y 0 +
74 chr1 151278832 151279227 Z 0 -
75 chr2 100000030 200000955 P 0 +
76 chr2 100000015 200000999 Q 0 +
77
78 </help>
79 </tool>