|
0
|
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>
|
