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/tools/filters/catWrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 79 lines | 54 code | 16 blank | 9 comment | 0 complexity | 3ec983798ed49b3fc9a00a9f27a11430 MD5 | raw file
 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
46Concatenates datasets
47
48-----
49
50**Example**
51
52Concatenating Dataset::
53
54    chrX  151087187  151087355  A  0  -
55    chrX  151572400  151572481  B  0  +
56
57with Dataset1::
58
59    chr1  151242630  151242955  X  0  +
60    chr1  151271715  151271999  Y  0  +
61    chr1  151278832  151279227  Z  0  -
62    
63and with Dataset2::
64
65    chr2  100000030  200000955  P  0  +
66    chr2  100000015  200000999  Q  0  +
67
68will 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>