Mercurial > repos > bgruening > text_processing
comparison cat.xml @ 1:43b1f073b693 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author | bgruening |
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date | Tue, 30 Jun 2015 16:23:23 -0400 |
parents | |
children | 616efa22d193 |
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0:5314e5d6f040 | 1:43b1f073b693 |
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1 <tool id="tp_cat" name="Concatenate datasets" version="0.1.0"> | |
2 <description>tail-to-head (cat)</description> | |
3 <requirements> | |
4 <requirement type="package" version="8.22">gnu_coreutils</requirement> | |
5 </requirements> | |
6 <version_command> | |
7 <![CDATA[ | |
8 cat --version | head -n 1 | |
9 ]]> | |
10 </version_command> | |
11 <command> | |
12 <![CDATA[ | |
13 cat | |
14 #for $file in $inputs: | |
15 "${file}" | |
16 #end for | |
17 > $out_file1 | |
18 ]]></command> | |
19 <inputs> | |
20 <param name="inputs" multiple="true" type="data" format="txt" label="datasets to concatenate"/> | |
21 </inputs> | |
22 <outputs> | |
23 <data name="out_file1" format_source="inputs" metadata_source="inputs"/> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="inputs" value="sort_result1.bed,sort_result2.bed,sort_result3.bed"/> | |
28 <output name="out_file1" file="cat_result1.txt"/> | |
29 </test> | |
30 </tests> | |
31 <help> | |
32 <![CDATA[ | |
33 | |
34 .. class:: warningmark | |
35 | |
36 **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. | |
37 | |
38 ----- | |
39 | |
40 **What it does** | |
41 | |
42 Concatenates datasets | |
43 | |
44 ----- | |
45 | |
46 **Example** | |
47 | |
48 Concatenating Dataset:: | |
49 | |
50 chrX 151087187 151087355 A 0 - | |
51 chrX 151572400 151572481 B 0 + | |
52 | |
53 with Dataset1:: | |
54 | |
55 chr1 151242630 151242955 X 0 + | |
56 chr1 151271715 151271999 Y 0 + | |
57 chr1 151278832 151279227 Z 0 - | |
58 | |
59 and with Dataset2:: | |
60 | |
61 chr2 100000030 200000955 P 0 + | |
62 chr2 100000015 200000999 Q 0 + | |
63 | |
64 will result in the following:: | |
65 | |
66 chrX 151087187 151087355 A 0 - | |
67 chrX 151572400 151572481 B 0 + | |
68 chr1 151242630 151242955 X 0 + | |
69 chr1 151271715 151271999 Y 0 + | |
70 chr1 151278832 151279227 Z 0 - | |
71 chr2 100000030 200000955 P 0 + | |
72 chr2 100000015 200000999 Q 0 + | |
73 ]]></help> | |
74 </tool> |