Mercurial > repos > artbio > concatenate_multiple_datasets
comparison catWrapper.xml @ 0:6f54dc6b37da draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
author | artbio |
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date | Sun, 11 Mar 2018 18:19:40 -0400 |
parents | |
children | 3a4694d4354f |
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-1:000000000000 | 0:6f54dc6b37da |
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1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="0.3"> | |
2 <description>tail-to-head</description> | |
3 <command><![CDATA[ | |
4 #if $headers == "No": | |
5 cat | |
6 #for $file in $input | |
7 "$file" | |
8 #end for | |
9 > "$out_file1" | |
10 #else: | |
11 #for $file in $input | |
12 printf "# ${file.element_identifier}\n" >> "$out_file1" && | |
13 cat "$file" >> "$out_file1" && | |
14 #end for | |
15 sleep 1 | |
16 #end if | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <param name="headers" type="select" label="include dataset names"> | |
21 <option value="No" selected="true">No</option> | |
22 <option value="Yes">Yes</option> | |
23 </param> | |
24 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/> | |
25 </inputs> | |
26 <outputs> | |
27 <data name="out_file1" format_source="input" metadata_source="input"/> | |
28 </outputs> | |
29 <tests> | |
30 <test> | |
31 <param name="headers" value="No" /> | |
32 <param name="input" value="1.bed,2.bed"/> | |
33 <output name="out_file1" file="cat_wrapper_out1.bed"/> | |
34 </test> | |
35 <test> | |
36 <param name="headers" value="Yes" /> | |
37 <param name="input" value="1.bed,2.bed"/> | |
38 <output name="out_file1" file="cat_wrapper_out2.bed"/> | |
39 </test> | |
40 | |
41 </tests> | |
42 <help> | |
43 | |
44 .. class:: warningmark | |
45 | |
46 **WARNING:** This tool does not check if the datasets being concatenated are in the same format. | |
47 | |
48 ----- | |
49 | |
50 **What it does** | |
51 | |
52 Concatenates datasets | |
53 | |
54 ----- | |
55 | |
56 **Example** | |
57 | |
58 Concatenating Dataset:: | |
59 | |
60 chrX 151087187 151087355 A 0 - | |
61 chrX 151572400 151572481 B 0 + | |
62 | |
63 with Dataset1:: | |
64 | |
65 chr1 151242630 151242955 X 0 + | |
66 chr1 151271715 151271999 Y 0 + | |
67 chr1 151278832 151279227 Z 0 - | |
68 | |
69 and with Dataset2:: | |
70 | |
71 chr2 100000030 200000955 P 0 + | |
72 chr2 100000015 200000999 Q 0 + | |
73 | |
74 will result in the following:: | |
75 | |
76 chrX 151087187 151087355 A 0 - | |
77 chrX 151572400 151572481 B 0 + | |
78 chr1 151242630 151242955 X 0 + | |
79 chr1 151271715 151271999 Y 0 + | |
80 chr1 151278832 151279227 Z 0 - | |
81 chr2 100000030 200000955 P 0 + | |
82 chr2 100000015 200000999 Q 0 + | |
83 | |
84 ----- | |
85 | |
86 Adapted from galaxy's catWrapper.xml to allow multiple input files. | |
87 | |
88 </help> | |
89 </tool> |