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
date Sun, 11 Mar 2018 18:19:40 -0400
parents
children 3a4694d4354f
comparison
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-1:000000000000 0:6f54dc6b37da
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>