Mercurial > repos > mvdbeek > concatenate_multiple_datasets

comparison catWrapper.xml @ 1:1bf1794dfcf6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
author mvdbeek
date Fri, 25 Sep 2015 11:07:07 -0400
parents cf750d0edbd8
children 745090cbbf75
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0:cf750d0edbd8 1:1bf1794dfcf6
1 <tool id="cat_multiple" name="Concatenate multiple datasets" version="0.1"> 1 <tool id="cat_multiple" name="Concatenate multiple datasets" version="0.2">
2 <description>tail-to-head</description> 2 <description>tail-to-head</description>
3 <command interpreter="python"> 3 <command><![CDATA[
4 catWrapper.py 4 cat
5 $out_file1
6 #for $file in $input 5 #for $file in $input
7 $file 6 "$file"
8 #end for 7 #end for
8 > "$out_file1"
9 ]]>
9 </command> 10 </command>
10 <inputs> 11 <inputs>
11 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/> 12 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
12 </inputs> 13 </inputs>
13 <outputs> 14 <outputs>
19 <output name="out_file1" file="cat_wrapper_out1.bed"/> 20 <output name="out_file1" file="cat_wrapper_out1.bed"/>
20 </test> 21 </test>
21 </tests> 22 </tests>
22 <help> 23 <help>
23 24
24 .. class:: warningmark 25 .. class:: warningmark
25 26
26 **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. 27 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This
28 tool does not check if the datasets being concatenated are in the same format.
27 29
28 ----- 30 -----
29 31
30 **What it does** 32 **What it does**
31 33
32 Concatenates datasets 34 Concatenates datasets
33 35
34 ----- 36 -----
35 37
36 **Example** 38 **Example**
37 39
38 Concatenating Dataset:: 40 Concatenating Dataset::
39 41
40 chrX 151087187 151087355 A 0 - 42 chrX 151087187 151087355 A 0 -
41 chrX 151572400 151572481 B 0 + 43 chrX 151572400 151572481 B 0 +
42 44
43 with Dataset1:: 45 with Dataset1::
44 46
45 chr1 151242630 151242955 X 0 + 47 chr1 151242630 151242955 X 0 +
46 chr1 151271715 151271999 Y 0 + 48 chr1 151271715 151271999 Y 0 +
47 chr1 151278832 151279227 Z 0 - 49 chr1 151278832 151279227 Z 0 -
48
49 and with Dataset2::
50 50
51 chr2 100000030 200000955 P 0 + 51 and with Dataset2::
52 chr2 100000015 200000999 Q 0 +
53 52
54 will result in the following:: 53 chr2 100000030 200000955 P 0 +
54 chr2 100000015 200000999 Q 0 +
55 55
56 chrX 151087187 151087355 A 0 - 56 will result in the following::
57 chrX 151572400 151572481 B 0 +
58 chr1 151242630 151242955 X 0 +
59 chr1 151271715 151271999 Y 0 +
60 chr1 151278832 151279227 Z 0 -
61 chr2 100000030 200000955 P 0 +
62 chr2 100000015 200000999 Q 0 +
63 57
64 ----- 58 chrX 151087187 151087355 A 0 -
59 chrX 151572400 151572481 B 0 +
60 chr1 151242630 151242955 X 0 +
61 chr1 151271715 151271999 Y 0 +
62 chr1 151278832 151279227 Z 0 -
63 chr2 100000030 200000955 P 0 +
64 chr2 100000015 200000999 Q 0 +
65 65
66 Adapted from the concatenate tool that comes with galaxy. 66 -----
67
68 Adapted from the concatenate tool that comes with galaxy.
67 </help> 69 </help>
68 </tool> 70 </tool>