Mercurial > repos > mvdbeek > concatenate_multiple_datasets

annotate catWrapper.xml @ 0:1e06fa2771f9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 11:09:17 -0400
parents
children 201c568972c3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
1 <tool id="cat_multiple" name="Concatenate multiple datasets" version="0.2">
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
2 <description>tail-to-head</description>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
3 <command><![CDATA[
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
4 cat
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
5 #for $file in $input
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
6 "$file"
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
7 #end for
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
8 > "$out_file1"
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
9 ]]>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
10 </command>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
11 <inputs>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
12 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
13 </inputs>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
14 <outputs>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
15 <data name="out_file1" format_source="input" metadata_source="input"/>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
16 </outputs>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
17 <tests>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
18 <test>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
19 <param name="input" value="1.bed,2.bed"/>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
20 <output name="out_file1" file="cat_wrapper_out1.bed"/>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
21 </test>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
22 </tests>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
23 <help>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
24
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
25 .. class:: warningmark
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
26
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
27 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
28 tool does not check if the datasets being concatenated are in the same format.
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
29
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
30 -----
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
31
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
32 **What it does**
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
33
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
34 Concatenates datasets
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
35
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
36 -----
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
37
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
38 **Example**
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
39
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
40 Concatenating Dataset::
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
41
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
42 chrX 151087187 151087355 A 0 -
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
43 chrX 151572400 151572481 B 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
44
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
45 with Dataset1::
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
46
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
47 chr1 151242630 151242955 X 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
48 chr1 151271715 151271999 Y 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
49 chr1 151278832 151279227 Z 0 -
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
50
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
51 and with Dataset2::
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
52
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
53 chr2 100000030 200000955 P 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
54 chr2 100000015 200000999 Q 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
55
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
56 will result in the following::
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
57
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
58 chrX 151087187 151087355 A 0 -
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
59 chrX 151572400 151572481 B 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
60 chr1 151242630 151242955 X 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
61 chr1 151271715 151271999 Y 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
62 chr1 151278832 151279227 Z 0 -
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
63 chr2 100000030 200000955 P 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
64 chr2 100000015 200000999 Q 0 +
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
65
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
66 -----
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
67
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
68 Adapted from the concatenate tool that comes with galaxy.
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
69 </help>
1e06fa2771f9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
mvdbeek
parents:
diff changeset
70 </tool>