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