annotate randomBed.xml @ 11:7308cc546a36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:35 -0400
parents 607c0576c6ab
children 44867b59dbf2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
1 <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 2
diff changeset
2 <description>generate random intervals in a genome</description>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
6 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="stdio" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
8 <command>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
9 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
10 bedtools random
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
11 -g $genome
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
12 -l $length
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
13 -n $intervals
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
14 #if str($seed.seed_choose) == "True":
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
15 -seed $seed.seed
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
16 #end if
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
17 > "$output"
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
18 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
19 </command>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
20 <inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
21 <expand macro="genome" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
24 <expand macro="seed" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
25 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
26 <outputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
27 <data format="bed" name="output" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
28 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
29 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
30 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
31 <param name="genome" value="mm9_chr1.len" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
32 <param name="seed_choose" value="False" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
33 <param name="length" value="5" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
34 <param name="intervals" value="3" />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
35 <output name="output">
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
36 <assert_contents>
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
37 <has_text_matching expression="chr1" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
38 <has_n_columns n="6" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
39 </assert_contents>
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
40 </output>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
41 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
42 </tests>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
43 <help>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
44 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
45 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
46
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
47 bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
48
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
49 @REFERENCES@
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
50 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
51 </help>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
52 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
53 </tool>