annotate blockbuster.xml @ 2:0f3d3f9f120f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 7a097197b6a5eda0ee430b36dd8e91bd3ce1db7b
author rnateam
date Fri, 15 Jan 2016 07:52:56 -0500
parents 293c1420bcd7
children 7c7ff7a3503f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
0f3d3f9f120f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 7a097197b6a5eda0ee430b36dd8e91bd3ce1db7b
rnateam
parents: 1
diff changeset
1 <tool id="blockbuster" name="blockbuster" version="0.1.1.1">
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
2 <description>detects blocks of overlapping reads using a gaussian-distribution approach</description>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
3 <requirements>
2
0f3d3f9f120f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 7a097197b6a5eda0ee430b36dd8e91bd3ce1db7b
rnateam
parents: 1
diff changeset
4 <requirement type="package" version="0.0.1.1">blockbuster</requirement>
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
5 </requirements>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
6 <command>
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
7 <![CDATA[
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
8 blockbuster.x
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
9 -distance $distance
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
10 -minClusterHeight $minClusterHeight
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
11 -minBlockHeight $minBlockHeight
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
12 -scale $scale
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
13 -merge $merge
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
14 -tagFilter $tagFilter
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
15 -print $print
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
16 $input
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
17 > data.blockbuster;
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
18 #if str($print)=="1"
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
19 awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $2"\t"$3"\t"$4"\tblock_"$1"\t"$6"\t"$5"\t"$3"\t"$4}' data.blockbuster
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
20 #else if str($print)=="2"
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
21 awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $1"\t"$2"\t"$3"\t"$3"\t"$4"\t"$5"\t"$6"\t"$2"\t"$3}' data.blockbuster
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
22 #end if
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
23 > $output
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
24 ]]>
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
25 </command>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
26 <inputs>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
27 <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
28 <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/>
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
29 <param name="minClusterHeight" type="float" value="50" label="minimum height (readno) of a cluster"/>
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
30 <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/>
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
31 <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/>
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
32 <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/>
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
33 <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/>
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
34 <param name="print" type="select" label="Type of output" >
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
35 <option value="1">blocks</option>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
36 <option value="2" selected="True">reads</option>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
37 </param>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
38 </inputs>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
39
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
40 <outputs>
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
41 <data format="bed" name="output" label="blockbuster on ${on_string}"/>
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
42 </outputs>
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
43 <help>
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
44 <![CDATA[
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
45
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
46 **What it does**
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
47
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
48 Blockbuster_ detects blocks of overlapping reads using a gaussian-distribution approach.
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
49
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
50
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
51 Once short read sequences are mapped to a reference genome, one will face the problem of dividing consecutive reads into blocks to detect specific expression patterns. Due to biological variability and sequencing inaccuracies, the read arrangement does not always show exact block boundaries. The blockbuster tool automatically assigns reads to blocks and gives a unique chance to actually see the different origins where the short reads come from.
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
52
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
53 .. _Blockbuster: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
54
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
55 **Input**
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
56
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
57 Input file can be a BED file or an Segemehl output file.
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
58
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
59
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
60 ]]>
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
61 </help>
1
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
62 <citations>
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
63 <citation type="doi">10.1093/bioinformatics/btp419</citation>
293c1420bcd7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 0
diff changeset
64 </citations>
0
6ae946589f04 initial Uploaded
rnateam
parents:
diff changeset
65 </tool>