Mercurial > repos > rnateam > blockbuster

annotate blockbuster.xml @ 2:f141f485e0e2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
author rnateam
date Wed, 07 Oct 2015 08:53:01 -0400
parents bfaa2f0d9515
children ea55fb635c5a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
1 <tool id="blockbuster" name="blockbuster" version="0.1.1">
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
2 <description>detects blocks of overlapping reads using a gaussian-distribution approach</description>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
3 <requirements>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
4 <requirement type="package" version="0.0.1">blockbuster</requirement>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
5 </requirements>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
6 <command>
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
7 <![CDATA[
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
8 blockbuster.x
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
9 -distance $distance
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
10 -minClusterHeight $minClusterHeight
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
11 -minBlockHeight $minBlockHeight
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
12 -scale $scale
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
13 -merge $merge
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
14 -tagFilter $tagFilter
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
15 -print $print
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
16 $input
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
17 > data.blockbuster;
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
18 #if str($print)=="1"
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
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"$4}' data.blockbuster
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
20 #else if str($print)=="2"
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
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
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
22 #end if
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
23 > $output
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
24 ]]>
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
25 </command>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
26 <inputs>
1
bfaa2f0d9515 Uploaded
rnateam
parents: 0
diff changeset
27 <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
28 <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/>
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
29 <param name="minClusterHeight" type="float" value="50" label="minimum height (readno) of a cluster"/>
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
30 <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/>
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
31 <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/>
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
32 <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/>
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
33 <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/>
1
bfaa2f0d9515 Uploaded
rnateam
parents: 0
diff changeset
34 <param name="print" type="select" label="Type of output" >
bfaa2f0d9515 Uploaded
rnateam
parents: 0
diff changeset
35 <option value="1">blocks</option>
bfaa2f0d9515 Uploaded
rnateam
parents: 0
diff changeset
36 <option value="2" selected="True">reads</option>
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
37 </param>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
38 </inputs>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
39
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
40 <outputs>
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
41 <data format="bed" name="output" label="blockbuster on ${on_string}"/>
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
42 </outputs>
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
43 <help>
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
44 <![CDATA[
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
45
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
46 **What it does**
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
47
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
48 Blockbuster_ detects blocks of overlapping reads using a gaussian-distribution approach.
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
49
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
50
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
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
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
52
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
53 .. _Blockbuster: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
54
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
55 **Input**
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
56
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
57 Input file can be a BED file or an Segemehl output file.
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
58
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
59
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
60 ]]>
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
61 </help>
2
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
62 <citations>
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
63 <citation type="doi">10.1093/bioinformatics/btp419</citation>
f141f485e0e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
rnateam
parents: 1
diff changeset
64 </citations>
0
2f9d4b518b03 Uploaded
rnateam
parents:
diff changeset
65 </tool>