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comparison blockbuster.xml @ 1:293c1420bcd7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty
author rnateam
date Wed, 07 Oct 2015 08:53:14 -0400
parents 6ae946589f04
children 0f3d3f9f120f
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0:6ae946589f04 1:293c1420bcd7
1 <tool id="blockbuster" name="blockbuster" version="0.1"> 1 <tool id="blockbuster" name="blockbuster" version="0.1.1">
2 <description>detects blocks of overlapping reads using a gaussian-distribution approach</description> 2 <description>detects blocks of overlapping reads using a gaussian-distribution approach</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.1">blockbuster</requirement> 4 <requirement type="package" version="0.0.1">blockbuster</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 blockbuster.x 7 <![CDATA[
8 -distance $distance 8 blockbuster.x
9 -minClusterHeight $minClusterHeight 9 -distance $distance
10 -minBlockHeight $minBlockHeight 10 -minClusterHeight $minClusterHeight
11 -scale $scale 11 -minBlockHeight $minBlockHeight
12 -merge $merge 12 -scale $scale
13 -tagFilter $tagFilter 13 -merge $merge
14 -print $print 14 -tagFilter $tagFilter
15 -print $print
15 $input 16 $input
16 17 > data.blockbuster;
18 #if str($print)=="1"
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"$4}' data.blockbuster
20 #else if str($print)=="2"
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
22 #end if
17 > $output 23 > $output
24 ]]>
18 </command> 25 </command>
19 <inputs> 26 <inputs>
20 <param name="input" type="data" format="bed" label="BED file containing read expressions"/> 27 <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
21 <param name="distance" type="integer" value="40" size="5" label="minimum distance between two clusters"/> 28 <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/>
22 <param name="minClusterHeight" type="float" value="50" size="5" label="minimum height (readno) of a cluster"/> 29 <param name="minClusterHeight" type="float" value="50" label="minimum height (readno) of a cluster"/>
23 <param name="minBlockHeight" type="float" value="1" size="5" label="minimum height (readno) of a block"/> 30 <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/>
24 <param name="scale" type="float" value="0.5" size="5" label="scale stddev for a single read"/> 31 <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/>
25 <param name="merge" type="integer" value="0" size="5" label="merge reads with almost similar means"/> 32 <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/>
26 <param name="tagFilter" type="integer" value="0" size="5" label="skip tags with expression smaller than this value"/> 33 <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/>
27 <param name="print" type="select" label="Type of output" > 34 <param name="print" type="select" label="Type of output" >
28 <option value="1">blocks</option> 35 <option value="1">blocks</option>
29 <option value="2" selected="True">reads</option> 36 <option value="2" selected="True">reads</option>
30 </param> 37 </param>
31 </inputs> 38 </inputs>
32 39
33 <outputs> 40 <outputs>
34 <data format="tabular" name="output" label="blockbuster on ${on_string}"/> 41 <data format="bed" name="output" label="blockbuster on ${on_string}"/>
35 </outputs> 42 </outputs>
36 <help> 43 <help>
44 <![CDATA[
37 45
38 .. class:: infomark 46 **What it does**
39
40 **What it does**
41 47
42 Blockbuster_ detects blocks of overlapping reads using a gaussian-distribution approach. 48 Blockbuster_ detects blocks of overlapping reads using a gaussian-distribution approach.
43 49
44 50
45 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. 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.
46 52
47 .. _Blockbuster: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html 53 .. _Blockbuster: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html
48 54
55 **Input**
49 56
50 **References** 57 Input file can be a BED file or an Segemehl output file.
51 58
52 59
53 If you use this program in your work you might want to cite: 60 ]]>
54
55 Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovitch P, Stadler PF: "Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data", Bioinformatics (2009) vol. 25 (18) pp. 2298-301
56
57
58 </help> 61 </help>
62 <citations>
63 <citation type="doi">10.1093/bioinformatics/btp419</citation>
64 </citations>
59 </tool> 65 </tool>