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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit e11f6de08dca72259d2286c442c5464b1f2236d6
author rnateam
date Sun, 17 Jan 2016 06:56:03 -0500
parents 0f3d3f9f120f
children
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2:0f3d3f9f120f 3:7c7ff7a3503f
1 <tool id="blockbuster" name="blockbuster" version="0.1.1.1"> 1 <tool id="blockbuster" name="blockbuster" version="0.1.2">
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="0.0.1.1">blockbuster</requirement> 4 <requirement type="package" version="0.0.1.1">blockbuster</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
10 -minClusterHeight $minClusterHeight 10 -minClusterHeight $minClusterHeight
11 -minBlockHeight $minBlockHeight 11 -minBlockHeight $minBlockHeight
12 -scale $scale 12 -scale $scale
13 -merge $merge 13 -merge $merge
14 -tagFilter $tagFilter 14 -tagFilter $tagFilter
15 -print $print 15 #if str($print).endswith( 'blocks' )
16 -print 1
17 #else
18 -print 2
19 #end if
16 $input 20 $input
17 > data.blockbuster; 21 > data.blockbuster;
18 #if str($print)=="1" 22 #if str($print) == 'bed_blocks'
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 23 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 > $output
20 #else if str($print)=="2" 24 #else if str($print) == 'bed_reads'
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 25 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 > $output
26 #else
27 mv data.blockbuster $output
22 #end if 28 #end if
23 > $output
24 ]]> 29 ]]>
25 </command> 30 </command>
26 <inputs> 31 <inputs>
27 <param name="input" type="data" format="bed" label="BED file containing read expressions"/> 32 <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
28 <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/> 33 <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/>
30 <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/> 35 <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/>
31 <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/> 36 <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/>
32 <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/> 37 <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/>
33 <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/> 38 <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/>
34 <param name="print" type="select" label="Type of output" > 39 <param name="print" type="select" label="Type of output" >
35 <option value="1">blocks</option> 40 <option value="bbf_blocks">blocks (blockbuster format)</option>
36 <option value="2" selected="True">reads</option> 41 <option value="bbf_reads" selected="True">reads (blockbuster format)</option>
42 <option value="bed_blocks">blocks (bed format)</option>
43 <option value="bed_reads" >reads (bed format)</option>
37 </param> 44 </param>
38 </inputs> 45 </inputs>
39 46
40 <outputs> 47 <outputs>
41 <data format="bed" name="output" label="blockbuster on ${on_string}"/> 48 <data format="bed" name="output" label="blockbuster on ${on_string}">
49 <change_format>
50 <when input="print" value="bbf_blocks" format="tabular" />
51 <when input="print" value="bbf_reads" format="tabular" />
52 </change_format>
53 </data>
42 </outputs> 54 </outputs>
55 <tests>
56 <test>
57 <param name="input" value="blockbuster_test_input.bed" ftype="bed" />
58 <param name="print" value="bed_blocks" />
59 <output name="output" file="blockbuster_test_result1.bed" ftype="bed" />
60 </test>
61 <test>
62 <param name="input" value="blockbuster_test_input.bed" ftype="bed" />
63 <param name="print" value="bbf_blocks" />
64 <output name="output" file="blockbuster_test_result2.blockbuster" ftype="tabular" />
65 </test>
66 </tests>
43 <help> 67 <help>
44 <![CDATA[ 68 <![CDATA[
45 69
46 **What it does** 70 **What it does**
47 71