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comparison baseline.xml @ 23:2770f49cb0dc

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re-uploading contra
author Franco Caramia <franco.caramia@petermac.org>
date Tue, 20 May 2014 09:59:00 +1000
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22:e8a98923965e 23:2770f49cb0dc
1 <tool id="baseline_tool" name="Baseline" version="1.0.0">
2 <description>: Control files for Contra</description>
3 <requirements>
4 <requirement type="package" version="2.17.0">bedtools</requirement>
5 <requirement type="package" name="samtools" version="0.1.18">samtools</requirement>
6 <requirement type="package" name="contra" version="2.0.4">contra</requirement>
7 </requirements>
8 <command interpreter="perl">
9
10 baseline_wrapper.pl
11
12 ##Required files
13 "PLAYEROPTION::-t=$target_file"
14
15 #for $group in $file_group
16 "BAMLISTENTRY::${group.bam}"
17 #end for
18
19 "PLAYEROPTION::--name=$sampleName"
20 "PLAYEROPTION::--trim=$trim"
21
22 ##File to generate the bam list
23 "BASELINEOUTPUT::$baseline_output"
24 </command>
25 <inputs>
26 <param name="target_file" type="data" format="bed" help="" optional="false" />
27 <repeat name="file_group" title="Bam file">
28 <param format="bam" name="bam" type="data" label="BAM File" help=""/>
29 </repeat>
30 <param name="sampleName" value="baseline" type="text" optional="true" />
31 <param name="trim" type="float" value="0.2" optional="true" />
32
33
34 </inputs>
35 <outputs>
36 <data name="baseline_output" title="Baseline Output" format="tabular" type="data" label="Baseline_Control.txt" />
37 </outputs>
38 <help>
39 |
40
41 **Reference**
42 http://contra-cnv.sourceforge.net/
43
44 -----
45
46 **What it does**
47
48 Creating a baseline control from multiple samples is can be useful when a matched control is not available. In the CONTRA download page, we have provided several baseline files for some of the platforms that we have tried. Alternatively, the “baseline.py” script that comes with CONTRA can be used to generate a custom baseline file.
49
50 -----
51
52 **Parameters**
53
54 ::
55
56 -t, --target Target region definition file [REQUIRED] [BED format]
57
58 -f, --files Files to be converted to baselines [REQUIRED] [BAM]
59
60 -o, --output Output folder [REQUIRED]
61
62 -c, --trim Portion of outliers to be removed before calculating
63 average [Default: 0.2]
64
65 -n, --name Output baseline file name [Default: baseline]
66
67
68 </help>
69 </tool>
70
71