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author greg
date Tue, 10 Dec 2013 10:09:39 -0500
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5:a80606f72321 6:5742b322f956
1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.1">
2 <description>uses the output from computeGCBias to generate corrected BAM files</description>
3 <expand macro="requirements" />
4 <macros>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <command>
8 #import tempfile
9 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
10
11 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
12 #set $temp_bam_path = $temp_bam_handle.name + '.bam'
13 #silent $temp_bam_handle.close()
14 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
15 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
16
17
18 correctGCBias
19
20 @THREADS@
21
22 --bamfile '$temp_bam_path'
23 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
24
25 @reference_genome_source@
26
27
28 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
29 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
30 #else:
31 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
32 #end if
33
34
35 #if $advancedOpt.showAdvancedOpt == "yes":
36 #if str($advancedOpt.region.value) != '':
37 --region '$advancedOpt.region'
38 #end if
39
40 --binSize '$advancedOpt.binSize'
41 #end if
42
43 #set newoutFileName="corrected."+str($outFileFormat)
44
45 --correctedFile $newoutFileName; mv $newoutFileName $outFileName
46
47 </command>
48
49 <inputs>
50
51 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
52
53 <param name="bamInput" format="bam" type="data" label="Input BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
54
55 <expand macro="reference_genome_source" />
56 <expand macro="effectiveGenomeSize" />
57
58 <param name="outFileFormat" type="select" label="File format of the output">
59 <option value="bam">bam</option>
60 <option value="bw">bigwig</option>
61 <option value="bg">bedgraph</option>
62 </param>
63
64 <conditional name="advancedOpt">
65 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
66 <option value="no" selected="true">no</option>
67 <option value="yes">yes</option>
68 </param>
69 <when value="no" />
70 <when value="yes">
71 <param name="region" type="text" value=""
72 label="Region of the genome to limit the operation to"
73 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
74
75 <param name="binSize" type="integer" value="50" min="1"
76 label="Bin size in bp"
77 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
78 </when>
79 </conditional>
80 </inputs>
81
82 <outputs>
83 <data format="bam" name="outFileName">
84 <change_format>
85 <when input="outFileFormat" value="bw" format="bigwig" />
86 <when input="outFileFormat" value="bam" format="bam" />
87 <when input="outFileFormat" value="bg" format="bedgraph" />
88 </change_format>
89 </data>
90 </outputs>
91 <help>
92
93 **What it does**
94
95 This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res.
96 The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
97
98 **Output files**:
99
100 - GC-normalized BAM file
101
102 -----
103
104 .. class:: infomark
105
106 @REFERENCES@
107
108 </help>
109 </tool>