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comparison correctGCBias.xml @ 26:2ad3b027dfcd draft

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author bgruening
date Thu, 06 Feb 2014 06:40:05 -0500
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25:d2898b81b912 26:2ad3b027dfcd
1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.4">
2 <description>uses the output from computeGCBias to generate corrected BAM files</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros>
6 <token name="@BINARY@">correctGCBias</token>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <command>
10 #import tempfile
11 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
12
13 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
14 #set $temp_bam_path = $temp_bam_handle.name + '.bam'
15 #silent $temp_bam_handle.close()
16 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
17 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
18
19
20 correctGCBias
21
22 @THREADS@
23
24 --bamfile '$temp_bam_path'
25 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
26
27 @reference_genome_source@
28
29
30 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
31 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
32 #else:
33 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
34 #end if
35
36 #if str($region).strip() != '':
37 --region '$region'
38 #end if
39
40 #if $advancedOpt.showAdvancedOpt == "yes":
41 --binSize '$advancedOpt.binSize'
42 #end if
43
44 ###set newoutFileName="corrected."+str($outFileFormat)
45 ##--correctedFile $newoutFileName;
46 --correctedFile "corrected.bam";
47
48 ##mv $newoutFileName $outFileName
49 mv "corrected.bam" $outFileName
50 </command>
51 <inputs>
52 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
53 <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
54 <expand macro="reference_genome_source" />
55 <expand macro="effectiveGenomeSize" />
56
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 <expand macro="region_limit_operation" />
65
66 <conditional name="advancedOpt">
67 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
68 <option value="no" selected="true">no</option>
69 <option value="yes">yes</option>
70 </param>
71 <when value="no" />
72 <when value="yes">
73 <param name="binSize" type="integer" value="50" min="1"
74 label="Bin size in bp"
75 help="Size of the bins in bp for the output of the bigwig/bedgraph file."/>
76 </when>
77 </conditional>
78 </inputs>
79 <outputs>
80 <data format="bam" name="outFileName">
81 <!--<change_format>
82 <when input="outFileFormat" value="bw" format="bigwig" />
83 <when input="outFileFormat" value="bam" format="bam" />
84 <when input="outFileFormat" value="bg" format="bedgraph" />
85 </change_format>-->
86 </data>
87 </outputs>
88 <help>
89
90 **What it does**
91
92 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
93 Benjamini and Speed (2012) Nucleic Acids Res.
94 The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
95
96 You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
97
98
99 **Output files**:
100
101 - GC-normalized BAM file
102
103 -----
104
105 @REFERENCES@
106
107 </help>
108 </tool>