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comparison correctGCBias.xml @ 13:b4c5dd45778a draft

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author bgruening
date Mon, 16 Dec 2013 04:36:19 -0500
parents 135f3bae5c56
children 5ea8782d650c
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12:aea72b24dea0 13:b4c5dd45778a
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" /> 4 <expand macro="stdio" />
5 <macros> 5 <macros>
6 <import>deepTools_macros.xml</import> 6 <import>deepTools_macros.xml</import>
7 </macros> 7 </macros>
8 <command> 8 <command>
9 #import tempfile 9 #import tempfile
10 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) 10 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
11 11
12 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) 12 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
13 #set $temp_bam_path = $temp_bam_handle.name + '.bam' 13 #set $temp_bam_path = $temp_bam_handle.name + '.bam'
14 #silent $temp_bam_handle.close() 14 #silent $temp_bam_handle.close()
15 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path)) 15 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
16 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path)) 16 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
17 17
18 18
19 correctGCBias 19 correctGCBias
20 20
21 @THREADS@ 21 @THREADS@
22 22
23 --bamfile '$temp_bam_path' 23 --bamfile '$temp_bam_path'
24 --GCbiasFrequenciesFile $GCbiasFrequenciesFile 24 --GCbiasFrequenciesFile $GCbiasFrequenciesFile
25 25
26 @reference_genome_source@ 26 @reference_genome_source@
27 27
28 28
29 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": 29 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
30 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize 30 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
31 #else: 31 #else:
32 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt 32 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
33 #end if 33 #end if
34 34
35 #if $advancedOpt.showAdvancedOpt == "yes":
36 #if str($advancedOpt.region.value) != '':
37 --region '$advancedOpt.region'
38 #end if
39 --binSize '$advancedOpt.binSize'
40 #end if
35 41
36 #if $advancedOpt.showAdvancedOpt == "yes": 42 #set newoutFileName="corrected."+str($outFileFormat)
37 #if str($advancedOpt.region.value) != '': 43 --correctedFile $newoutFileName;
38 --region '$advancedOpt.region'
39 #end if
40
41 --binSize '$advancedOpt.binSize'
42 #end if
43
44 #set newoutFileName="corrected."+str($outFileFormat)
45
46 --correctedFile $newoutFileName; mv $newoutFileName $outFileName
47 44
48 </command> 45 mv $newoutFileName $outFileName
49 46 </command>
50 <inputs> 47 <inputs>
51 48 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
52 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> 49 <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."/>
53
54 <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."/>
55
56 <expand macro="reference_genome_source" /> 50 <expand macro="reference_genome_source" />
57 <expand macro="effectiveGenomeSize" /> 51 <expand macro="effectiveGenomeSize" />
58 52
59 <param name="outFileFormat" type="select" label="File format of the output"> 53 <param name="outFileFormat" type="select" label="File format of the output">
60 <option value="bam">bam</option> 54 <option value="bam">bam</option>
61 <option value="bw">bigwig</option> 55 <option value="bw">bigwig</option>
62 <option value="bg">bedgraph</option> 56 <option value="bg">bedgraph</option>
63 </param> 57 </param>
64 58
65 <conditional name="advancedOpt"> 59 <conditional name="advancedOpt">
66 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 60 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
67 <option value="no" selected="true">no</option> 61 <option value="no" selected="true">no</option>
68 <option value="yes">yes</option> 62 <option value="yes">yes</option>
69 </param> 63 </param>
70 <when value="no" /> 64 <when value="no" />
71 <when value="yes"> 65 <when value="yes">
72 <param name="region" type="text" value="" 66 <param name="region" type="text" value=""
73 label="Region of the genome to limit the operation to" 67 label="Region of the genome to limit the operation to"
74 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;" /> 68 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;" />
75 69
76 <param name="binSize" type="integer" value="50" min="1" 70 <param name="binSize" type="integer" value="50" min="1"
77 label="Bin size in bp" 71 label="Bin size in bp"
78 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/> 72 help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
79 </when> 73 </when>
80 </conditional> 74 </conditional>
81 </inputs> 75 </inputs>
82 76 <outputs>
83 <outputs> 77 <data format="bam" name="outFileName">
84 <data format="bam" name="outFileName"> 78 <change_format>
85 <change_format> 79 <when input="outFileFormat" value="bw" format="bigwig" />
86 <when input="outFileFormat" value="bw" format="bigwig" /> 80 <when input="outFileFormat" value="bam" format="bam" />
87 <when input="outFileFormat" value="bam" format="bam" /> 81 <when input="outFileFormat" value="bg" format="bedgraph" />
88 <when input="outFileFormat" value="bg" format="bedgraph" /> 82 </change_format>
89 </change_format> 83 </data>
90 </data> 84 </outputs>
91 </outputs> 85 <help>
92 <help>
93 86
94 **What it does** 87 **What it does**
95 88
96 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. 89 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.
97 The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on. 90 The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.