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comparison computeGCBias.xml @ 5:c54d31467be4 draft

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Uploaded
author bgruening
date Fri, 29 Nov 2013 08:59:04 -0500
parents d957e25e18a3
children c53a73b8eef9
comparison
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4:ac935c35437a 5:c54d31467be4
6 </stdio> 6 </stdio>
7 <macros> 7 <macros>
8 <import>deepTools_macros.xml</import> 8 <import>deepTools_macros.xml</import>
9 </macros> 9 </macros>
10 <command> 10 <command>
11 #import tempfile 11 ln -s $bamInput local_bamInput.bam;
12 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) 12 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
13 13
14 #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) 14 computeGCBias
15 #set $temp_bam_path = $temp_bam_handle.name + '.bam'
16 #silent $temp_bam_handle.close()
17 #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
18 #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
19 15
20 computeGCBias 16 @THREADS@
21 17
22 @THREADS@ 18 --bamfile 'local_bamInput.bam'
19 --GCbiasFrequenciesFile $outFileName
20 --fragmentLength $fragmentLength
23 21
24 --bamfile '$temp_bam_path' 22 @reference_genome_source@
25 --GCbiasFrequenciesFile $outFileName
26 --fragmentLength $fragmentLength
27 23
28 @reference_genome_source@ 24 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
25 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
26 #else:
27 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
28 #end if
29 29
30 #if $advancedOpt.showAdvancedOpt == "yes":
31 #if str($advancedOpt.region.value) != '':
32 --region '$advancedOpt.region'
33 #end if
30 34
31 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": 35 --sampleSize '$advancedOpt.sampleSize'
32 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize 36 --regionSize '$advancedOpt.regionSize'
33 #else:
34 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
35 #end if
36 37
38 #if $advancedOpt.filterOut:
39 --filterOut $advancedOpt.filterOut
40 #end if
37 41
38 #if $advancedOpt.showAdvancedOpt == "yes": 42 #if $advancedOpt.extraSampling:
39 #if str($advancedOpt.region.value) != '': 43 --extraSampling $advancedOpt.extraSampling
40 --region '$advancedOpt.region' 44 #end if
41 #end if 45 #end if
42
43 --sampleSize '$advancedOpt.sampleSize'
44 --regionSize '$advancedOpt.regionSize'
45 46
46 #if $advancedOpt.filterOut: 47 #if $saveBiasPlot:
47 --filterOut $advancedOpt.filterOut 48 --biasPlot $biasPlot
48 #end if 49 #end if
49 50
50 #if $advancedOpt.extraSampling: 51 ## #if $output.showOutputSettings == "yes"
51 --extraSampling $advancedOpt.extraSampling 52 ## #if $output.saveBiasPlot:
52 #end if 53 ## --biasPlot biasPlot.png ;
53 54 ## mv biasPlot.png $biasPlot
54 #end if 55 ## #end if
55 56 ## #end if
56 #if $saveBiasPlot:
57 --biasPlot $biasPlot
58 #end if
59
60 ## #if $output.showOutputSettings == "yes"
61 ## #if $output.saveBiasPlot:
62 ## --biasPlot biasPlot.png ;
63 ## mv biasPlot.png $biasPlot
64 ## #end if
65 ## #end if
66
67 ; rm $temp_dir -rf
68 57
69 </command> 58 </command>
70 <inputs> 59 <inputs>
71 60
72 <param name="bamInput" format="bam" type="data" label="Input BAM file" 61 <param name="bamInput" format="bam" type="data" label="Input BAM file"